From 2ef6c7f51539cf3d09abd483a6c94a5a93758920 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Thu, 20 Jun 2024 01:54:02 +0000 Subject: [PATCH 1/5] Updated the data.yml sourced from australianbiocommons.github.io --- _data/data.yaml | 949 +++++++++++++++--------------------------------- 1 file changed, 293 insertions(+), 656 deletions(-) diff --git a/_data/data.yaml b/_data/data.yaml index 70a8ee4..936f480 100644 --- a/_data/data.yaml +++ b/_data/data.yaml @@ -2140,13 +2140,13 @@ edam-topics: - Mapping galaxy: - - description: 'Map with BWA: - map short reads (< 100 bp) against reference genome' - title: Map with BWA 0.7.17.5 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbwa%2Fbwa%2F0.7.17.5 - description: 'Map with BWA-MEM: - map medium and long reads (> 100 bp) against reference genome' - title: Map with BWA-MEM 0.7.17.2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbwa%2Fbwa_mem%2F0.7.17.2 + title: Map with BWA-MEM 0.7.18 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbwa%2Fbwa_mem%2F0.7.18 + - description: 'Map with BWA: - map short reads (< 100 bp) against reference genome' + title: Map with BWA 0.7.18 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbwa%2Fbwa%2F0.7.18 homepage: http://bio-bwa.sourceforge.net id: bwa license: MIT @@ -5097,8 +5097,8 @@ galaxy: - description: 'ENA Upload tool: Submission of (meta)data to the European Nucleotide Archive (ENA)' - title: ENA Upload tool 0.7.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fena_upload%2Fena_upload%2F0.7.1%2Bgalaxy1 + title: ENA Upload tool 0.7.3+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fena_upload%2Fena_upload%2F0.7.3%2Bgalaxy1 - description: 'ENA upload table builder: create tables for the ENA upload tool from metadata templates' title: ENA upload table builder 0.1.0+galaxy0 @@ -6290,6 +6290,9 @@ edam-operations: '' edam-topics: '' galaxy: + - description: 'Split file: to dataset collection' + title: Split file 0.5.2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsplit_file_to_collection%2Fsplit_file_to_collection%2F0.5.2 - description: 'Bundle Collection: Package up and download a collection of files as a single archive.' title: Bundle Collection 1.3.0 @@ -6363,6 +6366,12 @@ - description: 'FASTA-to-Tabular: converter' title: FASTA-to-Tabular 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffasta_to_tabular%2Ffasta2tab%2F1.1.1 + - description: 'Tabular-to-FASTA: converts tabular file to FASTA format' + title: Tabular-to-FASTA 1.1.1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftabular_to_fasta%2Ftab2fasta%2F1.1.1 + - description: 'Convert VCF to MAF: with vcf2maf' + title: Convert VCF to MAF 1.6.21+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvcf2maf%2Fvcf2maf%2F1.6.21%2Bgalaxy1 - description: 'BED-to-GFF: converter' title: BED-to-GFF 2.0.0 url: https://usegalaxy.org.au/root?tool_id=bed2gff1 @@ -6376,190 +6385,190 @@ - description: 'AXT to LAV: Converts an AXT formatted file to LAV format' title: AXT to LAV 1.0.0 url: https://usegalaxy.org.au/root?tool_id=axt_to_lav_1 - - description: 'Convert FASTA to Bowtie color space Index: ' - title: Convert FASTA to Bowtie color space Index 1.2.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index - - description: 'OpenBabel converter for molecular formats: ' - title: OpenBabel converter for molecular formats 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules - - description: 'Convert FASTA to fai file: ' - title: Convert FASTA to fai file 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai - - description: 'Convert GFF to BED: ' - title: Convert GFF to BED 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0 - - description: 'Convert neostore.zip files to neostore: ' - title: Convert neostore.zip files to neostore 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore - - description: 'Convert uncompressed file to compressed: ' - title: Convert uncompressed file to compressed 1.16+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz - - description: 'Convert XTC, DCD, and TRR: ' - title: Convert XTC, DCD, and TRR 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert - - description: 'Convert compressed file to uncompressed.: ' - title: Convert compressed file to uncompressed. 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed - - description: 'Convert BGZ VCF to tabix: ' - title: Convert BGZ VCF to tabix 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 - - description: 'Convert Interval to BGZIP: ' - title: Convert Interval to BGZIP 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0 + - description: 'Convert Wiggle to BigWig: ' + title: Convert Wiggle to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig + - description: 'Convert BED to GFF: ' + title: Convert BED to GFF 2.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0 + - description: 'Convert InChI to MOL: ' + title: Convert InChI to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol + - description: 'Convert compressed and uncompressed BCF files: ' + title: Convert compressed and uncompressed BCF files 0.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf + - description: 'Convert tar to directory: ' + title: Convert tar to directory 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory + - description: 'Convert SMILES to MOL: ' + title: Convert SMILES to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL + - description: 'Convert SAM to BigWig: ' + title: Convert SAM to BigWig 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 + - description: 'SMILES to SMILES: ' + title: SMILES to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles + - description: 'Convert FASTA to Bowtie base space Index: ' + title: Convert FASTA to Bowtie base space Index 1.3.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index - description: 'Convert Genomic Intervals To Strict BED12: ' title: Convert Genomic Intervals To Strict BED12 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0 + - description: 'Convert XTC, DCD, and TRR: ' + title: Convert XTC, DCD, and TRR 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert + - description: 'Convert FASTA to fai file: ' + title: Convert FASTA to fai file 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai + - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence + taxonomy file to a 2 column mothur taxonomy_outline format' + title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony + - description: 'Convert BAM to BigWig: ' + title: Convert BAM to BigWig 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0 + - description: 'Convert GFF to Interval Index: ' + title: Convert GFF to Interval Index 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0 - description: 'Convert Interval to tabix: ' title: Convert Interval to tabix 1.0.2 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0 - - description: 'Convert CRAM to BAM: ' - title: Convert CRAM to BAM 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 - - description: 'Convert compressed file to uncompressed.: ' - title: Convert compressed file to uncompressed. 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed - - description: 'Convert Genomic Intervals To Strict BED: ' - title: Convert Genomic Intervals To Strict BED 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 - - description: 'Convert BED, GFF, or VCF to BigWig: ' - title: Convert BED, GFF, or VCF to BigWig 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0 - - description: 'Convert Wiggle to Interval: ' - title: Convert Wiggle to Interval 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 - description: 'Convert MAF to Fasta: ' title: Convert MAF to Fasta 1.0.2 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_fasta_0 - - description: 'Convert SAM to BigWig: ' - title: Convert SAM to BigWig 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 - - description: 'Convert BAM to coordinate-sorted BAM: ' - title: Convert BAM to coordinate-sorted BAM 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam - - description: 'Convert FASTA to 2bit: ' - title: Convert FASTA to 2bit 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit - - description: 'Convert BED to Feature Location Index: ' - title: Convert BED to Feature Location Index 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0 - - description: 'Convert Bam to Bai: ' - title: Convert Bam to Bai 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0 - - description: 'Convert FASTQ files to seek locations: ' - title: Convert FASTQ files to seek locations 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0 - - description: 'Convert BigWig to Wiggle: Convert bigWig to wig' - title: Convert BigWig to Wiggle 377+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=bigwigtowig - - description: 'Convert Biom datasets: ' - title: Convert Biom datasets 2.1.5 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom - - description: 'Convert tabular to CSV: ' - title: Convert tabular to CSV 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv - - description: 'Convert GFF to Feature Location Index: ' - title: Convert GFF to Feature Location Index 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0 - - description: 'Convert PDB to GRO: ' - title: Convert PDB to GRO 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0 - - description: 'Convert BAM to BigWig: ' - title: Convert BAM to BigWig 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0 - - description: 'SMILES to SMILES: ' - title: SMILES to SMILES 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles - - description: 'Convert BED to GFF: ' - title: Convert BED to GFF 2.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0 + - description: 'Convert Picard Interval List to BED6: converter' + title: Convert Picard Interval List to BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 + - description: 'Convert plink pbed to linkage lped: ' + title: Convert plink pbed to linkage lped 0.02 + url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert + - description: 'Convert GRO to PDB: ' + title: Convert GRO to PDB 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0 + - description: 'Convert FASTA to Tabular: ' + title: Convert FASTA to Tabular 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular - description: 'Convert BedGraph to BigWig: ' title: Convert BedGraph to BigWig 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig + - description: 'Convert Genomic Intervals To Strict BED6: ' + title: Convert Genomic Intervals To Strict BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 + - description: 'Convert FASTQ files to seek locations: ' + title: Convert FASTQ files to seek locations 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0 - description: 'Convert Genomic Intervals To Coverage: ' title: Convert Genomic Intervals To Coverage 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0 - - description: 'Convert plink pbed to linkage lped: ' - title: Convert plink pbed to linkage lped 0.02 - url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert - - description: 'Convert GFF to Interval Index: ' - title: Convert GFF to Interval Index 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0 - - description: 'Convert Wiggle to BigWig: ' - title: Convert Wiggle to BigWig 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig + - description: 'Convert GFF to BED: ' + title: Convert GFF to BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0 + - description: 'Convert BED to Feature Location Index: ' + title: Convert BED to Feature Location Index 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0 + - description: 'OpenBabel converter for molecular formats: ' + title: OpenBabel converter for molecular formats 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules + - description: 'Convert Genomic Intervals To Strict BED: ' + title: Convert Genomic Intervals To Strict BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 + - description: 'Convert MAF to Genomic Intervals: ' + title: Convert MAF to Genomic Intervals 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0 + - description: 'Convert PDB to GRO: ' + title: Convert PDB to GRO 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0 + - description: 'Convert Bam to Bai: ' + title: Convert Bam to Bai 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0 - description: 'Convert lped to fped: ' title: Convert lped to fped 0.02 url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert + - description: 'Convert FASTA to 2bit: ' + title: Convert FASTA to 2bit 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit + - description: 'Convert tabular to CSV: ' + title: Convert tabular to CSV 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv - description: 'Convert SAM to BAM without sorting: ' title: Convert SAM to BAM without sorting 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam - - description: 'Convert MOL2 to MOL: ' - title: Convert MOL2 to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol - - description: 'Convert MAF to Genomic Intervals: ' - title: Convert MAF to Genomic Intervals 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0 - - description: 'Convert Len file to Linecount: ' - title: Convert Len file to Linecount 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount - - description: 'Convert FASTA to Tabular: ' - title: Convert FASTA to Tabular 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular - - description: 'Convert Picard Interval List to BED6: converter' - title: Convert Picard Interval List to BED6 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 - - description: 'Convert GRO to PDB: ' - title: Convert GRO to PDB 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0 - - description: 'Convert CSV to tabular: ' - title: Convert CSV to tabular 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular - - description: 'Convert FASTA to len file: ' - title: Convert FASTA to len file 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len - - description: 'Convert CML to SMILES: ' - title: Convert CML to SMILES 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles - - description: 'Convert lped to plink pbed: ' - title: Convert lped to plink pbed 0.02 - url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert - - description: 'Convert Genomic Intervals To Strict BED6: ' - title: Convert Genomic Intervals To Strict BED6 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 - description: 'Convert BAM to queryname-sorted BAM: ' title: Convert BAM to queryname-sorted BAM 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam - - description: 'Convert SMILES to MOL: ' - title: Convert SMILES to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL - - description: 'Convert FASTA to Bowtie base space Index: ' - title: Convert FASTA to Bowtie base space Index 1.3.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index - - description: 'Convert compressed and uncompressed BCF files: ' - title: Convert compressed and uncompressed BCF files 0.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf - - description: 'Convert InChI to MOL: ' - title: Convert InChI to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol - - description: 'Convert tar to directory: ' - title: Convert tar to directory 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory + - description: 'Convert lped to plink pbed: ' + title: Convert lped to plink pbed 0.02 + url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert + - description: 'Convert CSV to tabular: ' + title: Convert CSV to tabular 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular + - description: 'Convert Biom datasets: ' + title: Convert Biom datasets 2.1.5 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom + - description: 'Convert Interval to BGZIP: ' + title: Convert Interval to BGZIP 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0 - description: 'Convert tabular to dbnsfp: ' title: Convert tabular to dbnsfp 1.0.2 url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp - - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence - taxonomy file to a 2 column mothur taxonomy_outline format' - title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony + - description: 'Convert CML to SMILES: ' + title: Convert CML to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles + - description: 'Convert uncompressed file to compressed: ' + title: Convert uncompressed file to compressed 1.16+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz + - description: 'Convert GFF to Feature Location Index: ' + title: Convert GFF to Feature Location Index 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0 + - description: 'Convert BGZ VCF to tabix: ' + title: Convert BGZ VCF to tabix 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 + - description: 'Convert Len file to Linecount: ' + title: Convert Len file to Linecount 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount + - description: 'Convert FASTA to Bowtie color space Index: ' + title: Convert FASTA to Bowtie color space Index 1.2.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index + - description: 'Convert compressed file to uncompressed.: ' + title: Convert compressed file to uncompressed. 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed - description: 'Convert Genomic Intervals To BED: ' title: Convert Genomic Intervals To BED 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0 + - description: 'Convert Wiggle to Interval: ' + title: Convert Wiggle to Interval 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 + - description: 'Convert compressed file to uncompressed.: ' + title: Convert compressed file to uncompressed. 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed + - description: 'Convert neostore.zip files to neostore: ' + title: Convert neostore.zip files to neostore 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore + - description: 'Convert BigWig to Wiggle: Convert bigWig to wig' + title: Convert BigWig to Wiggle 377+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=bigwigtowig + - description: 'Convert CRAM to BAM: ' + title: Convert CRAM to BAM 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 - description: 'Convert Parquet to csv: ' title: Convert Parquet to csv 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv + - description: 'Convert BED, GFF, or VCF to BigWig: ' + title: Convert BED, GFF, or VCF to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0 - description: 'Convert plink pbed to ld reduced format: ' title: Convert plink pbed to ld reduced format 0.02 url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert + - description: 'Convert FASTA to len file: ' + title: Convert FASTA to len file 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len + - description: 'Convert MOL2 to MOL: ' + title: Convert MOL2 to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol + - description: 'Convert BAM to coordinate-sorted BAM: ' + title: Convert BAM to coordinate-sorted BAM 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam homepage: '' id: Galaxy CONVERTER license: '' @@ -6584,6 +6593,9 @@ - description: 'UCSC Archaea: table browser' title: UCSC Archaea 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=ucsc_table_direct_archaea1 + - description: 'SRA: server' + title: SRA 1.0.1 + url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=sra_source - description: 'EBI SRA: ENA SRA' title: EBI SRA 1.0.1 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=ebi_sra_main @@ -6608,6 +6620,9 @@ - description: 'Filter FASTA: on the headers and/or the sequences' title: Filter FASTA 2.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Ffilter_by_fasta_ids%2Ffilter_by_fasta_ids%2F2.3 + - description: 'Sub-sample sequences files: e.g. to reduce coverage' + title: Sub-sample sequences files 0.2.5 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpeterjc%2Fsample_seqs%2Fsample_seqs%2F0.2.5 - description: 'Filter: data on any column using simple expressions' title: Filter 1.1.1 url: https://usegalaxy.org.au/root?tool_id=Filter1 @@ -6647,9 +6662,15 @@ edam-operations: '' edam-topics: '' galaxy: + - description: 'Volcano Plot: create a volcano plot' + title: Volcano Plot 0.0.6 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvolcanoplot%2Fvolcanoplot%2F0.0.6 - description: 'Draw Stacked Bar Plots: for different categories and different criteria' title: Draw Stacked Bar Plots 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdraw_stacked_barplots%2Fdraw_stacked_barplots%2F1.0.0 + - description: 'Plotting tool: for multiple series and graph types' + title: Plotting tool 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fxy_plot%2FXY_Plot_1%2F1.0.2 - description: 'VCF to MAF Custom Track: for display at UCSC' title: VCF to MAF Custom Track 1.0.1 url: https://usegalaxy.org.au/root?tool_id=vcf_to_maf_customtrack1 @@ -6674,12 +6695,43 @@ edam-operations: '' edam-topics: '' galaxy: + - description: 'Extract Pairwise MAF blocks: given a set of genomic intervals' + title: Extract Pairwise MAF blocks 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=Interval2Maf_pairwise1 + - description: 'Extract MAF blocks: given a set of genomic intervals' + title: Extract MAF blocks 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=Interval2Maf1 + - description: 'Split MAF blocks: by Species' + title: Split MAF blocks 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=MAF_split_blocks_by_species1 - description: 'Stitch MAF blocks: given a set of genomic intervals' title: Stitch MAF blocks 1.0.1 url: https://usegalaxy.org.au/root?tool_id=Interval_Maf_Merged_Fasta2 - description: 'Stitch Gene blocks: given a set of coding exon intervals' title: Stitch Gene blocks 1.0.1 url: https://usegalaxy.org.au/root?tool_id=GeneBed_Maf_Fasta2 + - description: 'MAF Coverage Stats: Alignment coverage information' + title: MAF Coverage Stats 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=maf_stats1 + - description: 'Join MAF blocks: by Species' + title: Join MAF blocks 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=MAF_Thread_For_Species1 + - description: 'Filter MAF blocks: by Species' + title: Filter MAF blocks 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=MAF_Limit_To_Species1 + - description: 'Filter MAF blocks: by Size' + title: Filter MAF blocks 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=maf_limit_size1 + - description: 'Extract MAF by block number: given a set of block numbers and a + MAF file' + title: Extract MAF by block number 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=maf_by_block_number1 + - description: 'Reverse Complement: a MAF file' + title: Reverse Complement 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=MAF_Reverse_Complement_1 + - description: 'Filter MAF: by specified attributes' + title: Filter MAF 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=MAF_filter homepage: '' id: galaxy_fetch_alignments_sequences license: '' @@ -6789,12 +6841,21 @@ - description: 'Filter Tabular: ' title: Filter Tabular 3.3.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffilter_tabular%2Ffilter_tabular%2F3.3.0 + - description: 'Join two files: on column allowing a small difference' + title: Join two files 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fjoin_files_on_column_fuzzy%2Fjoin_files_on_column_fuzzy%2F1.0.1 - description: 'Replace column: by values which are defined in a convert file' title: Replace column 0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Freplace_column_by_key_value_file%2Freplace_column_with_key_value_file%2F0.2 - description: 'Replace column: by values which are defined in a convert file' title: Replace column 0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Freplace_column_by_key_value_file%2Freplace_column_with_key_value_file%2F0.2 + - description: 'SQLite to tabular: for SQL query' + title: SQLite to tabular 3.2.0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsqlite_to_tabular%2Fsqlite_to_tabular%2F3.2.0 + - description: 'Table Compute: computes operations on table data' + title: Table Compute 1.2.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftable_compute%2Ftable_compute%2F1.2.4%2Bgalaxy0 - description: 'Add column: to an existing dataset' title: Add column 1.0.0 url: https://usegalaxy.org.au/root?tool_id=addValue @@ -6958,6 +7019,12 @@ - description: 'Count GFF Features: ' title: Count GFF Features 0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcount_gff_features%2Fcount_gff_features%2F0.2 + - description: 'T Test for Two Samples: ' + title: T Test for Two Samples 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ft_test_two_samples%2Ft_test_two_samples%2F1.0.1 + - description: 'Summary Statistics: for any numerical column' + title: Summary Statistics 1.1.2 + url: https://usegalaxy.org.au/root?tool_id=Summary_Statistics1 homepage: '' id: galaxy_statistics license: '' @@ -8462,19 +8529,23 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: hifiasm-meta + biotools: hifiasm-meta bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved + de novo assembler for PacBio Hifi reads. + edam-operations: + - Sequence assembly + edam-topics: + - Sequence assembly + - Metagenomics galaxy: - description: 'Hifiasm_meta: for metagenome assembly using Hifi reads' title: Hifiasm_meta 0.3.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxy-australia%2Fhifiasm_meta%2Fhifiasm_meta%2F0.3.1%2Bgalaxy0 - homepage: '' + homepage: https://github.com/xfengnefx/hifiasm-meta id: hifiasm_meta - license: '' + license: MIT name: hifiasm_meta nci-gadi: '' nci-if89: '' @@ -9203,48 +9274,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Extract Pairwise MAF blocks: given a set of genomic intervals' - title: Extract Pairwise MAF blocks 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=Interval2Maf_pairwise1 - homepage: '' - id: Interval2Maf_pairwise1 - license: '' - name: Interval2Maf_pairwise1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Extract MAF blocks: given a set of genomic intervals' - title: Extract MAF blocks 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=Interval2Maf1 - homepage: '' - id: Interval2Maf1 - license: '' - name: Interval2Maf1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: ipyrad biotools: ipyrad bunya: @@ -9694,27 +9723,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Join two files: on column allowing a small difference' - title: Join two files 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fjoin_files_on_column_fuzzy%2Fjoin_files_on_column_fuzzy%2F1.0.1 - homepage: '' - id: join_files_on_column_fuzzy - license: '' - name: join_files_on_column_fuzzy - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: '' biotools: '' bunya: '' @@ -9955,17 +9963,21 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: kofamscan + biotools: kofamscan bunya: - 1.3.0--hdfd78af_2 - description: '' - edam-operations: '' - edam-topics: '' + description: KofamScan is a gene function annotation tool based on KEGG Orthology + and hidden Markov model. You need KOfam database to use this tool. + edam-operations: + - Sequence analysis + - Gene functional annotation + edam-topics: + - Genomics galaxy: '' - homepage: '' + homepage: https://github.com/takaram/kofam_scan id: kofamscan - license: '' + license: MIT name: kofamscan nci-gadi: '' nci-if89: '' @@ -10596,181 +10608,12 @@ - 1.3.0-gompi-2022a (D) description: '' edam-operations: '' - edam-topics: '' - galaxy: '' - homepage: '' - id: maeparser - license: '' - name: maeparser - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Extract MAF by block number: given a set of block numbers and a - MAF file' - title: Extract MAF by block number 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=maf_by_block_number1 - homepage: '' - id: maf_by_block_number1 - license: '' - name: maf_by_block_number1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Filter MAF: by specified attributes' - title: Filter MAF 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=MAF_filter - homepage: '' - id: MAF_filter - license: '' - name: MAF_filter - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Filter MAF blocks: by Size' - title: Filter MAF blocks 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=maf_limit_size1 - homepage: '' - id: maf_limit_size1 - license: '' - name: maf_limit_size1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Filter MAF blocks: by Species' - title: Filter MAF blocks 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=MAF_Limit_To_Species1 - homepage: '' - id: MAF_Limit_To_Species1 - license: '' - name: MAF_Limit_To_Species1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Reverse Complement: a MAF file' - title: Reverse Complement 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=MAF_Reverse_Complement_1 - homepage: '' - id: MAF_Reverse_Complement_1 - license: '' - name: MAF_Reverse_Complement_1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Split MAF blocks: by Species' - title: Split MAF blocks 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=MAF_split_blocks_by_species1 - homepage: '' - id: MAF_split_blocks_by_species1 - license: '' - name: MAF_split_blocks_by_species1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'MAF Coverage Stats: Alignment coverage information' - title: MAF Coverage Stats 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=maf_stats1 - homepage: '' - id: maf_stats1 - license: '' - name: maf_stats1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Join MAF blocks: by Species' - title: Join MAF blocks 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=MAF_Thread_For_Species1 + edam-topics: '' + galaxy: '' homepage: '' - id: MAF_Thread_For_Species1 + id: maeparser license: '' - name: MAF_Thread_For_Species1 + name: maeparser nci-gadi: '' nci-if89: '' pawsey: '' @@ -18112,27 +17955,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Sub-sample sequences files: e.g. to reduce coverage' - title: Sub-sample sequences files 0.2.5 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpeterjc%2Fsample_seqs%2Fsample_seqs%2F0.2.5 - homepage: '' - id: sample_seqs - license: '' - name: sample_seqs - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: samtools biotools: samtools bunya: @@ -19718,27 +19540,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Split file: to dataset collection' - title: Split file 0.5.2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsplit_file_to_collection%2Fsplit_file_to_collection%2F0.5.2 - homepage: '' - id: split_file_to_collection - license: '' - name: split_file_to_collection - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: '' biotools: '' bunya: '' @@ -19758,48 +19559,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'SQLite to tabular: for SQL query' - title: SQLite to tabular 3.2.0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsqlite_to_tabular%2Fsqlite_to_tabular%2F3.2.0 - homepage: '' - id: sqlite_to_tabular - license: '' - name: sqlite_to_tabular - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'SRA: server' - title: SRA 1.0.1 - url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=sra_source - homepage: '' - id: sra_source - license: '' - name: sra_source - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: sra-tools biotools: sra-tools bunya: @@ -20028,18 +19787,27 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: staramr + biotools: staramr bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: staramr (*AMR) scans bacterial genome contigs against the ResFinder, + PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and + other webservices offered by the Center for Genomic Epidemiology) and compiles + a summary report of detected antimicrobial resistance genes. The star|* in staramr + indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder + databases. + edam-operations: + - Antimicrobial resistance prediction + edam-topics: + - Microbiology + - Public health and epidemiology + - Infectious disease galaxy: - description: 'staramr: Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.' title: staramr 0.10.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fstaramr%2Fstaramr_search%2F0.10.0%2Bgalaxy1 - homepage: '' + homepage: https://github.com/phac-nml/staramr id: staramr license: '' name: staramr @@ -20144,27 +19912,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Summary Statistics: for any numerical column' - title: Summary Statistics 1.1.2 - url: https://usegalaxy.org.au/root?tool_id=Summary_Statistics1 - homepage: '' - id: Summary_Statistics1 - license: '' - name: Summary_Statistics1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: super-focus biotools: super-focus bunya: '' @@ -20302,69 +20049,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'T Test for Two Samples: ' - title: T Test for Two Samples 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ft_test_two_samples%2Ft_test_two_samples%2F1.0.1 - homepage: '' - id: t_test_two_samples - license: '' - name: t_test_two_samples - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Table Compute: computes operations on table data' - title: Table Compute 1.2.4+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftable_compute%2Ftable_compute%2F1.2.4%2Bgalaxy0 - homepage: '' - id: table_compute - license: '' - name: table_compute - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Tabular-to-FASTA: converts tabular file to FASTA format' - title: Tabular-to-FASTA 1.1.1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftabular_to_fasta%2Ftab2fasta%2F1.1.1 - homepage: '' - id: tabular_to_fasta - license: '' - name: tabular_to_fasta - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: targetfinder.org biotools: targetfinder.org bunya: '' @@ -20419,16 +20103,21 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: tbl2asn + biotools: tbl2asn bunya: - 20220427-linux64 - 20230119-linux64 (D) - description: '' - edam-operations: '' - edam-topics: '' + description: Tbl2asn is a command-line program that automates the creation of sequence + records for submission to GenBank. It uses many of the same functions as Genome + Workbench but is driven generally by data files. Tbl2asn generates .sqn files + for submission to GenBank. + edam-operations: + - Deposition + edam-topics: + - Data submission, annotation and curation galaxy: '' - homepage: '' + homepage: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ id: tbl2asn license: '' name: tbl2asn @@ -21508,27 +21197,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Convert VCF to MAF: with vcf2maf' - title: Convert VCF to MAF 1.6.21+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvcf2maf%2Fvcf2maf%2F1.6.21%2Bgalaxy1 - homepage: '' - id: vcf2maf - license: '' - name: vcf2maf - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: vcflib biotools: vcflib bunya: @@ -21740,27 +21408,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Volcano Plot: create a volcano plot' - title: Volcano Plot 0.0.6 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvolcanoplot%2Fvolcanoplot%2F0.0.6 - homepage: '' - id: volcanoplot - license: '' - name: volcanoplot - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: vsearch biotools: vsearch bunya: '' @@ -22225,27 +21872,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Plotting tool: for multiple series and graph types' - title: Plotting tool 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fxy_plot%2FXY_Plot_1%2F1.0.2 - homepage: '' - id: xy_plot - license: '' - name: xy_plot - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: yahs biotools: yahs bunya: '' @@ -22277,24 +21903,35 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: YeastMine + biotools: YeastMine bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: Search and retrieve S. cerevisiae data, populated by SGD and powered + by InterMine + edam-operations: + - Data retrieval + - Visualisation + - Gene-set enrichment analysis + - Query and retrieval + edam-topics: + - Data management + - Genomics + - Proteomics galaxy: - description: 'YeastMine: server' title: YeastMine 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=yeastmine - homepage: '' + homepage: https://yeastmine.yeastgenome.org/yeastmine id: yeastmine - license: '' + license: LGPL-2.1 name: yeastmine nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: 'InterMine: A flexible data warehouse system for the integration and analysis + of heterogeneous biological data' + url: https://doi.org/10.1093/bioinformatics/bts577 resources: - title: .nan url: .nan From 27a566121681c477f45161d546a94d4661202993 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Mon, 24 Jun 2024 03:35:12 +0000 Subject: [PATCH 2/5] Updated the data.yml sourced from australianbiocommons.github.io --- _data/data.yaml | 3397 +++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 2879 insertions(+), 518 deletions(-) diff --git a/_data/data.yaml b/_data/data.yaml index 936f480..cbf538b 100644 --- a/_data/data.yaml +++ b/_data/data.yaml @@ -4,10 +4,12 @@ - '201008' description: 3D de novo assembly (3D-DNA) is a pipeline for de novo assembly using HiC. + edam-inputs: [] edam-operations: - Scaffolding - De-novo assembly - Genome assembly + edam-outputs: [] edam-topics: - Sequence assembly - Mapping @@ -33,8 +35,21 @@ - 1.0.0-gompi-2021a description: Mass screening of contigs for antimicrobial resistance or virulence genes. + edam-inputs: + - formats: + - EMBL format + - GenBank format + - FASTA + term: FASTA + - formats: + - FASTA + term: FASTA edam-operations: - Antimicrobial resistance prediction + edam-outputs: + - formats: + - TSV + term: TSV edam-topics: - Genomics - Microbiology @@ -65,10 +80,19 @@ biotools: abyss bunya: '' description: De novo genome sequence assembler using short reads. + edam-inputs: + - formats: + - FASTQ + - FASTA + term: FASTA edam-operations: - Genome assembly - De-novo assembly - Scaffolding + edam-outputs: + - formats: + - FASTA + term: FASTA edam-topics: - Sequence assembly galaxy: @@ -99,8 +123,10 @@ (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.' + edam-inputs: [] edam-operations: - Modelling and simulation + edam-outputs: [] edam-topics: - Molecular modelling - Computational biology @@ -134,8 +160,10 @@ by themselves, and with Amber (Assisted Model Building with Energy Refinement) itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models. + edam-inputs: [] edam-operations: - Molecular dynamics simulation + edam-outputs: [] edam-topics: - Molecular modelling - Molecular dynamics @@ -165,10 +193,12 @@ \ as FASTA and GenBank, and it applies a set of statistical and visualization\ \ methods in different ways, to reveal information about codon context, codon\ \ usage, nucleotide repeats within open reading frames (ORFeome) and others." + edam-inputs: [] edam-operations: - Statistical inference - Nucleic acid sequence analysis - Coding region prediction + edam-outputs: [] edam-topics: - DNA - Gene expression @@ -194,7 +224,9 @@ "Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray."' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Export AnnData and loom files: Interconvert AnnData and Loom formats' @@ -231,8 +263,10 @@ using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. + edam-inputs: [] edam-operations: - Annotation + edam-outputs: [] edam-topics: '' galaxy: - description: 'annotateMyIDs: annotate a generic set of identifiers' @@ -256,10 +290,12 @@ metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. + edam-inputs: [] edam-operations: - Sequence clustering - Gene prediction - Differential gene expression analysis + edam-outputs: [] edam-topics: - Molecular interactions, pathways and networks - Gene and protein families @@ -294,9 +330,11 @@ bunya: - 0.4.2-gcccore-10.3.0 description: Convert various sequence formats to FASTA + edam-inputs: [] edam-operations: - Formatting - Sequence conversion + edam-outputs: [] edam-topics: - Data quality management - Genomics @@ -318,10 +356,12 @@ description: Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment. + edam-inputs: [] edam-operations: - Editing - Sequence annotation - Genome annotation + edam-outputs: [] edam-topics: - Data submission, annotation and curation - Gene transcripts @@ -346,8 +386,10 @@ biotools: aragorn bunya: '' description: ARAGORN detects tRNA, mtRNA info about tmRNA, and tmRNA genes + edam-inputs: [] edam-operations: - Gene prediction + edam-outputs: [] edam-topics: - Functional, regulatory and non-coding RNA - Genomics @@ -372,7 +414,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -394,9 +438,20 @@ based on the STAR aligner. In addition to fusions, it can detect exon duplications/inversions and truncations of genes (i.e., breakpoints in introns and intergenic regions). Arriba is the winner of the DREAM SMC-RNA Challenge. + edam-inputs: + - formats: + - BAM + - SAM + - CRAM + - FASTQ-illumina + term: FASTQ-illumina edam-operations: - Structural variation detection - Split read mapping + edam-outputs: + - formats: + - TSV + term: TSV edam-topics: - Gene transcripts - RNA splicing @@ -432,8 +487,10 @@ PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. + edam-inputs: [] edam-operations: - Gene prediction + edam-outputs: [] edam-topics: - Gene transcripts - Gene and protein families @@ -484,8 +541,10 @@ description: AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use. + edam-inputs: [] edam-operations: - Molecular docking + edam-outputs: [] edam-topics: - Drug discovery - Molecular modelling @@ -523,8 +582,29 @@ biotools: bakta bunya: '' description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids + edam-inputs: + - formats: + - FASTA + term: FASTA + - formats: + - TSV + term: TSV edam-operations: - Genome annotation + edam-outputs: + - formats: + - GenBank format + - EMBL format + - GFF3 + - JSON + - TSV + term: TSV + - formats: + - FASTA + term: FASTA + - formats: + - FASTA + term: FASTA edam-topics: - Genomics - Data submission, annotation and curation @@ -553,9 +633,11 @@ - 2.5.2-gcc-11.3.0 (D) description: BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. + edam-inputs: [] edam-operations: - Data handling - Sequence alignment analysis + edam-outputs: [] edam-topics: - Sequencing - Data management @@ -589,8 +671,10 @@ biotools: bamutil bunya: '' description: Bamutil provides a serie of programs to work on SAM/BAM files. + edam-inputs: [] edam-operations: - Data handling + edam-outputs: [] edam-topics: - Data management galaxy: @@ -617,8 +701,12 @@ description: GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. + edam-inputs: + - formats: [] + term: Sequence assembly edam-operations: - Sequence assembly visualisation + edam-outputs: [] edam-topics: - Genomics - Sequence assembly @@ -648,8 +736,16 @@ description: Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Gene prediction + edam-outputs: + - formats: + - GFF3 + term: GFF3 edam-topics: - Genomics - Model organisms @@ -674,7 +770,9 @@ bunya: - 1.5.3 matlab description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -696,6 +794,7 @@ description: BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. + edam-inputs: [] edam-operations: - RNA-Seq analysis - Sequence trimming @@ -703,6 +802,7 @@ - Sequence contamination filtering - Read binning - Sequence alignment + edam-outputs: [] edam-topics: - Sequencing - RNA splicing @@ -733,9 +833,13 @@ description: A tool for filling the gap created by genomic data processing/analysis by rebasing some analysis results against the parent features which were originally analysed. + edam-inputs: + - formats: [] + term: Identifier (by type of data) edam-operations: - Data handling - Formatting + edam-outputs: [] edam-topics: '' galaxy: - description: 'Rebase GFF3 features: against parent features' @@ -769,9 +873,19 @@ description: BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. + edam-inputs: + - formats: + - VCF + - BCF + term: BCF edam-operations: - Data handling - Variant calling + edam-outputs: + - formats: + - VCF + - BCF + term: BCF edam-topics: - Genetic variation - DNA polymorphism @@ -907,7 +1021,9 @@ bunya: - 2.20.0-gcc-11.3.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -927,9 +1043,11 @@ - 5.4.22jul22.46e-java-11 description: Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. + edam-inputs: [] edam-operations: - Phasing - Imputation + edam-outputs: [] edam-topics: - Population genetics galaxy: '' @@ -960,9 +1078,11 @@ - 4.0.0-gcc-11.3.0 (D) description: BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. + edam-inputs: [] edam-operations: - Phylogenetic inference - Standardisation and normalisation + edam-outputs: [] edam-topics: - Phylogenetics - Statistics and probability @@ -992,10 +1112,12 @@ inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. + edam-inputs: [] edam-operations: - Multiple sequence alignment - Phylogenetic tree generation (from molecular sequences) - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + edam-outputs: [] edam-topics: - Phylogenetics - Sequence analysis @@ -1030,9 +1152,11 @@ tree is weighted proportional to its posterior probability. It includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results. + edam-inputs: [] edam-operations: - Phylogenetic tree reconstruction - Phylogenetic tree analysis (shape) + edam-outputs: [] edam-topics: - Phylogenetics - Phylogenomics @@ -1056,8 +1180,10 @@ bunya: '' description: Convert a BED format file of the proteins from a proteomics search database into a tabular format for the Multiomics Visualization Platform (MVP). + edam-inputs: [] edam-operations: - Conversion + edam-outputs: [] edam-topics: - Literature and language galaxy: @@ -1082,8 +1208,10 @@ - 2.30.0-gcc-11.3.0 (D) description: BEDTools is an extensive suite of utilities for comparing genomic features in BED format. + edam-inputs: [] edam-operations: - Mapping + edam-outputs: [] edam-topics: - Genomics galaxy: @@ -1252,12 +1380,14 @@ The pipeline can be downloaded as a vragrant virtual machine (https://app.vagrantup.com/bellerophon/boxes/bellerophon). This is recommended, as it avoids backwards compatibility problems with TransRate' + edam-inputs: [] edam-operations: - De-novo assembly - Validation - de Novo sequencing - Transcriptome assembly - Chimera detection + edam-outputs: [] edam-topics: - Transcriptomics - Sequence assembly @@ -1285,9 +1415,14 @@ biotools: berokka bunya: '' description: Trim, circularise, orient and filter long read bacterial genome assemblies + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Filtering - Sequence trimming + edam-outputs: [] edam-topics: - Computer science galaxy: @@ -1310,7 +1445,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Convert image format: with Bioformats' @@ -1336,7 +1473,9 @@ - 1.7.3-gcc-10.3.0 - 1.7.3-gcc-11.3.0 (D) description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -1355,12 +1494,14 @@ bunya: '' description: Bio3D is an R package containing utilities for the analysis of protein structure, sequence and trajectory data. + edam-inputs: [] edam-operations: - Essential dynamics - Molecular dynamics - Protein structure analysis - Principal component visualisation - Sequence trimming + edam-outputs: [] edam-topics: - Structure analysis - Gene and protein families @@ -1397,7 +1538,9 @@ bunya: - '3.1' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -1416,8 +1559,10 @@ bunya: '' description: Tools for early stage NGS alignment file processing including fast sorting and duplicate marking. + edam-inputs: [] edam-operations: - Filtering + edam-outputs: [] edam-topics: - Sequencing galaxy: '' @@ -1440,7 +1585,9 @@ bunya: - 3.01-gcc-11.3.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://github.com/Ensembl/Bio-DB-HTS @@ -1463,8 +1610,10 @@ to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. + edam-inputs: [] edam-operations: - Formatting + edam-outputs: [] edam-topics: - Laboratory information management - Sequence analysis @@ -1492,7 +1641,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Bionano Hybrid Scaffold: automates the scaffolding process' @@ -1517,9 +1668,11 @@ description: A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. + edam-inputs: [] edam-operations: - Data handling - Service invocation + edam-outputs: [] edam-topics: - Genomics - Software engineering @@ -1545,11 +1698,13 @@ - 1.79-foss-2022a (D) description: Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. + edam-inputs: [] edam-operations: - Deposition - Service invocation - Query and retrieval - Aggregation + edam-outputs: [] edam-topics: - Bioinformatics - Data management @@ -1587,10 +1742,18 @@ bunya: '' description: BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. + edam-inputs: + - formats: + - SMILES + term: SMILES edam-operations: - Metabolic pathway prediction - PTM site prediction - Natural product identification + edam-outputs: + - formats: + - SMILES + term: SMILES edam-topics: - Small molecules - Endocrinology and metabolism @@ -1620,10 +1783,12 @@ bunya: '' description: Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion. + edam-inputs: [] edam-operations: - Methylation analysis - Read mapping - Bisulfite mapping + edam-outputs: [] edam-topics: - Epigenomics - Genomics @@ -1664,9 +1829,24 @@ description: A tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Sequence similarity search - Sequence alignment + edam-outputs: + - formats: + - BLAST XML results format + - BLAST XML v2 results format + - TSV + - CSV + - ASN.1 sequence format + - JSON + - Binary format + - Textual format + term: Textual format edam-topics: - Sequence analysis - Bioinformatics @@ -1703,9 +1883,24 @@ description: A tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Sequence similarity search - Sequence alignment + edam-outputs: + - formats: + - BLAST XML results format + - BLAST XML v2 results format + - TSV + - CSV + - ASN.1 sequence format + - JSON + - Binary format + - Textual format + term: Textual format edam-topics: - Sequence analysis - Bioinformatics @@ -1791,8 +1986,10 @@ bunya: - 3.7-gcc-11.3.0 description: Fast, accurate spliced alignment of DNA sequences. + edam-inputs: [] edam-operations: - Sequence alignment + edam-outputs: [] edam-topics: - Sequence analysis galaxy: '' @@ -1814,8 +2011,16 @@ biotools: blockbuster bunya: '' description: detect blocks of overlapping reads using a gaussian-distribution approach + edam-inputs: + - formats: + - BED + term: BED edam-operations: - RNA-Seq analysis + edam-outputs: + - formats: + - Textual format + term: Textual format edam-topics: - Genomics galaxy: @@ -1840,7 +2045,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'BlockClust: efficient clustering and classification of non-coding @@ -1863,7 +2070,9 @@ bunya: - 2.4.1-intel-2022a description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://alkesgroup.broadinstitute.org/BOLT-LMM/BOLT-LMM_manual.html @@ -1885,8 +2094,15 @@ description: Boost is a set of libraries for the C++ programming language that provides support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing. + edam-inputs: + - formats: + - Workflow format + term: Workflow format + - formats: [] + term: Image edam-operations: - Image analysis + edam-outputs: [] edam-topics: - Pure mathematics - Imaging @@ -1913,8 +2129,28 @@ bunya: - 1.3.1-gcc-11.3.0 description: Bowtie is an ultrafast, memory-efficient short read aligner. + edam-inputs: + - formats: + - HTML + - FASTA + term: FASTA + - formats: + - FASTQ-solexa + - FASTQ-sanger + - FASTQ-illumina + term: FASTQ-illumina edam-operations: - Sequence alignment + edam-outputs: + - formats: + - SAM + term: SAM + - formats: + - Textual format + term: Textual format + - formats: + - FASTQ + term: FASTQ edam-topics: - Mapping - Genomics @@ -1957,8 +2193,17 @@ an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.' + edam-inputs: + - formats: + - FASTQ + term: FASTQ edam-operations: - Read mapping + edam-outputs: + - formats: + - BAM + - SAM + term: SAM edam-topics: - Mapping - Genomics @@ -1997,8 +2242,10 @@ - 3.0.3 description: Pipeline for unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. + edam-inputs: [] edam-operations: - Genome annotation + edam-outputs: [] edam-topics: - RNA-Seq - RNA @@ -2025,8 +2272,22 @@ biotools: breseq bunya: '' description: Runs Breseq software on a set of fastq files. + edam-inputs: + - formats: + - FASTQ + term: FASTQ + - formats: + - SAM + term: SAM + - formats: + - TSV + term: TSV edam-operations: - Polymorphism detection + edam-outputs: + - formats: + - Textual format + term: Textual format edam-topics: - Sequencing - Sequence analysis @@ -2062,11 +2323,18 @@ description: Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Sequence assembly validation - Scaffolding - Genome assembly - Transcriptome assembly + edam-outputs: + - formats: [] + term: Sequence report edam-topics: - Sequence assembly - Genomics @@ -2101,10 +2369,12 @@ biotools: buttery_eel bunya: '' description: Accelerated nanopore basecalling with SLOW5 data format. + edam-inputs: [] edam-operations: - Base-calling - Formatting - Splitting + edam-outputs: [] edam-topics: - Computer science - Protein expression @@ -2135,8 +2405,15 @@ - 0.7.17-gcccore-11.3.0 (D) description: Fast, accurate, memory-efficient aligner for short and long sequencing reads + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Genome indexing + edam-outputs: + - formats: [] + term: Genome index edam-topics: - Mapping galaxy: @@ -2180,8 +2457,13 @@ description: Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Sequence alignment + edam-outputs: [] edam-topics: - Mapping galaxy: @@ -2208,7 +2490,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'bwameth: Fast and accurate aligner of BS-Seq reads.' @@ -2229,7 +2513,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://sourceforge.net/projects/bio-bwa/files/bwakit/ @@ -2250,7 +2536,9 @@ bunya: '' description: Tools for manipulating biological data, particularly multiple sequence alignments. + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: - Sequence analysis galaxy: @@ -2319,7 +2607,9 @@ users to specify customized operations when calling driver genes, and provides solid statistical evaluations and interpretable visualizations on the integration results + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: - Genetic variation - Oncology @@ -2345,9 +2635,11 @@ biotools: cactus bunya: '' description: Cactus is a reference-free whole-genome multiple alignment program. + edam-inputs: [] edam-operations: - Multiple sequence alignment - Genome alignment + edam-outputs: [] edam-topics: - Genomics - Sequence analysis @@ -2388,8 +2680,10 @@ description: Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments. + edam-inputs: [] edam-operations: - Sequence annotation + edam-outputs: [] edam-topics: - Metabolomics galaxy: @@ -2422,8 +2716,10 @@ - 2.2-gcccore-11.3.0 (D) description: De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. + edam-inputs: [] edam-operations: - De-novo assembly + edam-outputs: [] edam-topics: - Genomics galaxy: @@ -2454,11 +2750,13 @@ biotools: cap3 bunya: '' description: Web-based contig assembly. + edam-inputs: [] edam-operations: - Genome assembly - Mapping assembly - Sequence assembly - Scaffolding + edam-outputs: [] edam-topics: - Sequence assembly - Sequencing @@ -2487,10 +2785,20 @@ description: Implements statistical and computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification. + edam-inputs: + - formats: + - imzML metadata file + - ibd + term: ibd edam-operations: - Spectral analysis - Standardisation and normalisation - Mass spectra calibration + edam-outputs: + - formats: + - imzML metadata file + - ibd + term: ibd edam-topics: - Proteomics - Data visualisation @@ -2547,10 +2855,12 @@ gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. + edam-inputs: [] edam-operations: - Taxonomic classification - Sequence assembly - Coding region prediction + edam-outputs: [] edam-topics: - Metagenomics - Metagenomic sequencing @@ -2584,8 +2894,22 @@ - 4.8.1-gcc-10.3.0 - 4.8.1-gcc-11.3.0 (D) description: Cluster a nucleotide dataset into representative sequences. + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Sequence clustering + edam-outputs: + - formats: + - Textual format + term: Textual format + - formats: + - Textual format + term: Textual format + - formats: + - FASTA + term: FASTA edam-topics: - Sequencing galaxy: @@ -2623,9 +2947,11 @@ - 0.5.3 description: celseq2 is a Python framework for generating the UMI count matrix from CEL-Seq2 sequencing data. + edam-inputs: [] edam-operations: - Demultiplexing - RNA-Seq analysis + edam-outputs: [] edam-topics: - RNA-Seq - Transcriptomics @@ -2648,10 +2974,12 @@ bunya: '' description: Tool for quantifying data from biological images, particularly in high-throughput experiments. + edam-inputs: [] edam-operations: - Quantification - Image analysis - Parsing + edam-outputs: [] edam-topics: - Imaging - Microarray experiment @@ -2747,7 +3075,9 @@ bunya: - 7.1.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger @@ -2768,9 +3098,11 @@ description: cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas. + edam-inputs: [] edam-operations: - Visualisation - Essential dynamics + edam-outputs: [] edam-topics: - Transcriptomics - Cell biology @@ -2798,12 +3130,14 @@ - 1.2.2-foss-2022a (D) description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. + edam-inputs: [] edam-operations: - Sequence assembly validation - Validation - Sequence composition calculation - Sequencing quality control - Statistical calculation + edam-outputs: [] edam-topics: - Genomics - Phylogenomics @@ -2832,12 +3166,14 @@ - '2015_01_16' description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. + edam-inputs: [] edam-operations: - Sequence assembly validation - Validation - Sequence composition calculation - Sequencing quality control - Statistical calculation + edam-outputs: [] edam-topics: - Genomics - Phylogenomics @@ -2866,8 +3202,15 @@ description: Database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. + edam-inputs: + - formats: [] + term: Compound ID (ChEMBL) edam-operations: - Data retrieval + edam-outputs: + - formats: + - HTML + term: HTML edam-topics: - Small molecules - Chemical biology @@ -2911,10 +3254,12 @@ There are two ways to try out chemfp. From the download page page you can request an evaluation copy of the most recent version of chemfp, or you can download an earlier version for no cost under the MIT license' + edam-inputs: [] edam-operations: - Database search - Standardisation and normalisation - Formatting + edam-outputs: [] edam-topics: - Cheminformatics - Chemistry @@ -2961,10 +3306,12 @@ we provide four example workflows which illustrate the capabilities of the ChemicalToolbox, covering assembly of a compound library, hole filling, protein-ligand docking, and construction of a quantitative structure-activity relationship (QSAR) model. + edam-inputs: [] edam-operations: - Protein-ligand docking - Molecular dynamics - Sequence assembly + edam-outputs: [] edam-topics: - Cheminformatics - Molecular modelling @@ -3003,11 +3350,23 @@ the significance of overlap among ChIP peak data sets, and incorporate GEO database to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. + edam-inputs: + - formats: + - BED + - Sequence range format + term: Sequence range format edam-operations: - Sequence annotation - Visualisation - Gene-set enrichment analysis - Sequence feature comparison + edam-outputs: + - formats: + - Textual format + term: Textual format + - formats: + - Textual format + term: Textual format edam-topics: - ChIP-seq - Data visualisation @@ -3035,8 +3394,10 @@ bunya: '' description: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons (dotplot). + edam-inputs: [] edam-operations: - Dot plot plotting + edam-outputs: [] edam-topics: - Comparative genomics - Sequence analysis @@ -3061,7 +3422,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'CIRCexplorer: ' @@ -3083,7 +3446,9 @@ bunya: - 1.5.5--py_3 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://sanger-pathogens.github.io/circlator/ @@ -3102,8 +3467,19 @@ bunya: '' description: Circos is tool for visualizing data in a circular format. It was developed for genomic data but can work for many other kinds of data as well. + edam-inputs: + - formats: + - TSV + term: TSV edam-operations: - Visualisation + edam-outputs: + - formats: + - Textual format + term: Textual format + - formats: + - Image format + term: Image format edam-topics: - Comparative genomics - Data visualisation @@ -3171,7 +3547,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'CLIFinder: Find chimerics transcripts containing LINEs sequences' @@ -3192,7 +3570,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'climate stripes: from timeseries' @@ -3234,10 +3614,12 @@ clustermap.js is an interactive, reusable d3 chart designed to visualise homology between multiple gene clusters.' + edam-inputs: [] edam-operations: - Sequence clustering - Sequence cluster visualisation - Dendrogram visualisation + edam-outputs: [] edam-topics: - Molecular interactions, pathways and networks - Sequence analysis @@ -3265,7 +3647,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'ClipKIT. Alignment trimming software for phylogenetics.: ' @@ -3287,8 +3671,16 @@ bunya: '' description: "Multiple sequence alignment software. The name is occassionally spelled\ \ as ClustalOmega, Clustal \u03A9, Clustal\u03A9, Clustal O, ClustalO." + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Multiple sequence alignment + edam-outputs: + - formats: + - FASTA + term: FASTA edam-topics: - Sequence analysis galaxy: '' @@ -3316,8 +3708,16 @@ bunya: '' description: Multiple sequence alignment software. Old deprecated versions. Even older versions were CLUSTAL and CLUSTAL V (ClustalV). + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Multiple sequence alignment + edam-outputs: + - formats: + - FASTA + term: FASTA edam-topics: - Sequence analysis galaxy: @@ -3354,10 +3754,12 @@ bunya: '' description: ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. + edam-inputs: [] edam-operations: - Database search - Protein structure prediction - Fold recognition + edam-outputs: [] edam-topics: - Protein folds and structural domains - Protein folding, stability and design @@ -3386,7 +3788,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Compose text parameter value: from parameters' @@ -3407,7 +3811,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -3426,7 +3832,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Count: occurrences of each record' @@ -3452,9 +3860,11 @@ \ takes as input the nucleotides sequences or genomic coordinates of RNAs and\ \ outputs the probabilities p (0 \u2264 p \u2264 1), which measure the likelihood\ \ of protein coding." + edam-inputs: [] edam-operations: - Regression analysis - Query and retrieval + edam-outputs: [] edam-topics: - Functional, regulatory and non-coding RNA - Gene transcripts @@ -3484,7 +3894,9 @@ - 1.2.0 star-ccm+ description: Software to generate CRISPR guide RNAs against genomes annotated with individual variation. + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: - Genetic variation galaxy: '' @@ -3506,7 +3918,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'CTSM/FATES-EMERALD: Functionally Assembled Terrestrial Ecosystem @@ -3528,7 +3942,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://developer.nvidia.com/cuda-toolkit @@ -3555,7 +3971,9 @@ \ library of primitives for deep neural networks. cuDNN provides highly tuned\ \ implementations for standard routines such as forward and backward convolution,\ \ pooling, normalization, and activation layers." + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: - Machine learning galaxy: '' @@ -3581,9 +3999,22 @@ samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. + edam-inputs: + - formats: + - BAM + - SAM + term: SAM edam-operations: - RNA-seq time series data analysis - Transcriptome assembly + edam-outputs: + - formats: + - GTF + term: GTF + - formats: [] + term: Gene transcript report + - formats: [] + term: Gene expression data edam-topics: - RNA splicing - Transcriptomics @@ -3635,9 +4066,11 @@ description: Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations. + edam-inputs: [] edam-operations: - Sequence analysis - Sequence visualisation + edam-outputs: [] edam-topics: - Sequencing galaxy: @@ -3663,9 +4096,44 @@ bunya: '' description: Generate customized protein sequence database from RNA-Seq data for proteomics search. + edam-inputs: + - formats: + - BAM + - Textual format + - VCF + - FASTA + term: FASTA + - formats: + - BAM + - Textual format + - VCF + - FASTA + term: FASTA + - formats: + - BAM + - Textual format + - VCF + - FASTA + term: FASTA + - formats: + - BAM + - Textual format + - VCF + - FASTA + term: FASTA + - formats: + - BAM + - Textual format + - VCF + - FASTA + term: FASTA edam-operations: - Generation - Sequence annotation + edam-outputs: + - formats: + - FASTA + term: FASTA edam-topics: - Data integration and warehousing - RNA-Seq @@ -3696,10 +4164,26 @@ - 4.2-gcccore-11.3.0 (D) description: Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. + edam-inputs: + - formats: + - FASTQ + - FASTA + term: FASTA + - formats: + - BAM + term: BAM edam-operations: - Sequence trimming - Primer removal - Read pre-processing + edam-outputs: + - formats: + - FASTQ + - FASTA + term: FASTA + - formats: + - BAM + term: BAM edam-topics: - Genomics - Probes and primers @@ -3738,10 +4222,12 @@ without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis + edam-inputs: [] edam-operations: - Split read mapping - Genotyping - Structural variation detection + edam-outputs: [] edam-topics: - DNA structural variation - Sequencing @@ -3775,9 +4261,11 @@ sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. + edam-inputs: [] edam-operations: - Variant calling - DNA barcoding + edam-outputs: [] edam-topics: - Sequencing - Genetic variation @@ -3835,7 +4323,9 @@ bunya: - 2.0.5 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://dadi.readthedocs.io/en/latest/ @@ -3853,7 +4343,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Datamash: (operations on tabular data)' @@ -3874,7 +4366,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Protein Database Downloader: ' @@ -3895,7 +4389,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -3915,7 +4411,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -3934,7 +4432,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -3956,9 +4456,11 @@ - 3.5.2-foss-2022a (D) description: User-friendly tools for the normalization and visualization of deep-sequencing data. + edam-inputs: [] edam-operations: - Standardisation and normalisation - Visualisation + edam-outputs: [] edam-topics: - Genomics - ChIP-seq @@ -4050,12 +4552,14 @@ classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats. + edam-inputs: [] edam-operations: - Phylogenetic inference - Phylogenetic tree distances calculation - Phylogenetic tree editing - Phylogenetic tree topology analysis - Phylogenetic tree bootstrapping + edam-outputs: [] edam-topics: - Phylogenetics - Phylogenomics @@ -4080,9 +4584,17 @@ on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. + edam-inputs: + - formats: + - DSV + term: DSV edam-operations: - Differential gene expression analysis - RNA-Seq analysis + edam-outputs: + - formats: + - DSV + term: DSV edam-topics: - RNA-Seq galaxy: @@ -4113,9 +4625,11 @@ that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. + edam-inputs: [] edam-operations: - Enrichment analysis - Exonic splicing enhancer prediction + edam-outputs: [] edam-topics: - RNA-Seq galaxy: @@ -4149,10 +4663,12 @@ description: The Dfam database is a open collection of Transposable Element DNA sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations. + edam-inputs: [] edam-operations: - Genome annotation - Sequence visualisation - Pairwise sequence alignment + edam-outputs: [] edam-topics: - DNA - Phylogeny @@ -4187,10 +4703,12 @@ None required (for .raw, .mzML and .dia processing). Two executables are provided: DiaNN.exe (a command-line tool) and DIA-NN.exe (a GUI implemented as a wrapper for DiaNN.exe)' + edam-inputs: [] edam-operations: - Quantification - Spectral library search - Protein identification + edam-outputs: [] edam-topics: - Proteomics - Proteomics experiment @@ -4223,11 +4741,19 @@ It enables untargeted peptide and protein identification and quantitation using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation. + edam-inputs: + - formats: + - mzXML + term: mzXML edam-operations: - Peak detection - Spectrum calculation - Retention time prediction - Mass spectra calibration + edam-outputs: + - formats: + - MGF + term: MGF edam-topics: - Proteomics - Proteomics experiment @@ -4260,8 +4786,10 @@ protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. + edam-inputs: [] edam-operations: - Sequence alignment analysis + edam-outputs: [] edam-topics: - Sequence analysis - Proteins @@ -4295,10 +4823,12 @@ bunya: '' description: diaPASEF is an appproch for parallel accumulation-serial fragmentation combined with data-independent acquisition. + edam-inputs: [] edam-operations: - Deisotoping - Ion counting - Protein identification + edam-outputs: [] edam-topics: - Proteomics experiment - Proteomics @@ -4330,8 +4860,10 @@ description: Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. + edam-inputs: [] edam-operations: - Differential binding analysis + edam-outputs: [] edam-topics: - ChIP-seq galaxy: @@ -4355,7 +4887,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -4378,8 +4912,10 @@ data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. + edam-inputs: [] edam-operations: - Loading + edam-outputs: [] edam-topics: - Gene expression - RNA-seq @@ -4409,7 +4945,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Compute P-values and Correlation Coefficients for Feature Occurrences: @@ -4448,11 +4986,13 @@ bunya: - '1.10' description: Fast and Accurate Genome-wide Phasing and Imputation in a Single Tool. + edam-inputs: [] edam-operations: - Imputation - Phasing - Genotyping - Genome indexing + edam-outputs: [] edam-topics: - Genotype and phenotype - Sequencing @@ -4480,8 +5020,10 @@ description: EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. + edam-inputs: [] edam-operations: - Service management + edam-outputs: [] edam-topics: - Computer science galaxy: '' @@ -4505,8 +5047,21 @@ tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. + edam-inputs: + - formats: + - Sequence record format + term: Sequence record format edam-operations: - Differential gene expression analysis + edam-outputs: + - formats: + - Textual format + - Image format + term: Image format + - formats: + - Textual format + - Image format + term: Image format edam-topics: - Genetics - RNA-Seq @@ -4544,8 +5099,21 @@ tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. + edam-inputs: + - formats: + - Sequence record format + term: Sequence record format edam-operations: - Differential gene expression analysis + edam-outputs: + - formats: + - Textual format + - Image format + term: Image format + - formats: + - Textual format + - Image format + term: Image format edam-topics: - Genetics - RNA-Seq @@ -4583,8 +5151,10 @@ EDirect connects to Entrez through the Entrez Programming Utilities interface. It supports searching by indexed terms, looking up precomputed neighbors or links, filtering results by date or category, and downloading record summaries or reports. + edam-inputs: [] edam-operations: - Information retrieval + edam-outputs: [] edam-topics: - Data integration and warehousing galaxy: '' @@ -4611,8 +5181,10 @@ The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches, as it avoids transferring annotations from close paralogs.' + edam-inputs: [] edam-operations: - Database search + edam-outputs: [] edam-topics: - Metagenomics - Genomics @@ -4651,8 +5223,16 @@ bunya: '' description: This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. + edam-inputs: + - formats: + - TSV + term: TSV edam-operations: - Gene set testing + edam-outputs: + - formats: + - HTML + term: HTML edam-topics: - Systems biology galaxy: @@ -4695,8 +5275,10 @@ automated processing of large numbers of data sets, by means of scripting. Nowadays elastix is accompanied by SimpleElastix , making it available in languages like C++, Python, Java, R, Ruby, C# and Lua.' + edam-inputs: [] edam-operations: - Image analysis + edam-outputs: [] edam-topics: - Medical imaging - Oncology @@ -4729,12 +5311,14 @@ bunya: '' description: Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. + edam-inputs: [] edam-operations: - Sequence analysis - Local alignment - Sequence alignment analysis - Global alignment - Sequence alignment + edam-outputs: [] edam-topics: - Molecular biology - Sequence analysis @@ -5084,11 +5668,13 @@ contextual data relating to sequenced samples and experimental design. Serving both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data. + edam-inputs: [] edam-operations: - Sequence similarity search - Deposition - Sequence assembly - Data retrieval + edam-outputs: [] edam-topics: - Data submission, annotation and curation - Transcription factors and regulatory sites @@ -5124,8 +5710,16 @@ description: EncyclopeDIA is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. + edam-inputs: + - formats: + - TraML + term: TraML edam-operations: - Formatting + edam-outputs: + - formats: + - SQLite format + term: SQLite format edam-topics: - Proteomics - Proteomics experiment @@ -5165,7 +5759,9 @@ bunya: - 0.6.5 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://github.com/geronimp/enrichM @@ -5183,7 +5779,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -5211,8 +5809,10 @@ calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org + edam-inputs: [] edam-operations: - Phylogenetic analysis + edam-outputs: [] edam-topics: - Phylogenetics galaxy: '' @@ -5232,7 +5832,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'EtherCalc: ' @@ -5256,12 +5858,14 @@ Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. The database portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + edam-inputs: [] edam-operations: - Database search - Deposition - Generation - Query and retrieval - Data retrieval + edam-outputs: [] edam-topics: - Model organisms - Model organisms @@ -5289,10 +5893,12 @@ bunya: '' description: ExaBayes is a software package for Bayesian phylogenetic tree inference. It is particularly suitable for large-scale analyses on computer clusters. + edam-inputs: [] edam-operations: - Phylogenetic inference - Phylogenetic tree editing - Phylogenetic tree topology analysis + edam-outputs: [] edam-topics: - Phylogenetics galaxy: '' @@ -5312,8 +5918,10 @@ biotools: ExaML bunya: '' description: Tool for phylogenomic analyses on supercomputers. + edam-inputs: [] edam-operations: - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + edam-outputs: [] edam-topics: - Phylogeny - Phylogenomics @@ -5339,10 +5947,12 @@ - 2.4.0--hf34a1b8_7 description: A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. + edam-inputs: [] edam-operations: - Pairwise sequence alignment - Protein threading - Genome alignment + edam-outputs: [] edam-topics: - Sequence analysis - Sequence sites, features and motifs @@ -5370,7 +5980,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Export datasets: to remote files source' @@ -5393,8 +6005,10 @@ description: export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. + edam-inputs: [] edam-operations: - Conversion + edam-outputs: [] edam-topics: - Taxonomy - Metabolomics @@ -5426,8 +6040,23 @@ transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It can be used to resolve ambiguous mappings in other high-throughput sequencing based applications. + edam-inputs: + - formats: + - FASTA + term: FASTA + - formats: + - BAM + - SAM + term: SAM edam-operations: - Imputation + edam-outputs: + - formats: [] + term: Report + - formats: [] + term: Data + - formats: [] + term: Report edam-topics: - Gene expression - Metagenomics @@ -5463,10 +6092,12 @@ module in Nanopolish. Given a set of basecalled Nanopore reads and the raw signals, f5c detects the methylated cytosine bases. f5c can optionally utilise NVIDIA graphics cards for acceleration + edam-inputs: [] edam-operations: - Local alignment - Genotyping - Base-calling + edam-outputs: [] edam-topics: - Computer science - Epigenetics @@ -5494,8 +6125,10 @@ bunya: - 0.0.8--hdfd78af_1 description: Experimental PacBio diploid assembler. + edam-inputs: [] edam-operations: - Sequence assembly + edam-outputs: [] edam-topics: - Sequence assembly galaxy: '' @@ -5516,8 +6149,16 @@ biotools: compute_sequence_length bunya: '' description: Add length of sequence to fasta header. + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Data handling + edam-outputs: + - formats: + - FASTA + term: FASTA edam-topics: - Nucleic acids - Sequence analysis @@ -5547,7 +6188,9 @@ bunya: - 1.0.0-gcccore-10.3.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -5569,9 +6212,11 @@ Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. + edam-inputs: [] edam-operations: - Genome alignment - Sequence similarity search + edam-outputs: [] edam-topics: - Microbiology - Genetic variation @@ -5593,8 +6238,10 @@ - 0.1.4--h7132678_6 description: Read huge FastQ and FastA files (both normal and gzipped) an demanipulate them. + edam-inputs: [] edam-operations: - Formatting + edam-outputs: [] edam-topics: - Data management galaxy: '' @@ -5616,9 +6263,11 @@ description: A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. + edam-inputs: [] edam-operations: - Sequencing quality control - Sequence contamination filtering + edam-outputs: [] edam-topics: - Sequence analysis - Probes and primers @@ -5651,10 +6300,21 @@ can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. + edam-inputs: + - formats: + - FASTQ-like format (text) + - SAM + - FASTQ + - BAM + term: BAM edam-operations: - Sequence composition calculation - Sequencing quality control - Statistical calculation + edam-outputs: + - formats: + - HTML + term: HTML edam-topics: - Sequencing - Data quality management @@ -5684,8 +6344,10 @@ bunya: '' description: Compute quality stats for FASTQ files and print those stats as emoji... for some reason. + edam-inputs: [] edam-operations: - Sequencing quality control + edam-outputs: [] edam-topics: - Sequence analysis - Sequencing @@ -5710,9 +6372,11 @@ - 2.1.11-gcccore-10.3.0 description: Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. + edam-inputs: [] edam-operations: - Phylogenetic tree generation (from molecular sequences) - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + edam-outputs: [] edam-topics: - Phylogenetics - Sequence analysis @@ -5741,9 +6405,11 @@ bunya: '' description: Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. + edam-inputs: [] edam-operations: - Read pre-processing - Sequence editing + edam-outputs: [] edam-topics: - Sequence analysis galaxy: @@ -5792,9 +6458,11 @@ bunya: '' description: Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. + edam-inputs: [] edam-operations: - Read pre-processing - Sequence editing + edam-outputs: [] edam-topics: - Sequence analysis galaxy: @@ -5831,7 +6499,9 @@ bunya: - 20190320-gcccore-10.3.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -5850,8 +6520,10 @@ bunya: '' description: HMM-based gene structure prediction (multiple genes, both chains); Program for predicting multiple genes in genomic DNA sequences. + edam-inputs: [] edam-operations: - Gene prediction + edam-outputs: [] edam-topics: - Gene structure galaxy: @@ -5878,8 +6550,10 @@ Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. + edam-inputs: [] edam-operations: - Gene-set enrichment analysis + edam-outputs: [] edam-topics: - Genetics galaxy: @@ -5903,7 +6577,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Filter Combined Transcripts: using tracking file' @@ -5927,9 +6603,11 @@ a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. + edam-inputs: [] edam-operations: - Filtering - Sequencing quality control + edam-outputs: [] edam-topics: '' galaxy: - description: 'filtlong: Filtering long reads by quality' @@ -5951,8 +6629,18 @@ bunya: '' description: FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. + edam-inputs: + - formats: + - Thermo RAW + - Waters RAW + term: Waters RAW + - formats: + - TSV + - Textual format + term: Textual format edam-operations: - Label-free quantification + edam-outputs: [] edam-topics: - Proteomics experiment - Proteomics @@ -5979,7 +6667,9 @@ - 2.6.4-gcccore-11.3.0 - 2.6.4-gcccore-12.3.0 (D) description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -6002,11 +6692,13 @@ for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.' + edam-inputs: [] edam-operations: - Genome assembly - De-novo assembly - Mapping assembly - Cross-assembly + edam-outputs: [] edam-topics: - Sequence assembly - Metagenomics @@ -6041,11 +6733,23 @@ biotools: flymine bunya: '' description: An integrated database for Drosophila and Anopheles genomics. + edam-inputs: + - formats: [] + term: Sequence features + - formats: [] + term: Ontology data edam-operations: - Data retrieval - Visualisation - Gene-set enrichment analysis - Query and retrieval + edam-outputs: + - formats: [] + term: Over-representation data + - formats: [] + term: Query script + - formats: [] + term: Sequence features edam-topics: - Data management - Genomics @@ -6076,8 +6780,16 @@ description: Foldseek enables fast and sensitive comparisons of large structure sets. It reaches sensitivities similar to state-of-the-art structural aligners while being at least 20,000 times faster. + edam-inputs: + - formats: + - PDB + - mmCIF + term: mmCIF edam-operations: - Structure alignment + edam-outputs: + - formats: [] + term: Protein structure alignment edam-topics: - Proteins galaxy: '' @@ -6104,8 +6816,16 @@ alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket). + edam-inputs: + - formats: + - PDB + term: PDB edam-operations: - Molecular surface analysis + edam-outputs: + - formats: + - PDB + term: PDB edam-topics: - Protein structural motifs and surfaces galaxy: @@ -6134,8 +6854,25 @@ biotools: fraggenescan bunya: '' description: Application for finding (fragmented) genes in short reads + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Gene prediction + edam-outputs: + - formats: + - FASTA + term: FASTA + - formats: + - FASTA + term: FASTA + - formats: + - FASTA + term: FASTA + - formats: + - GFF + term: GFF edam-topics: - Genetics - Sequence analysis @@ -6166,9 +6903,11 @@ specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. + edam-inputs: [] edam-operations: - Variant calling - Statistical calculation + edam-outputs: [] edam-topics: - Genomics - Genetic variation @@ -6196,7 +6935,9 @@ bunya: - 20141119-gcccore-10.3.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -6215,8 +6956,10 @@ bunya: '' description: funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). + edam-inputs: [] edam-operations: - Genome annotation + edam-outputs: [] edam-topics: - Genomics galaxy: @@ -6250,8 +6993,10 @@ biotools: gaeval bunya: '' description: Gene Annotation EVAluation. + edam-inputs: [] edam-operations: - Sequence annotation + edam-outputs: [] edam-topics: - Sequence analysis - Gene structure @@ -6287,7 +7032,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Split file: to dataset collection' @@ -6303,6 +7050,9 @@ - description: 'Column join: on multiple datasets' title: Column join 0.0.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcollection_column_join%2Fcollection_column_join%2F0.0.3 + - description: 'Unzip: Unzip a file' + title: Unzip 6.0+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Funzip%2Funzip%2F6.0%2Bgalaxy0 - description: 'Unzip collection: ' title: Unzip collection 1.0.0 url: https://usegalaxy.org.au/root?tool_id=__UNZIP_COLLECTION__ @@ -6357,7 +7107,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Genbank to GFF3: converter' @@ -6366,6 +7118,9 @@ - description: 'FASTA-to-Tabular: converter' title: FASTA-to-Tabular 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffasta_to_tabular%2Ffasta2tab%2F1.1.1 + - description: 'Create InterMine Interchange: Dataset' + title: Create InterMine Interchange 0.0.1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fintermine_galaxy_exchange%2Fgalaxy_intermine_exchange%2F0.0.1 - description: 'Tabular-to-FASTA: converts tabular file to FASTA format' title: Tabular-to-FASTA 1.1.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftabular_to_fasta%2Ftab2fasta%2F1.1.1 @@ -6375,6 +7130,18 @@ - description: 'BED-to-GFF: converter' title: BED-to-GFF 2.0.0 url: https://usegalaxy.org.au/root?tool_id=bed2gff1 + - description: 'MAF to BED: Converts a MAF formatted file to the BED format' + title: MAF to BED 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=MAF_To_BED1 + - description: 'MAF to Interval: Converts a MAF formatted file to the Interval format' + title: MAF to Interval 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=MAF_To_Interval1 + - description: 'MAF to FASTA: Converts a MAF formatted file to FASTA format' + title: MAF to FASTA 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=MAF_To_Fasta1 + - description: 'SFF converter: ' + title: SFF converter 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=Sff_extractor - description: 'AXT to concatenated FASTA: Converts an AXT formatted file to a concatenated FASTA alignment' title: AXT to concatenated FASTA 1.0.0 @@ -6385,190 +7152,193 @@ - description: 'AXT to LAV: Converts an AXT formatted file to LAV format' title: AXT to LAV 1.0.0 url: https://usegalaxy.org.au/root?tool_id=axt_to_lav_1 - - description: 'Convert Wiggle to BigWig: ' - title: Convert Wiggle to BigWig 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig - - description: 'Convert BED to GFF: ' - title: Convert BED to GFF 2.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0 - - description: 'Convert InChI to MOL: ' - title: Convert InChI to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol - - description: 'Convert compressed and uncompressed BCF files: ' - title: Convert compressed and uncompressed BCF files 0.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf - - description: 'Convert tar to directory: ' - title: Convert tar to directory 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory - - description: 'Convert SMILES to MOL: ' - title: Convert SMILES to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL - - description: 'Convert SAM to BigWig: ' - title: Convert SAM to BigWig 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 - - description: 'SMILES to SMILES: ' - title: SMILES to SMILES 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles - - description: 'Convert FASTA to Bowtie base space Index: ' - title: Convert FASTA to Bowtie base space Index 1.3.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index - - description: 'Convert Genomic Intervals To Strict BED12: ' - title: Convert Genomic Intervals To Strict BED12 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0 + - description: 'LAV to BED: Converts a LAV formatted file to BED format' + title: LAV to BED 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=lav_to_bed1 + - description: 'Convert FASTA to Tabular: ' + title: Convert FASTA to Tabular 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular - description: 'Convert XTC, DCD, and TRR: ' title: Convert XTC, DCD, and TRR 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert - - description: 'Convert FASTA to fai file: ' - title: Convert FASTA to fai file 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai - - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence - taxonomy file to a 2 column mothur taxonomy_outline format' - title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony + - description: 'Convert uncompressed file to compressed: ' + title: Convert uncompressed file to compressed 1.16+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz + - description: 'Convert BED to Feature Location Index: ' + title: Convert BED to Feature Location Index 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0 + - description: 'Convert Genomic Intervals To Strict BED6: ' + title: Convert Genomic Intervals To Strict BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 + - description: 'Convert FASTA to len file: ' + title: Convert FASTA to len file 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len + - description: 'OpenBabel converter for molecular formats: ' + title: OpenBabel converter for molecular formats 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules + - description: 'Convert FASTA to Bowtie color space Index: ' + title: Convert FASTA to Bowtie color space Index 1.2.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index + - description: 'Convert compressed file to uncompressed.: ' + title: Convert compressed file to uncompressed. 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed - description: 'Convert BAM to BigWig: ' title: Convert BAM to BigWig 1.0.2 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0 + - description: 'Convert Interval to BGZIP: ' + title: Convert Interval to BGZIP 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0 + - description: 'Convert FASTQ files to seek locations: ' + title: Convert FASTQ files to seek locations 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0 + - description: 'Convert BED to GFF: ' + title: Convert BED to GFF 2.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0 + - description: 'Convert tabular to dbnsfp: ' + title: Convert tabular to dbnsfp 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp + - description: 'Convert Wiggle to Interval: ' + title: Convert Wiggle to Interval 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 + - description: 'Convert neostore.zip files to neostore: ' + title: Convert neostore.zip files to neostore 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore - description: 'Convert GFF to Interval Index: ' title: Convert GFF to Interval Index 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0 + - description: 'Convert tar to directory: ' + title: Convert tar to directory 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory - description: 'Convert Interval to tabix: ' title: Convert Interval to tabix 1.0.2 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0 + - description: 'Convert Len file to Linecount: ' + title: Convert Len file to Linecount 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount + - description: 'Convert Genomic Intervals To Strict BED12: ' + title: Convert Genomic Intervals To Strict BED12 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0 + - description: 'Convert Biom datasets: ' + title: Convert Biom datasets 2.1.5 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom + - description: 'Convert BAM to queryname-sorted BAM: ' + title: Convert BAM to queryname-sorted BAM 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam + - description: 'Convert compressed file to uncompressed.: ' + title: Convert compressed file to uncompressed. 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed + - description: 'Convert FASTA to Bowtie base space Index: ' + title: Convert FASTA to Bowtie base space Index 1.3.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index + - description: 'Convert FASTA to fai file: ' + title: Convert FASTA to fai file 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai + - description: 'Convert BED, GFF, or VCF to BigWig: ' + title: Convert BED, GFF, or VCF to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0 + - description: 'Convert tabular to CSV: ' + title: Convert tabular to CSV 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv + - description: 'Convert compressed and uncompressed BCF files: ' + title: Convert compressed and uncompressed BCF files 0.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf - description: 'Convert MAF to Fasta: ' title: Convert MAF to Fasta 1.0.2 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_fasta_0 - - description: 'Convert Picard Interval List to BED6: converter' - title: Convert Picard Interval List to BED6 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 - - description: 'Convert plink pbed to linkage lped: ' - title: Convert plink pbed to linkage lped 0.02 - url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert - - description: 'Convert GRO to PDB: ' - title: Convert GRO to PDB 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0 - - description: 'Convert FASTA to Tabular: ' - title: Convert FASTA to Tabular 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular - - description: 'Convert BedGraph to BigWig: ' - title: Convert BedGraph to BigWig 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig - - description: 'Convert Genomic Intervals To Strict BED6: ' - title: Convert Genomic Intervals To Strict BED6 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 - - description: 'Convert FASTQ files to seek locations: ' - title: Convert FASTQ files to seek locations 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0 - - description: 'Convert Genomic Intervals To Coverage: ' - title: Convert Genomic Intervals To Coverage 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0 - - description: 'Convert GFF to BED: ' - title: Convert GFF to BED 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0 - - description: 'Convert BED to Feature Location Index: ' - title: Convert BED to Feature Location Index 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0 - - description: 'OpenBabel converter for molecular formats: ' - title: OpenBabel converter for molecular formats 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules - - description: 'Convert Genomic Intervals To Strict BED: ' - title: Convert Genomic Intervals To Strict BED 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 - - description: 'Convert MAF to Genomic Intervals: ' - title: Convert MAF to Genomic Intervals 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0 + - description: 'Convert BGZ VCF to tabix: ' + title: Convert BGZ VCF to tabix 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 - description: 'Convert PDB to GRO: ' title: Convert PDB to GRO 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0 - - description: 'Convert Bam to Bai: ' - title: Convert Bam to Bai 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0 - - description: 'Convert lped to fped: ' - title: Convert lped to fped 0.02 - url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert + - description: 'Convert SMILES to MOL: ' + title: Convert SMILES to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL + - description: 'Convert BAM to coordinate-sorted BAM: ' + title: Convert BAM to coordinate-sorted BAM 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam - description: 'Convert FASTA to 2bit: ' title: Convert FASTA to 2bit 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit - - description: 'Convert tabular to CSV: ' - title: Convert tabular to CSV 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv - - description: 'Convert SAM to BAM without sorting: ' - title: Convert SAM to BAM without sorting 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam - - description: 'Convert BAM to queryname-sorted BAM: ' - title: Convert BAM to queryname-sorted BAM 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam + - description: 'Convert Parquet to csv: ' + title: Convert Parquet to csv 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv + - description: 'Convert BedGraph to BigWig: ' + title: Convert BedGraph to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig + - description: 'Convert GFF to Feature Location Index: ' + title: Convert GFF to Feature Location Index 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0 - description: 'Convert lped to plink pbed: ' title: Convert lped to plink pbed 0.02 url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert - description: 'Convert CSV to tabular: ' title: Convert CSV to tabular 1.0.0 url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular - - description: 'Convert Biom datasets: ' - title: Convert Biom datasets 2.1.5 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom - - description: 'Convert Interval to BGZIP: ' - title: Convert Interval to BGZIP 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0 - - description: 'Convert tabular to dbnsfp: ' - title: Convert tabular to dbnsfp 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp - - description: 'Convert CML to SMILES: ' - title: Convert CML to SMILES 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles - - description: 'Convert uncompressed file to compressed: ' - title: Convert uncompressed file to compressed 1.16+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz - - description: 'Convert GFF to Feature Location Index: ' - title: Convert GFF to Feature Location Index 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0 - - description: 'Convert BGZ VCF to tabix: ' - title: Convert BGZ VCF to tabix 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 - - description: 'Convert Len file to Linecount: ' - title: Convert Len file to Linecount 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount - - description: 'Convert FASTA to Bowtie color space Index: ' - title: Convert FASTA to Bowtie color space Index 1.2.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index - - description: 'Convert compressed file to uncompressed.: ' - title: Convert compressed file to uncompressed. 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed + - description: 'Convert Bam to Bai: ' + title: Convert Bam to Bai 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0 + - description: 'Convert MAF to Genomic Intervals: ' + title: Convert MAF to Genomic Intervals 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0 - description: 'Convert Genomic Intervals To BED: ' title: Convert Genomic Intervals To BED 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0 - - description: 'Convert Wiggle to Interval: ' - title: Convert Wiggle to Interval 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 - - description: 'Convert compressed file to uncompressed.: ' - title: Convert compressed file to uncompressed. 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed - - description: 'Convert neostore.zip files to neostore: ' - title: Convert neostore.zip files to neostore 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore + - description: 'Convert MOL2 to MOL: ' + title: Convert MOL2 to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol + - description: 'Convert SAM to BAM without sorting: ' + title: Convert SAM to BAM without sorting 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam - description: 'Convert BigWig to Wiggle: Convert bigWig to wig' title: Convert BigWig to Wiggle 377+galaxy0 url: https://usegalaxy.org.au/root?tool_id=bigwigtowig - - description: 'Convert CRAM to BAM: ' - title: Convert CRAM to BAM 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 - - description: 'Convert Parquet to csv: ' - title: Convert Parquet to csv 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv - - description: 'Convert BED, GFF, or VCF to BigWig: ' - title: Convert BED, GFF, or VCF to BigWig 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0 + - description: 'Convert plink pbed to linkage lped: ' + title: Convert plink pbed to linkage lped 0.02 + url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert + - description: 'Convert GRO to PDB: ' + title: Convert GRO to PDB 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0 + - description: 'Convert Genomic Intervals To Coverage: ' + title: Convert Genomic Intervals To Coverage 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0 + - description: 'Convert CML to SMILES: ' + title: Convert CML to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles + - description: 'Convert Genomic Intervals To Strict BED: ' + title: Convert Genomic Intervals To Strict BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 + - description: 'Convert SAM to BigWig: ' + title: Convert SAM to BigWig 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 + - description: 'Convert lped to fped: ' + title: Convert lped to fped 0.02 + url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert - description: 'Convert plink pbed to ld reduced format: ' title: Convert plink pbed to ld reduced format 0.02 url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert - - description: 'Convert FASTA to len file: ' - title: Convert FASTA to len file 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len - - description: 'Convert MOL2 to MOL: ' - title: Convert MOL2 to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol - - description: 'Convert BAM to coordinate-sorted BAM: ' - title: Convert BAM to coordinate-sorted BAM 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam + - description: 'Convert InChI to MOL: ' + title: Convert InChI to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol + - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence + taxonomy file to a 2 column mothur taxonomy_outline format' + title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony + - description: 'Convert Wiggle to BigWig: ' + title: Convert Wiggle to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig + - description: 'SMILES to SMILES: ' + title: SMILES to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles + - description: 'Convert Picard Interval List to BED6: converter' + title: Convert Picard Interval List to BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 + - description: 'Convert GFF to BED: ' + title: Convert GFF to BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0 + - description: 'Convert CRAM to BAM: ' + title: Convert CRAM to BAM 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 homepage: '' id: Galaxy CONVERTER license: '' @@ -6584,7 +7354,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'UCSC Main: table browser' @@ -6599,6 +7371,18 @@ - description: 'EBI SRA: ENA SRA' title: EBI SRA 1.0.1 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=ebi_sra_main + - description: 'modENCODE fly: server' + title: modENCODE fly 1.0.1 + url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=modENCODEfly + - description: 'modENCODE modMine: server' + title: modENCODE modMine 1.0.0 + url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=modmine + - description: 'Ratmine: server' + title: Ratmine 1.0.0 + url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=ratmine + - description: 'modENCODE worm: server' + title: modENCODE worm 1.0.1 + url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=modENCODEworm homepage: '' id: galaxy_data_sources license: '' @@ -6614,7 +7398,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Filter FASTA: on the headers and/or the sequences' @@ -6659,7 +7445,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Volcano Plot: create a volcano plot' @@ -6668,6 +7456,12 @@ - description: 'Draw Stacked Bar Plots: for different categories and different criteria' title: Draw Stacked Bar Plots 1.0.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdraw_stacked_barplots%2Fdraw_stacked_barplots%2F1.0.0 + - description: 'Histogram: of a numeric column' + title: Histogram 1.0.4 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fhistogram%2Fhistogram_rpy%2F1.0.4 + - description: 'proportional venn: from 2-3 sets' + title: proportional venn 0.5 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fidot%2Fprop_venn%2Fprop_venn%2F0.5 - description: 'Plotting tool: for multiple series and graph types' title: Plotting tool 1.0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fxy_plot%2FXY_Plot_1%2F1.0.2 @@ -6677,6 +7471,9 @@ - description: 'Bar chart: for multiple columns' title: Bar chart 1.0.0 url: https://usegalaxy.org.au/root?tool_id=barchart_gnuplot + - description: 'Boxplot: of quality statistics' + title: Boxplot 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=qual_stats_boxplot homepage: '' id: galaxy_graph_display license: '' @@ -6692,7 +7489,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Extract Pairwise MAF blocks: given a set of genomic intervals' @@ -6747,7 +7546,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Gene BED To Exon/Intron/Codon BED: expander' @@ -6768,7 +7569,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Reverse: columns in a tabular file' @@ -6802,7 +7605,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Number lines: ' @@ -6919,7 +7724,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Concatenate: FASTA alignment by species' @@ -7001,7 +7808,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Categorize Elements: satisfying criteria' @@ -7019,6 +7828,10 @@ - description: 'Count GFF Features: ' title: Count GFF Features 0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcount_gff_features%2Fcount_gff_features%2F0.2 + - description: 'Row Means: Calculates the mean of a row of numbers for an entire + table' + title: Row Means 0.1 + url: https://usegalaxy.org.au/root?tool_id=testtoolshed.g2.bx.psu.edu%2Frepos%2Fsimon-gladman%2Frow_means%2Frow_means%2F0.1 - description: 'T Test for Two Samples: ' title: T Test for Two Samples 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ft_test_two_samples%2Ft_test_two_samples%2F1.0.1 @@ -7046,11 +7859,13 @@ \ whole genome and exome sequencing data. GATK4 expands functionality into copy\ \ number and somatic analyses and offers pipeline scripts for workflows. \n\n\ Version 4 (GATK4) is open-source at https://github.com/broadinstitute/gatk." + edam-inputs: [] edam-operations: - Polymorphism detection - Sequence analysis - Genotyping - Statistical calculation + edam-outputs: [] edam-topics: - Sequence analysis - Genetic variation @@ -7080,8 +7895,22 @@ biotools: gblocks bunya: '' description: Cleaning aligned sequences. + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Sequence alignment analysis + edam-outputs: + - formats: + - Textual format + term: Textual format + - formats: + - FASTA + term: FASTA + - formats: + - HTML + term: HTML edam-topics: - Sequence analysis galaxy: @@ -7115,8 +7944,10 @@ variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits. + edam-inputs: [] edam-operations: - Genetic variation analysis + edam-outputs: [] edam-topics: - GWAS study galaxy: '' @@ -7139,8 +7970,19 @@ description: Software aimed at pairwise sequence comparison generating high quality results (equivalent to MUMmer) with controlled memory consumption and comparable or faster execution times particularly with long sequences. + edam-inputs: + - formats: + - FASTA + term: FASTA + - formats: + - FASTA + term: FASTA edam-operations: - Sequence analysis + edam-outputs: + - formats: + - Binary format + term: Binary format edam-topics: - Sequence analysis galaxy: @@ -7169,9 +8011,11 @@ well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. + edam-inputs: [] edam-operations: - Sequence analysis - Genetic variation analysis + edam-outputs: [] edam-topics: - Sequence analysis galaxy: @@ -7275,8 +8119,10 @@ annotation of protein-coding genes in a target genome. Thereby, it utilizes amino acid sequence and intron position conservation. In addition, it allows to incorporate RNA-seq evidence for splice site prediction. + edam-inputs: [] edam-operations: - Genome annotation + edam-outputs: [] edam-topics: - Genomics - Homology modeling @@ -7309,10 +8155,12 @@ Visually driven real-time analysis of genomic data.' + edam-inputs: [] edam-operations: - Variant prioritisation - Variant calling - Variant classification + edam-outputs: [] edam-topics: - Exome sequencing - Genomics @@ -7341,7 +8189,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Generate count matrix: from individual files' @@ -7362,7 +8212,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Generate A Matrix: for using PC and LDA' @@ -7383,7 +8235,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -7406,9 +8260,11 @@ detailed mathematical model of how k-mer frequencies will be distributed in heterozygous and polyploid genomes | Average k-mer coverage for polyploid genome | Upload results from running Jellyfish or KMC + edam-inputs: [] edam-operations: - Genotyping - k-mer counting + edam-outputs: [] edam-topics: - Sequence assembly - Mathematics @@ -7436,8 +8292,10 @@ biotools: genometools bunya: '' description: Free collection of bioinformatics tools for genome informatics. + edam-inputs: [] edam-operations: - Sequence analysis + edam-outputs: [] edam-topics: - Nucleic acid sites, features and motifs - Sequence analysis @@ -7461,7 +8319,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Genrich: Detecting sites of genomic enrichment' @@ -7482,7 +8342,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Get PDB file: from Protein Data Bank' @@ -7507,12 +8369,14 @@ This toolkit assemblies organelle genome from genomic skimming data.' + edam-inputs: [] edam-operations: - De-novo assembly - Genome assembly - Mapping assembly - Mapping - Sequence trimming + edam-outputs: [] edam-topics: - Cell biology - Sequence assembly @@ -7541,7 +8405,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'GFA to FASTA: Convert Graphical Fragment Assembly files to FASTA @@ -7565,8 +8431,12 @@ description: gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. + edam-inputs: + - formats: [] + term: Nucleic acid sequence edam-operations: - Data handling + edam-outputs: [] edam-topics: - Computational biology galaxy: @@ -7589,7 +8459,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'GFF-to-BED: converter' @@ -7611,7 +8483,9 @@ bunya: - 0.1.a1a2bc9--hdfd78af_2 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -7631,8 +8505,10 @@ - 0.12.2-gcc-10.3.0 description: Program for comparing, annotating, merging and tracking transcripts in GFF files. + edam-inputs: [] edam-operations: - Sequence annotation + edam-outputs: [] edam-topics: - Nucleic acids - Sequence analysis @@ -7655,7 +8531,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Convert gffCompare annotated GTF to BED: for StringTie results' @@ -7677,8 +8555,10 @@ bunya: - 0.12.7-gcccore-10.3.0 description: program for filtering, converting and manipulating GFF files + edam-inputs: [] edam-operations: - Sequence annotation + edam-outputs: [] edam-topics: - Nucleic acids - Sequence analysis @@ -7702,8 +8582,13 @@ biotools: ggplot2 bunya: '' description: Plotting system for R, based on the grammar of graphics. + edam-inputs: [] edam-operations: - Visualisation + edam-outputs: + - formats: + - Image format + term: Image format edam-topics: - Data visualisation galaxy: @@ -7744,7 +8629,9 @@ - 9.54.0-gcccore-10.3.0 - 9.56.1-gcccore-11.3.0 (D) description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -7762,7 +8649,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'GMAJ: Multiple Alignment Viewer' @@ -7784,9 +8673,30 @@ bunya: - 2023.04.28 description: Genomic Mapping and Alignment Program for mRNA and EST Sequences. + edam-inputs: + - formats: + - FASTQ-illumina + - FASTQ-sanger + - FASTA + term: FASTA + - formats: + - FASTQ-illumina + - FASTQ-sanger + - FASTA + term: FASTA + - formats: + - Textual format + term: Textual format + - formats: + - FASTA + term: FASTA edam-operations: - Genetic mapping - Sequence alignment + edam-outputs: + - formats: + - Textual format + term: Textual format edam-topics: - Mapping galaxy: '' @@ -7816,8 +8726,12 @@ a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU parallel can then split the input and pipe it into commands in parallel. + edam-inputs: + - formats: [] + term: URL edam-operations: - Splitting + edam-outputs: [] edam-topics: '' galaxy: '' homepage: https://www.gnu.org/software/parallel/ @@ -7839,7 +8753,9 @@ - 2.7-gcc-11.3.0 (D) description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://www.gnu.org/software/gsl/ @@ -7867,8 +8783,21 @@ The tool features an optional graph clustering algorithm to reduce the redundancy\ \ in the set of enriched GO terms and simplify its output.\nIt was developed by\ \ the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ci\xEAncia." + edam-inputs: + - formats: + - Textual format + term: Textual format + - formats: + - OBO format + - OWL format + term: OWL format edam-operations: - Gene-set enrichment analysis + edam-outputs: + - formats: + - png + - Textual format + term: Textual format edam-topics: - Transcriptomics galaxy: @@ -7895,8 +8824,10 @@ bunya: '' description: Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. + edam-inputs: [] edam-operations: - Gene functional annotation + edam-outputs: [] edam-topics: - RNA-Seq galaxy: @@ -7920,7 +8851,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'GrameneMart: Central server' @@ -7944,11 +8877,13 @@ of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. + edam-inputs: [] edam-operations: - Phylogenetic inference - Phylogenetic tree visualisation - Phylogenetic tree editing - Taxonomic classification + edam-outputs: [] edam-topics: - Metagenomics - Phylogenetics @@ -7985,8 +8920,13 @@ acids that have a lot of complicated bonded interactions, but since it is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. + edam-inputs: + - formats: + - PDB + term: PDB edam-operations: - Molecular dynamics + edam-outputs: [] edam-topics: - Molecular dynamics galaxy: @@ -8095,11 +9035,13 @@ metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).' + edam-inputs: [] edam-operations: - Genome alignment - Taxonomic classification - Sequence assembly - Query and retrieval + edam-outputs: [] edam-topics: - Metagenomics - Taxonomy @@ -8127,7 +9069,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'GTF-to-BEDGraph: converter' @@ -8148,7 +9092,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'GTF2GeneList: extracts a complete annotation table or subsets thereof @@ -8171,10 +9117,12 @@ bunya: '' description: Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. + edam-inputs: [] edam-operations: - Genotyping - Phylogenetic inference - Ancestral reconstruction + edam-outputs: [] edam-topics: - Phylogeny - Genotype and phenotype @@ -8202,7 +9150,9 @@ - 1.10-gcccore-10.3.0 - 1.12-gcccore-11.3.0 (D) description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Compress file(s): ' @@ -8227,9 +9177,23 @@ across a range of long- and short-read sequencing technologies. The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md' + edam-inputs: + - formats: + - BAM + term: BAM + - formats: + - VCF + term: VCF edam-operations: - Haplotype mapping - Variant classification + edam-outputs: + - formats: + - plain text format (unformatted) + term: plain text format (unformatted) + - formats: + - VCF + term: VCF edam-topics: '' galaxy: - description: 'Hapcut2: - haplotype assembly for diploid organisms' @@ -8250,7 +9214,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'HbVar: Human Hemoglobin Variants and Thalassemias' @@ -8271,8 +9237,10 @@ biotools: heinz bunya: '' description: Tool for single-species active module discovery. + edam-inputs: [] edam-operations: - Pathway or network analysis + edam-outputs: [] edam-topics: - Genetics - Gene expression @@ -8309,10 +9277,18 @@ bunya: '' description: This tool provides functional annotation for a list of genes by connecting with DAVID database. + edam-inputs: + - formats: + - TSV + term: TSV edam-operations: - Database search - Service invocation - Gene functional annotation + edam-outputs: + - formats: + - HTML + term: HTML edam-topics: - Ontology and terminology - Gene expression @@ -8344,10 +9320,18 @@ bunya: '' description: This tool can be used to analyze the patterns of linkage disequilibrium (LD) between polymorphic sites in a locus. + edam-inputs: + - formats: + - TSV + term: TSV edam-operations: - Data handling - Linkage disequilibrium calculation - Variant pattern analysis + edam-outputs: + - formats: + - TSV + term: TSV edam-topics: - Mapping - Molecular interactions, pathways and networks @@ -8381,10 +9365,18 @@ bunya: '' description: This tool creates a link to the g:GOSt tool (Gene Group Functional Profiling), which provides functional profiling of gene lists. + edam-inputs: + - formats: + - TSV + term: TSV edam-operations: - Data handling - Service invocation - Gene functional annotation + edam-outputs: + - formats: + - HTML + term: HTML edam-topics: - Ontology and terminology - Function analysis @@ -8419,10 +9411,12 @@ \ data analysis, quality control and visualization.\n\nHiCExplorer \u2014 HiCExplorer\ \ 3.6 documentation.\n\nscHiCExplorer \u2014 scHiCExplorer 7 documentation.\n\n\ Free document hosting provided by Read the Docs." + edam-inputs: [] edam-operations: - Validation - Visualisation - Standardisation and normalisation + edam-outputs: [] edam-topics: - Workflows - DNA @@ -8466,11 +9460,13 @@ bunya: '' description: Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz). + edam-inputs: [] edam-operations: - Primer removal - De-novo assembly - Genome assembly - Sequence trimming + edam-outputs: [] edam-topics: - Sequence assembly - Agricultural science @@ -8502,9 +9498,11 @@ bunya: - 0.16.1-gcccore-10.3.0 description: 'Hifiasm: a haplotype-resolved assembler for accurate Hifi reads' + edam-inputs: [] edam-operations: - Genome assembly - De-novo assembly + edam-outputs: [] edam-topics: - Sequence assembly galaxy: @@ -8534,8 +9532,10 @@ bunya: '' description: Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. + edam-inputs: [] edam-operations: - Sequence assembly + edam-outputs: [] edam-topics: - Sequence assembly - Metagenomics @@ -8563,8 +9563,10 @@ description: Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). + edam-inputs: [] edam-operations: - Sequence alignment + edam-outputs: [] edam-topics: - RNA-seq galaxy: @@ -8594,28 +9596,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Histogram: of a numeric column' - title: Histogram 1.0.4 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fhistogram%2Fhistogram_rpy%2F1.0.4 - homepage: '' - id: histogram - license: '' - name: histogram - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -8639,8 +9622,14 @@ protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. + edam-inputs: + - formats: [] + term: Sequence alignment edam-operations: - Formatting + edam-outputs: + - formats: [] + term: Sequence alignment edam-topics: - Sequence analysis - Sequence sites, features and motifs @@ -8710,7 +9699,9 @@ description: Horovod is a distributed deep learning training framework for TensorFlow, Keras, PyTorch, and Apache MXNet. The goal of Horovod is to make distributed deep learning fast and easy to use. + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: - Machine learning galaxy: '' @@ -8733,8 +9724,10 @@ - 2.0.2-foss-2022a description: Python framework to process and analyse high-throughput sequencing (HTS) data + edam-inputs: [] edam-operations: - Nucleic acid sequence analysis + edam-outputs: [] edam-topics: - Sequence analysis galaxy: @@ -8765,8 +9758,32 @@ and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools. + edam-inputs: + - formats: + - SAM + - BAM + - CRAM + - FASTA + - FASTQ + term: FASTQ + - formats: + - VCF + - BCF + term: BCF edam-operations: - Data handling + edam-outputs: + - formats: + - SAM + - BAM + - CRAM + - FASTA + - FASTQ + term: FASTQ + - formats: + - VCF + - BCF + term: BCF edam-topics: - Data management galaxy: '' @@ -8798,10 +9815,12 @@ \ potential of a microbial community and its members. More generally, functional\ \ profiling answers the question \u201CWhat are the microbes in my community-of-interest\ \ doing (or are capable of doing)?\u201D" + edam-inputs: [] edam-operations: - Species frequency estimation - Taxonomic classification - Phylogenetic analysis + edam-outputs: [] edam-topics: - Metagenomics - Phylogenomics @@ -8868,8 +9887,10 @@ \ the metabolic potential of a microbial community and its members. More generally,\ \ functional profiling answers the question \u201CWhat are the microbes in my\ \ community-of-interest doing (or capable of doing)?\u201D" + edam-inputs: [] edam-operations: - Metabolic pathway prediction + edam-outputs: [] edam-topics: '' galaxy: - description: 'Combine MetaPhlAn2 and HUMAnN2 outputs: to relate genus/species @@ -8928,10 +9949,12 @@ are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.' + edam-inputs: [] edam-operations: - Sequence trimming - Sequence assembly - Read mapping + edam-outputs: [] edam-topics: - Phylogenetics - Plant biology @@ -8960,8 +9983,10 @@ bunya: '' description: Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. + edam-inputs: [] edam-operations: - Statistical calculation + edam-outputs: [] edam-topics: - Phylogeny - Small molecules @@ -8992,7 +10017,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://www.l3harrisgeospatial.com/Software-Technology/IDL @@ -9014,7 +10041,9 @@ - 7.0.11-14-gcccore-10.3.0 - 7.1.0-37-gcccore-11.3.0 (D) description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://imagemagick.org/script/index.php @@ -9035,9 +10064,11 @@ description: Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies + edam-inputs: [] edam-operations: - Genome assembly - Phasing + edam-outputs: [] edam-topics: - Sequence assembly galaxy: '' @@ -9064,8 +10095,15 @@ sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. + edam-inputs: + - formats: + - Sequence profile format + term: Sequence profile format edam-operations: - Nucleic acid feature detection + edam-outputs: + - formats: [] + term: Database search results edam-topics: - Sequence sites, features and motifs - Structural genomics @@ -9106,7 +10144,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -9128,8 +10168,10 @@ large, integrated datasets. It supports a wide variety of data types and format, including short-read alignments in the SAM/BAM format. Data can be viewed from local files or over the web via http. + edam-inputs: [] edam-operations: - Visualisation + edam-outputs: [] edam-topics: - Genomics - Data visualisation @@ -9159,11 +10201,22 @@ biotools: integron_finder bunya: '' description: A tool to detect Integron in DNA sequences. + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Nucleic acid feature detection - Sequence motif recognition - Protein feature detection - Genome annotation + edam-outputs: + - formats: + - GenBank format + term: GenBank format + - formats: + - TSV + term: TSV edam-topics: - Functional genomics - Mobile genetic elements @@ -9198,8 +10251,16 @@ accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding your own data. + edam-inputs: + - formats: + - Textual format + term: Textual format edam-operations: - Database search + edam-outputs: + - formats: + - Textual format + term: Textual format edam-topics: - Data integration and warehousing - Rare diseases @@ -9223,35 +10284,22 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Create InterMine Interchange: Dataset' - title: Create InterMine Interchange 0.0.1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fintermine_galaxy_exchange%2Fgalaxy_intermine_exchange%2F0.0.1 - homepage: '' - id: intermine_galaxy_exchange - license: '' - name: intermine_galaxy_exchange - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: interproscan_4 biotools: interproscan_4 bunya: - 5.55-88.0-foss-2021a description: Scan sequences against the InterPro protein signature databases. + edam-inputs: + - formats: [] + term: Protein sequence edam-operations: - Sequence motif recognition - Protein feature detection + edam-outputs: + - formats: [] + term: Sequence signature matches + - formats: [] + term: Protein features edam-topics: - Gene and protein families - Sequence analysis @@ -9283,10 +10331,12 @@ \ toolkit for assembly and analysis of restriction-site associated genomic data\ \ sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.\n\ \nWelcome to ipyrad \u2014 ipyrad documentation." + edam-inputs: [] edam-operations: - Sequence assembly - de Novo sequencing - Haplotype mapping + edam-outputs: [] edam-topics: - Sequence assembly - Phylogenetics @@ -9314,8 +10364,10 @@ trees and assessing branch supports with the ultrafast bootstrap approximation. It is based on the IQPNNI algorithm with 10-fold speedup together with substantially additional features. + edam-inputs: [] edam-operations: - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + edam-outputs: [] edam-topics: - Phylogenetics - Statistics and probability @@ -9347,8 +10399,10 @@ row- and column-level metadata. Particular attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results. + edam-inputs: [] edam-operations: - Clustering + edam-outputs: [] edam-topics: - Gene expression - Transcriptomics @@ -9375,8 +10429,10 @@ bunya: '' description: Automated identification of insertion sequence elements in prokaryotic genomes. + edam-inputs: [] edam-operations: - Structural variation detection + edam-outputs: [] edam-topics: - Genomics - DNA structural variation @@ -9408,9 +10464,11 @@ includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. + edam-inputs: [] edam-operations: - Sequence comparison - Sequence analysis + edam-outputs: [] edam-topics: - Computational biology - Gene transcripts @@ -9439,12 +10497,14 @@ single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique. + edam-inputs: [] edam-operations: - Demultiplexing - Sequence trimming - Clustering - Primer removal - DNA barcoding + edam-outputs: [] edam-topics: - Gene transcripts galaxy: '' @@ -9467,10 +10527,12 @@ iVar - DataBase of Genomics Variants.' + edam-inputs: [] edam-operations: - Variant classification - Text annotation - Variant calling + edam-outputs: [] edam-topics: - Biological databases - Evolutionary biology @@ -9516,8 +10578,10 @@ inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset. + edam-inputs: [] edam-operations: - Differential gene expression analysis + edam-outputs: [] edam-topics: - Statistics and probability galaxy: @@ -9550,7 +10614,9 @@ - 4.3.0-foss-2021a description: JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: - Statistics and probability galaxy: '' @@ -9577,11 +10643,13 @@ forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples. + edam-inputs: [] edam-operations: - Genotyping - Variant calling - Genome indexing - Visualisation + edam-outputs: [] edam-topics: - Structural variation - DNA polymorphism @@ -9607,7 +10675,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -9628,7 +10698,9 @@ - 2.1-gcccore-10.3.0 - 2.1-gcccore-11.3.0 (D) description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -9648,8 +10720,10 @@ description: Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. + edam-inputs: [] edam-operations: - Genome visualisation + edam-outputs: [] edam-topics: - Genomics galaxy: @@ -9677,7 +10751,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Genome annotation statistics: ' @@ -9700,8 +10776,17 @@ - 2.3.0-gcc-10.3.0 - 2.3.0-gcc-11.3.0 (D) description: A command-line algorithm for counting k-mers in DNA sequence. + edam-inputs: + - formats: + - FASTA + - FASTQ + term: FASTQ edam-operations: - k-mer counting + edam-outputs: + - formats: + - K-mer countgraph + term: K-mer countgraph edam-topics: - Sequence analysis - Genomics @@ -9727,7 +10812,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'JQ: process JSON' @@ -9751,9 +10838,11 @@ description: Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps. + edam-inputs: [] edam-operations: - Genome indexing - Visualisation + edam-outputs: [] edam-topics: - Sequencing - Mapping @@ -9778,7 +10867,9 @@ bunya: - 3.5.0-gcccore-11.3.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -9803,8 +10894,10 @@ or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. + edam-inputs: [] edam-operations: - Gene expression profiling + edam-outputs: [] edam-topics: - Transcriptomics - RNA-seq @@ -9834,9 +10927,11 @@ bunya: '' description: Suite of tools that generate, analyse and compare k-mer spectra produced from sequence files + edam-inputs: [] edam-operations: - Sequence composition calculation - Sequence feature detection + edam-outputs: [] edam-topics: - Sequence analysis - Genomics @@ -9860,7 +10955,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://github.com/ucscGenomeBrowser/kent @@ -9882,8 +10979,18 @@ data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. + edam-inputs: + - formats: + - FASTQ-like format (text) + - FASTA + term: FASTA edam-operations: - Standardisation and normalisation + edam-outputs: + - formats: + - FASTQ-like format (text) + - FASTA + term: FASTA edam-topics: - Sequence assembly galaxy: @@ -9942,8 +11049,10 @@ bunya: '' description: KMC is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. + edam-inputs: [] edam-operations: - k-mer counting + edam-outputs: [] edam-topics: - Whole genome sequencing - Genomics @@ -9969,9 +11078,14 @@ - 1.3.0--hdfd78af_2 description: KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Sequence analysis - Gene functional annotation + edam-outputs: [] edam-topics: - Genomics galaxy: '' @@ -9996,8 +11110,16 @@ but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. + edam-inputs: + - formats: + - FASTA-like + term: FASTA-like edam-operations: - Taxonomic classification + edam-outputs: + - formats: + - TSV + term: TSV edam-topics: - Taxonomy - Metagenomics @@ -10053,8 +11175,17 @@ speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. + edam-inputs: + - formats: + - FASTQ + - FASTA + term: FASTA edam-operations: - Taxonomic classification + edam-outputs: + - formats: + - TSV + term: TSV edam-topics: - Taxonomy - Metagenomics @@ -10080,8 +11211,13 @@ bunya: '' description: KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files + edam-inputs: + - formats: + - TSV + term: TSV edam-operations: - Visualisation + edam-outputs: [] edam-topics: - Taxonomy - Metagenomics @@ -10117,8 +11253,10 @@ bunya: '' description: Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). + edam-inputs: [] edam-operations: - Visualisation + edam-outputs: [] edam-topics: - Metagenomics galaxy: @@ -10146,7 +11284,9 @@ bunya: - 2.8.1-gcccore-11.3.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -10171,10 +11311,12 @@ Welcome to LAMA, an open source pipeline to automatically identify embryo dysmorphology from 3D volumetric images.' + edam-inputs: [] edam-operations: - Image analysis - Image annotation - Standardisation and normalisation + edam-outputs: [] edam-topics: - Tomography - Genotype and phenotype @@ -10202,9 +11344,11 @@ bunya: '' description: A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. + edam-inputs: [] edam-operations: - Sequence alignment - Read mapping + edam-outputs: [] edam-topics: - Genomics galaxy: @@ -10233,28 +11377,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' - edam-topics: '' - galaxy: - - description: 'LAV to BED: Converts a LAV formatted file to BED format' - title: LAV to BED 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=lav_to_bed1 - homepage: '' - id: lav_to_bed1 - license: '' - name: lav_to_bed1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Gene length and GC content: from GTF and FASTA file' @@ -10285,12 +11410,14 @@ \ features and offers numerous publication-quality result output graphics and\ \ tables to facilitate statistical and exploratory analysis of label-free quantitative\ \ datasets" + edam-inputs: [] edam-operations: - Essential dynamics - Principal component visualisation - Label-free quantification - Imputation - Standardisation and normalisation + edam-outputs: [] edam-topics: - Proteomics - Sequence analysis @@ -10320,7 +11447,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Convert genome coordinates: between assemblies and genomes' @@ -10342,8 +11471,16 @@ bunya: '' description: Data analysis, linear models and differential expression for microarray data. + edam-inputs: + - formats: + - Textual format + term: Textual format edam-operations: - RNA-Seq analysis + edam-outputs: + - formats: + - Image format + term: Image format edam-topics: - Molecular biology - Genetics @@ -10373,12 +11510,14 @@ Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. + edam-inputs: [] edam-operations: - Scaffolding - Genome assembly - Read mapping - Read pre-processing - Sequence trimming + edam-outputs: [] edam-topics: - Sequence assembly - Mapping @@ -10409,8 +11548,10 @@ use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering. + edam-inputs: [] edam-operations: - Variant calling + edam-outputs: [] edam-topics: - Genomics - Genetic variation @@ -10454,8 +11595,10 @@ It can output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs), but it can genotype indels if they are given in an input VCF. + edam-inputs: [] edam-operations: - Variant calling + edam-outputs: [] edam-topics: - Genetic variation galaxy: '' @@ -10480,7 +11623,9 @@ - 5.5.2.11-gcc-10.3.0 - 5.5.2.11-gcc-11.3.0 (D) description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: http://lpsolve.sourceforge.net/5.5/ @@ -10501,8 +11646,10 @@ description: LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package. + edam-inputs: [] edam-operations: - Sequence assembly + edam-outputs: [] edam-topics: - Sequence assembly galaxy: '' @@ -10527,7 +11674,9 @@ - 5.4.3-gcccore-10.3.0 - 5.4.4-gcccore-11.3.0 (D) description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://www.lua.org/ @@ -10546,10 +11695,31 @@ bunya: - 2.2.9.1 description: Model-based Analysis of ChIP-seq data. + edam-inputs: + - formats: + - TSV + term: TSV + - formats: + - BAM + - BED + - SAM + - TSV + term: TSV edam-operations: - Peak calling - Enrichment analysis - Gene regulatory network analysis + edam-outputs: + - formats: + - BED + - WIG + term: WIG + - formats: + - TSV + term: TSV + - formats: + - HTML + term: HTML edam-topics: - ChIP-seq - Molecular interactions, pathways and networks @@ -10607,7 +11777,9 @@ - 1.3.0-gompi-2021a - 1.3.0-gompi-2022a (D) description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -10621,77 +11793,22 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'MAF to BED: Converts a MAF formatted file to the BED format' - title: MAF to BED 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=MAF_To_BED1 - homepage: '' - id: MAF_To_BED1 - license: '' - name: MAF_To_BED1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'MAF to FASTA: Converts a MAF formatted file to FASTA format' - title: MAF to FASTA 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=MAF_To_Fasta1 - homepage: '' - id: MAF_To_Fasta1 - license: '' - name: MAF_To_Fasta1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'MAF to Interval: Converts a MAF formatted file to the Interval format' - title: MAF to Interval 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=MAF_To_Interval1 - homepage: '' - id: MAF_To_Interval1 - license: '' - name: MAF_To_Interval1 - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: MAFFT biotools: MAFFT bunya: - 7.490-gcc-10.3.0-with-extensions description: MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Multiple sequence alignment + edam-outputs: + - formats: + - FASTA + term: FASTA edam-topics: - Sequence analysis galaxy: @@ -10734,8 +11851,10 @@ bunya: '' description: Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. + edam-inputs: [] edam-operations: - Genetic variation analysis + edam-outputs: [] edam-topics: - Genetics - Genetic variation @@ -10779,8 +11898,10 @@ description: "Portable and easily configurable genome annotation pipeline. It\u2019\ s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently\ \ annotate their genomes and to create genome databases." + edam-inputs: [] edam-operations: - Genome annotation + edam-outputs: [] edam-topics: - Genomics - DNA @@ -10819,12 +11940,14 @@ morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions. + edam-inputs: [] edam-operations: - Quantification - Visualisation - Spectrum calculation - Peak detection - Mass spectra calibration + edam-outputs: [] edam-topics: - Proteomics experiment - Proteomics @@ -10856,8 +11979,10 @@ bunya: - 2.3-gcc-10.3.0 description: Fast genome and metagenome distance estimation using MinHash. + edam-inputs: [] edam-operations: - Sequence distance matrix generation + edam-outputs: [] edam-topics: - Genomics - Metagenomics @@ -10882,7 +12007,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'mash screen: determines how well query sequences are contained within @@ -10904,7 +12031,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'mash sketch: Create a reduced representation of a sequence or set @@ -10926,7 +12055,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'MasterVar to pgSnp: Convert from MasterVar to pgSnp format' @@ -10950,8 +12081,10 @@ \ de\_Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can\ \ assemble data sets containing only short reads from Illumina sequencing or a\ \ mixture of short reads and long reads (Sanger, 454)." + edam-inputs: [] edam-operations: - Genome assembly + edam-outputs: [] edam-topics: - Sequence assembly - Whole genome sequencing @@ -10978,10 +12111,25 @@ biotools: matchms bunya: '' description: Tool to import, process, clean, and compare mass spectrometry data. + edam-inputs: + - formats: + - MGF + - JSON + term: JSON edam-operations: - Spectral library search - Format validation - Filtering + edam-outputs: + - formats: + - JSON + term: JSON + - formats: + - JSON + term: JSON + - formats: + - Mass spectrometry data format + term: Mass spectrometry data format edam-topics: - Metabolomics galaxy: @@ -11044,9 +12192,11 @@ description: Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python. Matplotlib makes easy things easy and hard things possible. + edam-inputs: [] edam-operations: - Data handling - Visualisation + edam-outputs: [] edam-topics: '' galaxy: '' homepage: https://matplotlib.org/ @@ -11065,8 +12215,10 @@ bunya: '' description: Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. + edam-inputs: [] edam-operations: - Sequence assembly + edam-outputs: [] edam-topics: - Metagenomics - Sequence assembly @@ -11094,6 +12246,13 @@ - 2.2.0.0-gcccore-11.3.0 description: Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. + edam-inputs: + - formats: + - CSV + - TSV + - SEQUEST .out file + - xlsx + term: xlsx edam-operations: - Imputation - Visualisation @@ -11103,6 +12262,14 @@ - Heat map generation - Clustering - Principal component plotting + edam-outputs: + - formats: + - CSV + term: CSV + - formats: + - JPG + - PNG + term: PNG edam-topics: - Proteomics experiment - Proteomics @@ -11143,10 +12310,14 @@ bunya: '' description: MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. + edam-inputs: + - formats: [] + term: Pathway or network edam-operations: - Clustering - Network analysis - Gene regulatory network analysis + edam-outputs: [] edam-topics: - Molecular interactions, pathways and networks galaxy: '' @@ -11172,8 +12343,10 @@ it also reads other formats (e.g. PDB files and XYZ format trajectories; see the supported coordinate formats for the full list). It can write most of these formats, too, together with atom selections for use in Gromacs, CHARMM, VMD and PyMol + edam-inputs: [] edam-operations: - Molecular dynamics + edam-outputs: [] edam-topics: - Molecular dynamics galaxy: @@ -11197,7 +12370,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Slice MD trajectories: using the MDTraj package' @@ -11225,10 +12400,12 @@ description: medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. + edam-inputs: [] edam-operations: - Base-calling - Variant calling - Sequence assembly + edam-outputs: [] edam-topics: - Sequence assembly - Machine learning @@ -11265,8 +12442,10 @@ description: Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. + edam-inputs: [] edam-operations: - Genome assembly + edam-outputs: [] edam-topics: - Metagenomics - Sequencing @@ -11294,7 +12473,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Merge Columns: together' @@ -11325,12 +12506,14 @@ Merqury provides a set of tools for this purpose.' + edam-inputs: [] edam-operations: - Genome assembly - k-mer counting - Scaffolding - Phasing - De-novo assembly + edam-outputs: [] edam-topics: - Sequence assembly - Whole genome sequencing @@ -11362,8 +12545,17 @@ description: Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. + edam-inputs: + - formats: + - FASTA + - FASTQ + term: FASTQ edam-operations: - k-mer counting + edam-outputs: + - formats: + - K-mer countgraph + term: K-mer countgraph edam-topics: - Whole genome sequencing - Genomics @@ -11395,10 +12587,12 @@ "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning + edam-inputs: [] edam-operations: - Read binning - Sequence assembly - Genome annotation + edam-outputs: [] edam-topics: - Metagenomics - Sequence assembly @@ -11428,7 +12622,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'metabolicMine: server' @@ -11458,10 +12654,12 @@ This history is empty. You can load your own data or get data from an external source' + edam-inputs: [] edam-operations: - Read pre-processing - Standardisation and normalisation - Sequence merging + edam-outputs: [] edam-topics: - Metagenomics - Metagenomic sequencing @@ -11521,8 +12719,16 @@ - 6-gcc-11.3.0 (D) description: MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Homology-based gene prediction + edam-outputs: + - formats: + - FASTA + term: FASTA edam-topics: - Metagenomics - Gene and protein families @@ -11548,9 +12754,11 @@ bunya: '' description: Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. + edam-inputs: [] edam-operations: - Nucleic acid sequence analysis - Phylogenetic tree analysis + edam-outputs: [] edam-topics: - Metagenomics - Phylogenomics @@ -11589,6 +12797,22 @@ information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. + edam-inputs: + - formats: + - Textual format + term: Textual format + - formats: + - Textual format + term: Textual format + - formats: + - Textual format + term: Textual format + - formats: + - Textual format + term: Textual format + - formats: + - Textual format + term: Textual format edam-operations: - Principal component visualisation - Visualisation @@ -11600,6 +12824,16 @@ - Indexing - Filtering - Statistical inference + edam-outputs: + - formats: + - Image format + term: Image format + - formats: + - Image format + term: Image format + - formats: + - Image format + term: Image format edam-topics: - Proteomics - Metatranscriptomics @@ -11648,8 +12882,34 @@ biotools: metaspades bunya: '' description: Genome assembler for metagenomics datasets. + edam-inputs: + - formats: + - FASTQ + term: FASTQ + - formats: + - FASTQ + term: FASTQ + - formats: + - FASTQ + term: FASTQ edam-operations: - Genome alignment + edam-outputs: + - formats: + - FASTA + term: FASTA + - formats: + - TSV + term: TSV + - formats: + - FASTA + term: FASTA + - formats: + - TSV + term: TSV + - formats: + - Textual format + term: Textual format edam-topics: - Metagenomics - Sequence analysis @@ -11683,12 +12943,14 @@ accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.' + edam-inputs: [] edam-operations: - Read binning - Sequence assembly - Genome annotation - Sequence trimming - Demultiplexing + edam-outputs: [] edam-topics: - Whole genome sequencing - Metagenomic sequencing @@ -11716,9 +12978,17 @@ biotools: methyldackel bunya: '' description: A (mostly) universal methylation extractor for BS-seq experiments. + edam-inputs: + - formats: + - BAM + term: BAM edam-operations: - Sequence alignment conversion - Methylation calling + edam-outputs: + - formats: + - bedgraph + term: bedgraph edam-topics: - Epigenomics galaxy: @@ -11740,7 +13010,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'metilene: calling differentially methylated regions from bisulfite @@ -11764,10 +13036,12 @@ description: Estimates effective population sizes,past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes, and population divergences or admixture. + edam-inputs: [] edam-operations: - Haplotype mapping - Phylogenetic tree generation (maximum likelihood and Bayesian methods) - Cell migration analysis + edam-outputs: [] edam-topics: - Population genetics - Nucleic acid structure analysis @@ -11795,10 +13069,12 @@ - 2.2.4--py39h70b41aa_0 description: A lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data and to select the best models in each locus. + edam-inputs: [] edam-operations: - Splice transcript prediction - Gene prediction - RNA-Seq analysis + edam-outputs: [] edam-topics: - RNA-seq - Gene transcripts @@ -11821,7 +13097,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'MiModD Read Alignment: maps sequence reads to a reference genome @@ -11896,8 +13174,17 @@ bunya: '' description: Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. + edam-inputs: + - formats: + - FASTQ-like format (text) + - FASTA + term: FASTA edam-operations: - Genome assembly + edam-outputs: + - formats: + - FASTA + term: FASTA edam-topics: - Sequence assembly galaxy: @@ -11924,8 +13211,10 @@ description: Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. + edam-inputs: [] edam-operations: - De-novo assembly + edam-outputs: [] edam-topics: - Genomics - Sequence assembly @@ -11953,7 +13242,9 @@ bunya: - 4.12.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://docs.conda.io/en/latest/miniconda.html @@ -11973,8 +13264,10 @@ bunya: - 2.24-gcccore-11.3.0 description: Pairwise aligner for genomic and spliced nucleotide sequences + edam-inputs: [] edam-operations: - Pairwise sequence alignment + edam-outputs: [] edam-topics: - Mapping galaxy: @@ -12005,9 +13298,11 @@ description: Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. + edam-inputs: [] edam-operations: - Sequence alignment - Protein sequence analysis + edam-outputs: [] edam-topics: - Sequence sites, features and motifs - Sequence analysis @@ -12029,11 +13324,13 @@ bunya: - 4.9.6--1 description: MIRA 3 - Whole Genome Shotgun and EST Sequence Assembler + edam-inputs: [] edam-operations: - Local alignment - k-mer counting - Sequence assembly - Read mapping + edam-outputs: [] edam-topics: - Sequence assembly - RNA-Seq @@ -12056,7 +13353,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'miRcounts: Counts miRNA alignments from small RNA sequence data' @@ -12078,9 +13377,11 @@ bunya: '' description: miRDeep2 discovers active known or novel miRNAs from deep sequencing data. + edam-inputs: [] edam-operations: - miRNA target prediction - miRNA expression analysis + edam-outputs: [] edam-topics: - Functional, regulatory and non-coding RNA - RNA immunoprecipitation @@ -12110,7 +13411,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'MITObim: mitochondrial baiting and iterative mapping' @@ -12131,11 +13434,13 @@ biotools: mitohifi bunya: '' description: Find, circularise and annotate mitogenome from PacBio assemblies + edam-inputs: [] edam-operations: - Genome assembly - De-novo assembly - Genome annotation - Sequence classification + edam-outputs: [] edam-topics: - Sequence assembly - Sequence analysis @@ -12162,8 +13467,18 @@ biotools: mitos bunya: '' description: De novo metazoan mitochondrial genome annotation. + edam-inputs: + - formats: + - FASTA + term: FASTA edam-operations: - Genome annotation + edam-outputs: + - formats: + - BED + - GFF + - FASTA + term: FASTA edam-topics: - Zoology - Whole genome sequencing @@ -12190,8 +13505,17 @@ - 2.23.0--hdfd78af_1 description: Multi Locus Sequence Typing from an assembled genome or from a set of reads. + edam-inputs: + - formats: + - FASTA-like + - FASTA + term: FASTA edam-operations: - Multilocus sequence typing + edam-outputs: + - formats: + - Binary format + term: Binary format edam-topics: - Immunoproteins and antigens galaxy: @@ -12228,9 +13552,18 @@ \ algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion\ \ metagenomic sequence fragments in 10\u2009h on a single server to 50% sequence\ \ identity." + edam-inputs: + - formats: + - FASTQ-like format (text) + - FASTA-like (text) + term: FASTA-like (text) edam-operations: - Sequence similarity search - Sequence alignment + edam-outputs: + - formats: + - BLAST results + term: BLAST results edam-topics: - Metagenomics - Sequence analysis @@ -12280,11 +13613,13 @@ adaption of bacteria to new niches through horizontal transmission of novel traits to different genetic backgrounds. The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.' + edam-inputs: [] edam-operations: - Clustering - Plasmid map drawing - Sequence assembly - Deposition + edam-outputs: [] edam-topics: - Mobile genetic elements - Whole genome sequencing @@ -12312,75 +13647,18 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'modENCODE fly: server' - title: modENCODE fly 1.0.1 - url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=modENCODEfly - homepage: '' - id: modENCODEfly - license: '' - name: modENCODEfly - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'modENCODE worm: server' - title: modENCODE worm 1.0.1 - url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=modENCODEworm - homepage: '' - id: modENCODEworm - license: '' - name: modENCODEworm - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'modENCODE modMine: server' - title: modENCODE modMine 1.0.0 - url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=modmine - homepage: '' - id: modmine - license: '' - name: modmine - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: moff biotools: moff bunya: '' description: A modest Feature Finder to extract features in MS1 Data. + edam-inputs: + - formats: [] + term: Mass spectrometry data edam-operations: - Protein feature detection + edam-outputs: + - formats: [] + term: Sequence motif (protein) edam-topics: - Proteomics galaxy: @@ -12404,7 +13682,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -12426,8 +13706,10 @@ bunya: '' description: A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. + edam-inputs: [] edam-operations: - Peptide database search + edam-outputs: [] edam-topics: - Proteomics galaxy: @@ -12454,6 +13736,7 @@ bunya: '' description: Open-source, platform-independent, community-supported software for describing and comparing microbial communities + edam-inputs: [] edam-operations: - DNA barcoding - Sequencing quality control @@ -12462,6 +13745,7 @@ - Visualisation - Sequence read processing - Phylogenetic analysis + edam-outputs: [] edam-topics: - Microbial ecology - Taxonomy @@ -12906,8 +14190,10 @@ (MGI). Supports powerful query, reporting, and analysis capabilities, the ability to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer. + edam-inputs: [] edam-operations: - Query and retrieval + edam-outputs: [] edam-topics: - Model organisms - Genotype and phenotype @@ -12935,8 +14221,10 @@ description: Program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. + edam-inputs: [] edam-operations: - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + edam-outputs: [] edam-topics: - Phylogenetics galaxy: '' @@ -12973,9 +14261,11 @@ applications. In this article, we provide a high-level overview of the features of the MRtrix3 framework and general-purpose image processing applications provided with the software + edam-inputs: [] edam-operations: - Image analysis - Visualisation + edam-outputs: [] edam-topics: - MRI - Medical imaging @@ -13002,9 +14292,27 @@ mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. + edam-inputs: + - formats: + - Textual format + - Thermo RAW + - mzXML + - mzML + - MGF + - mzIdentML + term: mzIdentML edam-operations: - Filtering - Formatting + edam-outputs: + - formats: + - Textual format + - Thermo RAW + - mzXML + - mzML + - MGF + - mzIdentML + term: mzIdentML edam-topics: - Proteomics - Proteomics experiment @@ -13029,9 +14337,47 @@ biotools: msmetaenhancer bunya: '' description: Tool for mass spectra metadata annotation. + edam-inputs: + - formats: + - MGF + - JSON + - CSV + - TSV + - xlsx + term: xlsx + - formats: + - SMILES + - InChI + - InChIKey + - Textual format + term: Textual format edam-operations: - Annotation - Standardisation and normalisation + edam-outputs: + - formats: + - MGF + - JSON + - CSV + - TSV + - xlsx + term: xlsx + - formats: [] + term: Sample annotation + - formats: + - InChI + - SMILES + term: SMILES + - formats: [] + term: Database ID + - formats: [] + term: PubChem ID + - formats: [] + term: Chemical name (IUPAC) + - formats: [] + term: CAS number + - formats: [] + term: ChEBI ID edam-topics: - Metabolomics - Compound libraries and screening @@ -13057,6 +14403,10 @@ biotools: msstats bunya: '' description: Statistical tool for quantitative mass spectrometry-based proteomics. + edam-inputs: + - formats: + - CSV + term: CSV edam-operations: - Statistical modelling - Data handling @@ -13064,6 +14414,10 @@ - Statistical inference - Quantification - Standardisation and normalisation + edam-outputs: + - formats: + - CSV + term: CSV edam-topics: - Proteomics - Proteomics experiment @@ -13088,21 +14442,31 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: msstatstmt + biotools: msstatstmt bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: Tools for detecting differentially abundant peptides and proteins in + shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) + labeling + edam-inputs: [] + edam-operations: + - Spectrum calculation + - Tag-based peptide identification + - Differential protein expression profiling + edam-outputs: [] + edam-topics: + - Proteomics + - Proteomics experiment + - Protein expression galaxy: - description: 'MSstatsTMT: protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling' title: MSstatsTMT 2.0.0+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmsstatstmt%2Fmsstatstmt%2F2.0.0%2Bgalaxy1 - homepage: '' + homepage: https://msstats.org/msstatstmt/ id: bioconductor-msstatstmt license: '' - name: msstatstmt + name: MSstatsTMT nci-gadi: '' nci-if89: '' pawsey: '' @@ -13115,7 +14479,9 @@ bunya: - '20230414' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -13138,9 +14504,21 @@ many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + edam-inputs: [] edam-operations: - Validation - Sequencing quality control + edam-outputs: + - formats: + - CSV + - JSON + - HTML + - YAML + - TSV + term: TSV + - formats: + - HTML + term: HTML edam-topics: - Sequencing - Bioinformatics @@ -13171,9 +14549,11 @@ description: MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Basically it is a ultra-fast alignment of large-scale DNA and protein sequences + edam-inputs: [] edam-operations: - Sequence alignment - Read mapping + edam-outputs: [] edam-topics: - Genomics - Mapping @@ -13221,7 +14601,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Construct Expression Set Object: Create an ExpressionSet object @@ -13247,18 +14629,24 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: mztosqlite + biotools: mztosqlite bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: Convert proteomics data files into a SQLite database + edam-inputs: [] + edam-operations: + - Conversion + - Peptide database search + edam-outputs: [] + edam-topics: + - Proteomics + - Biological databases galaxy: - description: 'mz to sqlite: Extract mzIdentML and associated proteomics datasets into a SQLite DB' title: mz to sqlite 2.1.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Fmz_to_sqlite%2Fmz_to_sqlite%2F2.1.1%2Bgalaxy0 - homepage: '' + homepage: https://github.com/galaxyproteomics/mzToSQLite id: mztosqlite license: '' name: mztosqlite @@ -13273,7 +14661,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://www.nag.com/ @@ -13316,11 +14706,13 @@ such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro' + edam-inputs: [] edam-operations: - Post-translation modification site prediction - PolyA signal detection - Genotyping - k-mer counting + edam-outputs: [] edam-topics: - Functional, regulatory and non-coding RNA - RNA-Seq @@ -13348,7 +14740,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'NanoFilt: Filtering and trimming of long read sequencing data' @@ -13371,9 +14765,15 @@ description: NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences + edam-inputs: + - formats: + - FASTA-like + - nucleotide + term: nucleotide edam-operations: - Scatter plot plotting - Box-Whisker plot plotting + edam-outputs: [] edam-topics: - Genomics galaxy: @@ -13400,12 +14800,22 @@ - 0.14.0--hb24e783_1 description: A package for detecting cytosine methylations and genetic variations from nanopore MinION sequencing data. + edam-inputs: + - formats: + - FASTA-like (text) + term: FASTA-like (text) + - formats: + - FASTA + term: FASTA edam-operations: - Statistical calculation - Genetic variation analysis - Sequence assembly - Methylation analysis - Mapping + edam-outputs: + - formats: [] + term: Sequence alignment report edam-topics: - Sequence analysis - Sequencing @@ -13444,7 +14854,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -13463,7 +14875,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Natural Product likeness calculator: - calculates the similarity @@ -13487,10 +14901,12 @@ description: NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. + edam-inputs: [] edam-operations: - Data handling - Sequence database search - Data retrieval + edam-outputs: [] edam-topics: - Biological databases galaxy: '' @@ -13509,25 +14925,66 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: ncbi_resources + biotools: ncbi_resources bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: The National Center for Biotechnology Information (NCBI) provides analysis + and retrieval resources for the data in GenBank and other biological data made + available through the NCBI web site. + edam-inputs: [] + edam-operations: + - Deposition + - Service discovery + - Query and retrieval + - PCR primer design + edam-outputs: [] + edam-topics: + - Data integration and warehousing + - Database management + - Data mining + - Molecular interactions, pathways and networks + - Rare diseases galaxy: - description: 'NCBI Accession Download: Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API' title: NCBI Accession Download 0.2.8+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fncbi_acc_download%2Fncbi_acc_download%2F0.2.8%2Bgalaxy0 - homepage: '' + homepage: http://www.ncbi.nlm.nih.gov id: ncbi_acc_download license: '' name: ncbi_acc_download nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: Database resources of the National Center for Biotechnology Information. + url: https://doi.org/10.1093/nar/gkp967 + - title: Database resources of the national center for biotechnology information + url: https://doi.org/10.1093/nar/gkq1172 + - title: Database resources of the National Center for Biotechnology Information + url: https://doi.org/10.1093/nar/gkr1184 + - title: Database resources of the National Center for Biotechnology Information + url: https://doi.org/10.1093/nar/gki062 + - title: Database resources of the National Center for Biotechnology Information + url: https://doi.org/10.1093/nar/gkl1031 + - title: Database resources of the National Center for Biotechnology Information + url: https://doi.org/10.1093/nar/gkm1000 + - title: Database resources of the National Center for Biotechnology Information + url: https://doi.org/10.1093/nar/gku1130 + - title: Database resources of the National Center for Biotechnology Information + url: https://doi.org/10.1093/nar/gkv1290 + - title: Database resources of the national center for biotechnology information + url: https://doi.org/10.1093/nar/gkab1112 + - title: Database resources of the National Center for Biotechnology Information + url: https://doi.org/10.1093/nar/gkaa892 + - title: Database resources of the National Center for Biotechnology Information + url: https://doi.org/10.1093/nar/gkx1095 + - title: Database resources of the National Center for Biotechnology Information + url: https://doi.org/10.1093/nar/gkz899 + - title: Database resources of the National Center for Biotechnology Information + url: https://doi.org/10.1093/nar/gky1069 + - title: Database Resources of the National Center for Biotechnology Information + url: https://doi.org/10.1093/nar/gkw1071 resources: - title: .nan url: .nan @@ -13537,7 +14994,9 @@ - 2.10.9-gompi-2021a - 3.0.2-gompi-2022a (D) description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://github.com/ncbi/ncbi-vdb @@ -13559,8 +15018,10 @@ done in local memory without requiring temporary files. Highly recommended for regression testing scientific models or datasets in a test-driven development environment. + edam-inputs: [] edam-operations: - Regression analysis + edam-outputs: [] edam-topics: '' galaxy: '' homepage: https://gitlab.com/remikz/nccmp @@ -13579,7 +15040,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://www.ncl.ucar.edu/index.shtml @@ -13599,7 +15062,9 @@ bunya: '' description: The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: http://nco.sourceforge.net/ @@ -13620,8 +15085,10 @@ biotools: ncview bunya: '' description: Ncview is a netCDF visual browser. + edam-inputs: [] edam-operations: - Visualisation + edam-outputs: [] edam-topics: '' galaxy: '' homepage: https://cirrus.ucsd.edu/ncview/ @@ -13644,7 +15111,9 @@ description: NetCDF (Network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://www.unidata.ucar.edu/software/netcdf/ @@ -13678,10 +15147,12 @@ phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. + edam-inputs: [] edam-operations: - Phylogenetic tree generation - Phylogenetic tree analysis - Phylogenetic tree reconstruction + edam-outputs: [] edam-topics: - Phylogeny - Genomics @@ -13703,20 +15174,28 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: nextclade + biotools: nextclade bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: Nextclade is an open-source project for viral genome alignment, mutation + calling, clade assignment, quality checks and phylogenetic placement. + edam-inputs: [] + edam-operations: + - Methylation analysis + - Variant calling + edam-outputs: [] + edam-topics: + - Genomics + - Sequence analysis + - Cladistics galaxy: - description: 'Nextclade: Viral genome clade assignment, mutation calling, and sequence quality checks' title: Nextclade 2.7.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fnextclade%2Fnextclade%2F2.7.0%2Bgalaxy0 - homepage: '' + homepage: https://github.com/nextstrain/nextclade id: nextclade - license: '' + license: MIT name: nextclade nci-gadi: '' nci-if89: '' @@ -13732,9 +15211,11 @@ description: Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. + edam-inputs: [] edam-operations: - Service composition - Service invocation + edam-outputs: [] edam-topics: - Software engineering - Workflows @@ -13772,10 +15253,12 @@ to correct the error bases in reference genome. To correct the raw third-generation sequencing (TGS) long reads with approximately 15-10% sequencing errors, please use NextDenovo' + edam-inputs: [] edam-operations: - Genome assembly - Scaffolding - k-mer counting + edam-outputs: [] edam-topics: - Sequence assembly - Plant biology @@ -13794,22 +15277,43 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: NextPolish + biotools: NextPolish bunya: - 0.1.0--hd03093a_0 - description: '' - edam-operations: '' - edam-topics: '' + description: 'A fast and efficient genome polishing tool for long read assembly. + + + Fast and accurately polish the genome generated by noisy long reads. + + + NextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy + long reads, it can be used with short read data only or long read data only or + a combination of both. It contains two core modules, and use a stepwise fashion + to correct the error bases in reference genome. To correct the raw third-generation + sequencing (TGS) long reads with approximately 15-10% sequencing errors, please + use NextDenovo' + edam-inputs: [] + edam-operations: + - Genome assembly + - Scaffolding + - k-mer counting + edam-outputs: [] + edam-topics: + - Sequence assembly + - Plant biology + - Mapping galaxy: '' - homepage: '' + homepage: https://github.com/Nextomics/NextPolish id: nextpolish2 license: '' name: NextPolish2 nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: 'NextPolish: A fast and efficient genome polishing tool for long-read assembly' + url: https://doi.org/10.1093/BIOINFORMATICS/BTZ891 resources: - title: .nan url: .nan @@ -13818,7 +15322,9 @@ bunya: - 2.10.9-gcccore-10.3.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://github.com/ncbi/ngs @@ -13837,12 +15343,14 @@ bunya: '' description: NGSUtils is a suite of software tools for working with next-generation sequencing datasets + edam-inputs: [] edam-operations: - Read pre-processing - Sequencing quality control - Variant calling - Formatting - Sequence contamination filtering + edam-outputs: [] edam-topics: - Genomics - Transcriptomics @@ -13870,7 +15378,9 @@ - 1.10.2-gcccore-10.3.0 - 1.10.2-gcccore-11.3.0 (D) description: Nearly Infinite Neighbor Joining Application + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: - Phylogeny galaxy: '' @@ -13890,7 +15400,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'NOVOplasty: de novo assembler for short circular genomes' @@ -13911,7 +15423,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -13930,7 +15444,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Naive Variant Caller (NVC): - tabulate variable sites from BAM datasets' @@ -13953,8 +15469,10 @@ description: Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. + edam-inputs: [] edam-operations: - Sequence analysis + edam-outputs: [] edam-topics: - Sequence analysis - DNA @@ -14011,7 +15529,9 @@ bunya: - 4.1.1--pyhdfd78af_0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -14033,6 +15553,55 @@ that can be combined to a workflow with the integrated workflow editor TOPPAS. Raw and intermediate mass spectrometry data can be visualised with the included viewer TOPPView. + edam-inputs: + - formats: + - pepXML + - mzQuantML + - dta + - FASTA + - protXML + - idXML + - OBO + - XML + - TraML + - mzML + - mzIdentML + - mzXML + - MGF + - qcML + term: qcML + - formats: + - pepXML + - mzQuantML + - dta + - FASTA + - protXML + - idXML + - OBO + - XML + - TraML + - mzML + - mzIdentML + - mzXML + - MGF + - qcML + term: qcML + - formats: + - pepXML + - mzQuantML + - dta + - FASTA + - protXML + - idXML + - OBO + - XML + - TraML + - mzML + - mzIdentML + - mzXML + - MGF + - qcML + term: qcML edam-operations: - Protein identification - Parsing @@ -14058,6 +15627,33 @@ - Prediction and recognition (protein) - Comparison - Standardisation and normalisation + edam-outputs: + - formats: + - pepXML + - mzQuantML + - dta + - FASTA + - idXML + - mzXML + - TraML + - mzML + - mzIdentML + - MGF + - qcML + term: qcML + - formats: + - pepXML + - mzQuantML + - dta + - FASTA + - idXML + - mzXML + - TraML + - mzML + - mzIdentML + - MGF + - qcML + term: qcML edam-topics: - Proteomics experiment - Proteomics @@ -14213,7 +15809,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -14237,11 +15835,13 @@ It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. + edam-inputs: [] edam-operations: - Genome comparison - Phylogenetic tree generation (from molecular sequences) - Phylogenetic tree analysis - Genome alignment + edam-outputs: [] edam-topics: - Phylogenetics - Phylogenomics @@ -14271,7 +15871,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Calculate community metrics: calculate community metrics from abundance @@ -14309,7 +15911,9 @@ bunya: - 3.1.2 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://pandoc.org/ @@ -14332,12 +15936,18 @@ of interest; Pangolin will predict changes in splice site strength due to each variant, and return a file of the same format. Pangolin's models can also be used with custom sequences. + edam-inputs: + - formats: + - VCF + - CSV + term: CSV edam-operations: - Splice site prediction - Sequence merging - Alternative splicing prediction - Genotyping - Variant classification + edam-outputs: [] edam-topics: - RNA splicing - Genetic variation @@ -14365,7 +15975,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Parse parameter value: from dataset' @@ -14390,8 +16002,10 @@ \ data using qualitative and quantitative techniques. The data exploration can\ \ be done interactively in 3D or programmatically using ParaView\u2019s batch\ \ processing capabilities." + edam-inputs: [] edam-operations: - Visualisation + edam-outputs: [] edam-topics: - Data visualisation - Imaging @@ -14421,7 +16035,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Parse mitochondrial blast: overlap-conscious coverage calculation @@ -14446,9 +16062,11 @@ description: Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees. + edam-inputs: [] edam-operations: - SNP detection - Genome alignment + edam-outputs: [] edam-topics: - DNA polymorphism - Phylogenetics @@ -14474,9 +16092,11 @@ pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. + edam-inputs: [] edam-operations: - Pathway or network analysis - Pathway or network visualisation + edam-outputs: [] edam-topics: - Molecular interactions, pathways and networks - Systems biology @@ -14508,9 +16128,11 @@ contaminants as well as many non-pathogenic microbiota. Researchers can analyze, display and transform results from the Kraken and Centrifuge classifiers using interactive tables, heatmaps and flow diagrams. + edam-inputs: [] edam-operations: - Annotation - Taxonomic classification + edam-outputs: [] edam-topics: - Metagenomics - Model organisms @@ -14535,9 +16157,11 @@ biotools: pblat bunya: '' description: Multithread blat algorithm speeding up aligning sequences to genomes. + edam-inputs: [] edam-operations: - Protein threading - Read mapping + edam-outputs: [] edam-topics: - RNA-seq - Mapping @@ -14563,11 +16187,13 @@ bunya: '' description: Productive visualization of high-throughput sequencing data using the SeqCode open portable platform. + edam-inputs: [] edam-operations: - Visualisation - Peak calling - Essential dynamics - Phylogenetic footprinting + edam-outputs: [] edam-topics: - ChIP-seq - RNA-Seq @@ -14599,8 +16225,10 @@ description: Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. + edam-inputs: [] edam-operations: - Sequence merging + edam-outputs: [] edam-topics: - Sequence assembly galaxy: @@ -14624,7 +16252,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'PepPointer: classify genomic location of peptides' @@ -14650,6 +16280,16 @@ and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data + edam-inputs: + - formats: + - FASTA + term: FASTA + - formats: + - mzIdentML + term: mzIdentML + - formats: + - MGF + term: MGF edam-operations: - PTM localisation - Protein identification @@ -14658,6 +16298,20 @@ - Peptide identification - Mass spectrum visualisation - Enrichment analysis + edam-outputs: + - formats: + - JPG + - SVG + term: SVG + - formats: + - Textual format + term: Textual format + - formats: + - Image format + term: Image format + - formats: + - TSV + term: TSV edam-topics: - Proteomics - Proteomics experiment @@ -14696,7 +16350,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Peptide Genomic Coordinate: Get Peptide''s genomic coordinate using @@ -14718,6 +16374,10 @@ biotools: percolator bunya: '' description: Semi-supervised learning for peptide identification from MS/MS data. + edam-inputs: + - formats: + - XML + term: XML edam-operations: - Protein fragment weight comparison - Protein identification @@ -14725,6 +16385,10 @@ - Peptide identification - Target-Decoy - Validation of peptide-spectrum matches + edam-outputs: + - formats: + - XML + term: XML edam-topics: - Proteomics - Proteomics experiment @@ -14762,7 +16426,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -14782,8 +16448,10 @@ bunya: '' description: This tool is used to search a FASTA sequence against a library of Pfam HMM. + edam-inputs: [] edam-operations: - Protein sequence analysis + edam-outputs: [] edam-topics: - Sequence analysis galaxy: @@ -14806,12 +16474,14 @@ bunya: '' description: Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. + edam-inputs: [] edam-operations: - Genome annotation - Antimicrobial resistance prediction - tRNA gene prediction - Formatting - Sequence assembly + edam-outputs: [] edam-topics: - Metagenomics - Sequence sites, features and motifs @@ -14839,7 +16509,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Phinch Visualisation: ' @@ -14860,7 +16532,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://www.php.net/ @@ -14880,10 +16554,12 @@ bunya: '' description: Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. + edam-inputs: [] edam-operations: - Deposition - Analysis - Visualisation + edam-outputs: [] edam-topics: - Microbiology - Sequence analysis @@ -14913,8 +16589,19 @@ biotools: phyml bunya: '' description: Phylogenetic estimation software using Maximum Likelihood + edam-inputs: + - formats: + - Phylip format variant + term: Phylip format variant + - formats: + - Phylip format variant + term: Phylip format variant edam-operations: - Phylogenetic tree generation (maximum likelihood and Bayesian methods) + edam-outputs: + - formats: + - newick + term: newick edam-topics: - Phylogenetics - Bioinformatics @@ -14951,8 +16638,10 @@ description: A set of command line tools for manipulating high-throughput sequencing (HTS) data in formats such as SAM/BAM/CRAM and VCF. Available as a standalone program or within the GATK4 program. + edam-inputs: [] edam-operations: - Genetic variation analysis + edam-outputs: [] edam-topics: - Sequencing - Data management @@ -15086,11 +16775,13 @@ of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. + edam-inputs: [] edam-operations: - Phylogenetic reconstruction - Expression analysis - Genome annotation - DNA barcoding + edam-outputs: [] edam-topics: - Metagenomics - Microbial ecology @@ -15139,11 +16830,13 @@ description: PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. + edam-inputs: [] edam-operations: - Phylogenetic reconstruction - Expression analysis - Rarefaction - Pathway analysis + edam-outputs: [] edam-topics: - Metagenomics - Microbiology @@ -15190,7 +16883,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Pileup-to-Interval: condenses pileup format into ranges of bases' @@ -15211,7 +16906,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Filter pileup: on coverage and SNPs' @@ -15233,8 +16930,10 @@ bunya: '' description: Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. + edam-inputs: [] edam-operations: - Sequence assembly + edam-outputs: [] edam-topics: - Assembly galaxy: @@ -15269,12 +16968,14 @@ as those without any programming or development expertise, to perform complex analysis in a simple to use, transparent, accessible, reproducible, and user-friendly environment' + edam-inputs: [] edam-operations: - Essential dynamics - Quantification - Standardisation and normalisation - Imputation - Parsing + edam-outputs: [] edam-topics: - PCR experiment - Transcriptomics @@ -15297,19 +16998,24 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: plasflow + biotools: plasflow bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: PlasFlow is a set of scripts used for prediction of plasmid sequences + in metagenomic contigs. + edam-inputs: [] + edam-operations: + - Sequence analysis + edam-outputs: [] + edam-topics: + - Metagenomics galaxy: - description: 'PlasFlow: Prediction of plasmid sequences in metagenomic contigs' title: PlasFlow 1.1.0+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fplasflow%2FPlasFlow%2F1.1.0%2Bgalaxy0 - homepage: '' + homepage: https://github.com/smaegol/PlasFlow id: PlasFlow - license: '' + license: GPL-3.0 name: PlasFlow nci-gadi: '' nci-if89: '' @@ -15325,8 +17031,10 @@ description: Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + edam-inputs: [] edam-operations: - Genetic variation analysis + edam-outputs: [] edam-topics: - GWAS study galaxy: '' @@ -15349,7 +17057,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Plot confusion matrix, precision, recall and ROC and AUC curves: @@ -15377,8 +17087,10 @@ biotools: pnetcdf bunya: '' description: 'PnetCDF: A Parallel I/O Library for NetCDF File Access' + edam-inputs: [] edam-operations: - Aggregation + edam-outputs: [] edam-topics: - Computer science galaxy: '' @@ -15400,7 +17112,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Poisson two-sample test: ' @@ -15421,7 +17135,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Porechop: adapter trimmer for Oxford Nanopore reads' @@ -15443,8 +17159,10 @@ bunya: '' description: Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. + edam-inputs: [] edam-operations: - Nucleic acid sequence analysis + edam-outputs: [] edam-topics: - DNA - Sequencing @@ -15508,8 +17226,10 @@ - 1.1.alpha19 description: Tools for performing taxonomic assignment based on phylogeny using pplacer and clst. + edam-inputs: [] edam-operations: - Taxonomic classification + edam-outputs: [] edam-topics: - Taxonomy galaxy: '' @@ -15530,7 +17250,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'PretextMap: converts SAM or BAM files into genome contact maps' @@ -15551,8 +17273,10 @@ biotools: pretextview bunya: '' description: Pretext is an OpenGL-powered pretext contact map viewer. + edam-inputs: [] edam-operations: - Scaffolding + edam-outputs: [] edam-topics: - Mapping galaxy: @@ -15582,8 +17306,10 @@ a majority of the highest-scoring PRODIGAL selected sites coincide. If such a position is found, it is accepted, and the predictions are changed for the outlying genes. + edam-inputs: [] edam-operations: - Gene prediction + edam-outputs: [] edam-topics: - DNA - Sequence analysis @@ -15612,8 +17338,10 @@ separation, or handle low resolution data only. Here we present the package that implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) and generates the peak table. + edam-inputs: [] edam-operations: - Peak calling + edam-outputs: [] edam-topics: - Metabolomics galaxy: @@ -15637,7 +17365,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -15659,10 +17389,12 @@ - 1.14.5-gompi-2022a (D) description: Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. + edam-inputs: [] edam-operations: - Gene prediction - Coding region prediction - Genome annotation + edam-outputs: [] edam-topics: - Genomics - Model organisms @@ -15688,28 +17420,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' - edam-topics: '' - galaxy: - - description: 'proportional venn: from 2-3 sets' - title: proportional venn 0.5 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fidot%2Fprop_venn%2Fprop_venn%2F0.5 - homepage: '' - id: prop_venn - license: '' - name: prop_venn - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://anaconda.org/bioconda/ucsc-pslcdnafilter @@ -15736,10 +17449,12 @@ be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences' + edam-inputs: [] edam-operations: - Genome assembly - Read binning - Scaffolding + edam-outputs: [] edam-topics: - Sequence assembly galaxy: @@ -15766,7 +17481,9 @@ - 0.3.18-foss-2021a - 0.3.18-foss-2022a (D) description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -15786,9 +17503,11 @@ - 2.5.2-foss-2021a description: PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. + edam-inputs: [] edam-operations: - Sequencing quality control - Statistical calculation + edam-outputs: [] edam-topics: - Sequence analysis - Data quality management @@ -15819,9 +17538,11 @@ pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.' + edam-inputs: [] edam-operations: - Visualisation - Formatting + edam-outputs: [] edam-topics: - Model organisms - Imaging @@ -15847,7 +17568,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'PyProphet merge: Merge multiple osw files' @@ -15880,9 +17603,11 @@ - 0.16.0.1-gcc-10.3.0 - 0.19.1-gcc-11.3.0 (D) description: A Python module for reading and manipulating SAM/BAM/VCF/BCF files. + edam-inputs: [] edam-operations: - Data handling - Sequence file editing + edam-outputs: [] edam-topics: - Sequencing - Mapping @@ -15905,7 +17630,9 @@ bunya: '' description: PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: - Machine learning - Computer science @@ -15932,11 +17659,13 @@ - '2022.8' description: "QIIME 2\u2122 is a next-generation microbiome bioinformatics platform\ \ that is extensible, free, open source, and community developed." + edam-inputs: [] edam-operations: - Demultiplexing - Visualisation - Taxonomic classification - Phylogenetic analysis + edam-outputs: [] edam-topics: - Microbial ecology - Phylogeny @@ -16536,35 +18265,16 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Boxplot: of quality statistics' - title: Boxplot 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=qual_stats_boxplot - homepage: '' - id: qual_stats_boxplot - license: '' - name: qual_stats_boxplot - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: qualimap biotools: qualimap bunya: '' description: Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. + edam-inputs: [] edam-operations: - Sequencing quality control + edam-outputs: [] edam-topics: - Data quality management galaxy: @@ -16606,10 +18316,12 @@ licensed under the Apache License, Version 2.0. The source code, documentation, and file specifications are available at: https: phac-nml.github.io quasitools Contact gary.vandomselaar@canada.ca' + edam-inputs: [] edam-operations: - Sequence trimming - Genotyping - Base-calling + edam-outputs: [] edam-topics: - Virology - Small molecules @@ -16674,9 +18386,11 @@ - 5.2.0-foss-2022a (D) description: "QUAST stands for QUality ASsessment Tool. \nIt evaluates a quality\ \ of genome assemblies by computing various metrics and providing nice reports." + edam-inputs: [] edam-operations: - Visualisation - Sequence assembly validation + edam-outputs: [] edam-topics: - Sequence assembly galaxy: @@ -16706,11 +18420,19 @@ a Galaxy workflow. The SQLite database can be saved to the Galaxy history, and further process to generate tabular outputs containing desired information and formatting. + edam-inputs: + - formats: + - TSV + term: TSV edam-operations: - Data handling - Parsing - Query and retrieval - Filtering + edam-outputs: + - formats: + - TSV + term: TSV edam-topics: - Bioinformatics - Workflows @@ -16738,10 +18460,12 @@ - 4.2.1-foss-2021a - 4.2.1-foss-2022a (D) description: Free software environment for statistical computing and graphics. + edam-inputs: [] edam-operations: - Analysis - Data handling - Visualisation + edam-outputs: [] edam-topics: - Mathematics - Data architecture, analysis and design @@ -16768,7 +18492,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Initial processing using RaceID: performs filtering, normalisation, @@ -16816,9 +18542,11 @@ and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.' + edam-inputs: [] edam-operations: - Genome assembly - Mapping assembly + edam-outputs: [] edam-topics: - Whole genome sequencing - Sequence assembly @@ -16847,11 +18575,30 @@ bunya: '' description: A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. + edam-inputs: + - formats: + - Binary format + - CSV + term: CSV + - formats: + - Binary format + - CSV + term: CSV + - formats: + - Binary format + - CSV + term: CSV edam-operations: - Imputation - Standardisation and normalisation - Clustering - Correlation + edam-outputs: + - formats: [] + term: Mass spectrum + - formats: + - CSV + term: CSV edam-topics: - Metabolomics galaxy: @@ -16886,12 +18633,14 @@ \ using colored de Bruijn graphs.\n\nRatatosk is a phased error correction tool\ \ for erroneous long reads based on compacted and colored de Bruijn graphs built\ \ from accurate short reads." + edam-inputs: [] edam-operations: - De-novo assembly - Sequencing error detection - Variant calling - Phasing - Read binning + edam-outputs: [] edam-topics: - DNA polymorphism - Sequence assembly @@ -16910,27 +18659,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Ratmine: server' - title: Ratmine 1.0.0 - url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=ratmine - homepage: '' - id: ratmine - license: '' - name: ratmine - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: raven biotools: raven bunya: '' @@ -16938,10 +18666,12 @@ Raven is a de novo genome assembler for long uncorrected reads.' + edam-inputs: [] edam-operations: - De-novo assembly - Genome assembly - Read pre-processing + edam-outputs: [] edam-topics: - Sequence assembly - Whole genome sequencing @@ -16968,8 +18698,16 @@ bunya: '' description: A standalone tool for extracting data directly from raw files generated by Thermo Orbitrap family instruments. + edam-inputs: + - formats: + - Thermo RAW + term: Thermo RAW edam-operations: - Parsing + edam-outputs: + - formats: + - Textual format + term: Textual format edam-topics: - Proteomics experiment - Proteomics @@ -16997,9 +18735,11 @@ bunya: - 8.2.12 description: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. + edam-inputs: [] edam-operations: - Sequence analysis - Phylogenetic tree analysis + edam-outputs: [] edam-topics: - Phylogenetics - Sequence analysis @@ -17028,10 +18768,12 @@ bunya: '' description: RDKit is an Open-Source Cheminformatics Software. Fast, Efficient Fragment-Based Coordinate Generation for Open Babel. + edam-inputs: [] edam-operations: - Nucleic acid structure prediction - Molecular dynamics - Protein geometry validation + edam-outputs: [] edam-topics: - Cheminformatics - Medicinal chemistry @@ -17061,7 +18803,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Create Frankenstein ligand: for docking active site definition' @@ -17083,9 +18827,11 @@ bunya: '' description: Tool for calculating the probability of nucleosome formation along a DNA sequence input by the user. + edam-inputs: [] edam-operations: - Nucleosome formation or exclusion sequence prediction - Formatting + edam-outputs: [] edam-topics: - DNA - DNA binding sites @@ -17114,12 +18860,26 @@ The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. + edam-inputs: + - formats: + - mzML + term: mzML edam-operations: - Chromatographic alignment - Quantification - Peak detection - Feature extraction - Alignment + edam-outputs: + - formats: + - Binary format + term: Binary format + - formats: + - Binary format + term: Binary format + - formats: + - Binary format + term: Binary format edam-topics: - Metabolomics galaxy: @@ -17170,8 +18930,10 @@ bunya: '' description: This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. + edam-inputs: [] edam-operations: - RNA-Seq analysis + edam-outputs: [] edam-topics: - RNA - Sequencing @@ -17199,7 +18961,9 @@ bunya: - 3.2.9 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://rgcgithub.github.io/regenie/ @@ -17222,8 +18986,10 @@ of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).' + edam-inputs: [] edam-operations: - Genome annotation + edam-outputs: [] edam-topics: - Sequence analysis - Sequence composition, complexity and repeats @@ -17254,10 +19020,12 @@ programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. + edam-inputs: [] edam-operations: - Genome assembly - de Novo sequencing - Genome annotation + edam-outputs: [] edam-topics: - Model organisms - Sequence composition, complexity and repeats @@ -17288,8 +19056,10 @@ biotools: RepeatScout bunya: '' description: RepeatScout is a tool to discover repetitive substrings in DNA. + edam-inputs: [] edam-operations: - k-mer counting + edam-outputs: [] edam-topics: - DNA galaxy: '' @@ -17311,7 +19081,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'RepEnrich: Repeat Element Profiling' @@ -17337,7 +19109,9 @@ a sequence of dependent samples from the posterior distribution of the parameters.' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: - Statistics and probability galaxy: '' @@ -17360,8 +19134,16 @@ MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records. + edam-inputs: + - formats: + - XML + term: XML edam-operations: - Clustering + edam-outputs: + - formats: + - Mass spectrometry data format + term: Mass spectrometry data format edam-topics: - Metabolomics galaxy: @@ -17387,7 +19169,9 @@ bunya: - 4.1.2 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -17407,8 +19191,12 @@ description: RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler. + edam-inputs: + - formats: [] + term: Sequence edam-operations: - Sequence analysis + edam-outputs: [] edam-topics: - Genomics galaxy: '' @@ -17429,7 +19217,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Analyse canonical genes against ''peak'' data: using RnaChipIntegrator' @@ -17456,8 +19246,10 @@ description: A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. + edam-inputs: [] edam-operations: - Genome assembly + edam-outputs: [] edam-topics: - DNA - Genomics @@ -17480,28 +19272,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'Row Means: Calculates the mean of a row of numbers for an entire - table' - title: Row Means 0.1 - url: https://usegalaxy.org.au/root?tool_id=testtoolshed.g2.bx.psu.edu%2Frepos%2Fsimon-gladman%2Frow_means%2Frow_means%2F0.1 - homepage: '' - id: row_means - license: '' - name: row_means - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: rsem biotools: rsem bunya: @@ -17512,8 +19282,10 @@ previous methods. Our improved accuracy is the result of handling read mapping uncertainty with a statistical model and the estimation of gene expression levels as the sum of isoform expression levels. + edam-inputs: [] edam-operations: - RNA-Seq quantification + edam-outputs: [] edam-topics: - RNA-Seq galaxy: '' @@ -17538,8 +19310,10 @@ inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. + edam-inputs: [] edam-operations: - Data handling + edam-outputs: [] edam-topics: - Sequencing galaxy: @@ -17641,9 +19415,11 @@ biotools: rstudio bunya: '' description: Integrated development environment (IDE) for the R programming language. + edam-inputs: [] edam-operations: - Data handling - Visualisation + edam-outputs: [] edam-topics: - Mathematics - Data architecture, analysis and design @@ -17670,9 +19446,11 @@ bunya: '' description: 'RTG Core: Software for alignment and analysis of next-gen sequencing data.' + edam-inputs: [] edam-operations: - Sequence alignment - Sequence alignment analysis + edam-outputs: [] edam-topics: - Genomics galaxy: '' @@ -17692,7 +19470,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'rxDock cavity definition: - generate the active site definition @@ -17719,8 +19499,10 @@ description: A software tool that implements a novel, is an alignment-free algorithm for the estimation of isoform abundances directly from a set of reference sequences and RNA-seq reads. + edam-inputs: [] edam-operations: - RNA-Seq analysis + edam-outputs: [] edam-topics: - RNA-Seq - RNA @@ -17750,10 +19532,22 @@ - 1.4.0-gompi-2021a - 1.9.0-gcc-11.3.0 (D) description: A tool for transcript expression quantification from RNA-seq data + edam-inputs: + - formats: + - FASTQ + - FASTA + term: FASTA + - formats: + - FASTA + term: FASTA edam-operations: - Sequence composition calculation - RNA-Seq quantification - Gene expression analysis + edam-outputs: + - formats: + - TSV + term: TSV edam-topics: - RNA-Seq - Gene expression @@ -17781,7 +19575,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'salmonKallistoMtxTo10x: Transforms .mtx matrix and associated labels @@ -17810,10 +19606,12 @@ with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch' + edam-inputs: [] edam-operations: - Genome assembly - De-novo assembly - Scaffolding + edam-outputs: [] edam-topics: - Sequence assembly - DNA binding sites @@ -17839,7 +19637,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Filter SAM: on bitwise flag values' @@ -17860,7 +19660,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Generate pileup: from BAM dataset' @@ -17881,7 +19683,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Convert SAM: to interval' @@ -17903,9 +19707,11 @@ bunya: '' description: This tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats. + edam-inputs: [] edam-operations: - Sequence analysis - Sequence alignment + edam-outputs: [] edam-topics: - DNA - Sequence analysis @@ -17934,8 +19740,10 @@ bunya: '' description: A tool to mark duplicates and extract discordant and split reads from SAM files. + edam-inputs: [] edam-operations: - Split read mapping + edam-outputs: [] edam-topics: - DNA - Sequencing @@ -17965,6 +19773,12 @@ high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. + edam-inputs: + - formats: + - BAM + - SAM + - CRAM + term: CRAM edam-operations: - Indexing - Editing @@ -17973,6 +19787,12 @@ - Formatting - Sorting - Filtering + edam-outputs: + - formats: + - BAM + - SAM + - CRAM + term: CRAM edam-topics: - Mapping - Sequence analysis @@ -18071,8 +19891,10 @@ includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. + edam-inputs: [] edam-operations: - Differential gene expression analysis + edam-outputs: [] edam-topics: - Gene expression - Cell biology @@ -18201,10 +20023,12 @@ bunya: '' description: Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. + edam-inputs: [] edam-operations: - Read pre-processing - Sequencing quality control - Sequence visualisation + edam-outputs: [] edam-topics: - RNA-seq - Quality affairs @@ -18249,7 +20073,9 @@ bunya: - 0.11.1-gcccore-10.3.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -18268,11 +20094,13 @@ bunya: '' description: Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. + edam-inputs: [] edam-operations: - Image analysis - Image annotation - Visualisation - Data handling + edam-outputs: [] edam-topics: - Imaging - Software engineering @@ -18316,7 +20144,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Estimator attributes: get important attributes from an estimator @@ -18383,7 +20213,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://www.webscipio.org/ @@ -18402,7 +20234,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Extract values from an SD-file: into a tabular file using RDKit' @@ -18423,7 +20257,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Send to cloud: ' @@ -18447,8 +20283,14 @@ - 4.5.1-foss-2022a (D) description: "SEPP stands for SAT\xE9-Enabled Phylogenetic Placement and addresses\ \ the problem of phylogenetic placement for meta-genomic short reads" + edam-inputs: + - formats: [] + term: Phylogenetic tree edam-operations: - Phylogenetic analysis + edam-outputs: + - formats: [] + term: Phylogenetic data edam-topics: - Phylogenetics galaxy: '' @@ -18470,7 +20312,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Filter sequences by ID: from a tabular file' @@ -18491,7 +20335,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Select sequences by ID: from a tabular file' @@ -18521,11 +20367,21 @@ in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. + edam-inputs: + - formats: + - FASTA + - FASTQ + term: FASTQ edam-operations: - DNA transcription - Sequence trimming - DNA translation - Sequence conversion + edam-outputs: + - formats: + - FASTA + - FASTQ + term: FASTQ edam-topics: - Database management - Sequence analysis @@ -18557,7 +20413,9 @@ bunya: - 1.2.0-gcc-10.3.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -18578,9 +20436,11 @@ - 1.3-gcc-11.3.0 (D) description: A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. + edam-inputs: [] edam-operations: - Data handling - Sequence file editing + edam-outputs: [] edam-topics: - Data management galaxy: @@ -18653,7 +20513,9 @@ single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: - RNA-Seq - Transcriptomics @@ -18674,33 +20536,20 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' - galaxy: - - description: 'SFF converter: ' - title: SFF converter 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=Sff_extractor - homepage: '' - id: Sff_extractor - license: '' - name: Sff_extractor - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: shasta biotools: shasta bunya: '' description: De novo assembly from Oxford Nanopore reads. + edam-inputs: + - formats: + - FASTQ + term: FASTQ edam-operations: - Genome assembly + edam-outputs: + - formats: + - FASTQ + term: FASTQ edam-topics: - Genomics - Sequence assembly @@ -18732,8 +20581,16 @@ Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. + edam-inputs: + - formats: + - FASTQ + term: FASTQ edam-operations: - Genome assembly + edam-outputs: + - formats: + - FASTA + term: FASTA edam-topics: - Genomics - Microbiology @@ -18758,8 +20615,10 @@ bunya: '' description: A clustering approach for identification of enriched domains from histone modification ChIP-seq data. + edam-inputs: [] edam-operations: - Sequence contamination filtering + edam-outputs: [] edam-topics: - ChIP-seq - Epigenomics @@ -18797,11 +20656,13 @@ For all PMIDs in each row of a table the according abstracts are saved in additional columns.' + edam-inputs: [] edam-operations: - Text mining - Database search - Text annotation - Clustering + edam-outputs: [] edam-topics: - Natural language processing - Workflows @@ -18832,7 +20693,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -18853,10 +20716,12 @@ description: The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching. + edam-inputs: [] edam-operations: - Genome assembly - Visualisation - Multilocus sequence typing + edam-outputs: [] edam-topics: - Whole genome sequencing - Immunoproteins and antigens @@ -18886,7 +20751,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -18905,7 +20772,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -18939,7 +20808,9 @@ the data storage footprint while still permitting efficient parallel access. Detailed benchmarking experiments have shown that SLOW5 format is an order of magnitude faster and significantly smaller than FAST5.' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://github.com/hasindu2008/slow5tools @@ -18962,7 +20833,9 @@ bunya: - 20160702-gcccore-10.3.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -18990,10 +20863,12 @@ etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568' + edam-inputs: [] edam-operations: - Sequence trimming - Genotyping - k-mer counting + edam-outputs: [] edam-topics: - Sequence assembly - Genetic variation @@ -19025,8 +20900,10 @@ workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style. + edam-inputs: [] edam-operations: - Service composition + edam-outputs: [] edam-topics: - Bioinformatics - Workflows @@ -19051,8 +20928,10 @@ bunya: - '2013_11_29' description: The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. + edam-inputs: [] edam-operations: - Gene prediction + edam-outputs: [] edam-topics: - DNA - DNA polymorphism @@ -19091,10 +20970,12 @@ \ works please visit the documentation page. SNAPPy was design for Linux based\ \ operative systems | Welcome to snappy\u2019s documentation! \u2014 SNAPPy-HIV1-Subtyping\ \ 1.0.0 documentation | Free document hosting provided by Read the Docs" + edam-inputs: [] edam-operations: - Sequence trimming - Parsing - Genotyping + edam-outputs: [] edam-topics: - Phylogenetics - Workflows @@ -19119,9 +21000,17 @@ bunya: '' description: An algorithm for structural variation detection from third generation sequencing alignment. + edam-inputs: + - formats: + - BAM + term: BAM edam-operations: - Sequence analysis - Structural variation detection + edam-outputs: + - formats: + - VCF + term: VCF edam-topics: - DNA structural variation - Sequencing @@ -19148,10 +21037,12 @@ biotools: snippy bunya: '' description: Rapid haploid variant calling and core SNP phylogeny generation. + edam-inputs: [] edam-operations: - Phylogenetic tree visualisation - Phylogenetic tree generation - Variant calling + edam-outputs: [] edam-topics: - Genomics - Model organisms @@ -19184,7 +21075,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Finds SNP sites: from a multi-FASTA alignment file' @@ -19205,7 +21098,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'SNP distance matrix: Compute distance in SNPs between all sequences @@ -19228,8 +21123,33 @@ bunya: '' description: Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). + edam-inputs: + - formats: + - TSV + - Textual format + term: Textual format + - formats: + - VCF + term: VCF + - formats: + - BED + term: BED + - formats: + - GFF + - GTF + term: GTF + - formats: + - FASTA + term: FASTA edam-operations: - SNP detection + edam-outputs: + - formats: + - TSV + term: TSV + - formats: + - HTML + term: HTML edam-topics: - DNA polymorphism - Genetic variation @@ -19270,7 +21190,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'snpFreq: significant SNPs in case-control data' @@ -19291,7 +21213,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Variant Frequency Plot: Generates a heatmap of allele frequencies @@ -19313,8 +21237,10 @@ biotools: snpsift bunya: '' description: Toolbox that allows you to filter and manipulate annotated vcf files. + edam-inputs: [] edam-operations: - Variant filtering + edam-outputs: [] edam-topics: - Data management - Data architecture, analysis and design @@ -19362,11 +21288,13 @@ biotools: soapdenovo2 bunya: '' description: SOAPdenovo2 is a next generation sequencing reads de novo assembler. + edam-inputs: [] edam-operations: - Scaffolding - De-novo assembly - Genome assembly - Sorting + edam-outputs: [] edam-topics: - Sequence assembly - Sequencing @@ -19392,10 +21320,12 @@ bunya: - 4.3.6--h9ee0642_0 description: Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. + edam-inputs: [] edam-operations: - Sequence similarity search - Sequence comparison - Sequence alignment analysis + edam-outputs: [] edam-topics: - Metatranscriptomics - Metagenomics @@ -19422,7 +21352,9 @@ bunya: - 2.0.1-gcc-11.3.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://www.10xgenomics.com/support/software/space-ranger/latest @@ -19446,8 +21378,28 @@ \ or IonTorrent reads and is capable of providing hybrid assemblies using PacBio,\ \ Oxford Nanopore and Sanger reads. Additional contigs can be provided and can\ \ be used as long reads." + edam-inputs: + - formats: + - FASTQ + term: FASTQ + - formats: + - FASTA + term: FASTA edam-operations: - Genome assembly + edam-outputs: + - formats: + - TSV + term: TSV + - formats: + - FASTA + term: FASTA + - formats: + - TSV + term: TSV + - formats: + - Textual format + term: Textual format edam-topics: - Sequence assembly galaxy: @@ -19501,7 +21453,9 @@ bunya: - 1.0.1-gcccore-11.3.0 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -19520,8 +21474,10 @@ bunya: '' description: Spectral Repeat Finder (SRF) is a program to find repeats through an analysis of the power spectrum of a given DNA sequence. + edam-inputs: [] edam-operations: - Analysis + edam-outputs: [] edam-topics: - Computational biology galaxy: '' @@ -19544,7 +21500,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://www.sqlite.org/index.html @@ -19566,8 +21524,10 @@ - 3.0.3--h87f3376_0 description: The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. + edam-inputs: [] edam-operations: - Data handling + edam-outputs: [] edam-topics: - DNA - Genomics @@ -19601,7 +21561,9 @@ bunya: - 0.2.0--py_4 description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://github.com/katholt/srst2 @@ -19621,9 +21583,11 @@ - 1.1-gcccore-10.3.0 description: A fast implementation of the Smith-Waterman algorithm whose API that can be flexibly used by programs written in C, C++ and other languages. + edam-inputs: [] edam-operations: - Data handling - Sequence alignment + edam-outputs: [] edam-topics: - Sample collections - Genomics @@ -19649,8 +21613,10 @@ description: Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. + edam-inputs: [] edam-operations: - Data handling + edam-outputs: [] edam-topics: - Mapping - Population genetics @@ -19759,8 +21725,19 @@ - 2.7.10b-gcc-11.3.0 (D) - 2.7.10a--h9ee0642_0 description: Ultrafast universal RNA-seq data aligner + edam-inputs: + - formats: + - FASTQ + term: FASTQ edam-operations: - Sequence alignment + edam-outputs: + - formats: + - BAM + - SAM + term: SAM + - formats: [] + term: Gene expression matrix edam-topics: - RNA-Seq - Transcriptomics @@ -19796,8 +21773,10 @@ a summary report of detected antimicrobial resistance genes. The star|* in staramr indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases. + edam-inputs: [] edam-operations: - Antimicrobial resistance prediction + edam-outputs: [] edam-topics: - Microbiology - Public health and epidemiology @@ -19823,8 +21802,10 @@ bunya: '' description: STAR-Fusion, a method that is both fast and accurate in identifying fusion transcripts from RNA-Seq data + edam-inputs: [] edam-operations: - Sequence analysis + edam-outputs: [] edam-topics: - Gene structure - RNA-Seq @@ -19851,9 +21832,11 @@ transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. + edam-inputs: [] edam-operations: - Transcriptome assembly - RNA-Seq analysis + edam-outputs: [] edam-topics: - Transcriptomics - RNA-seq @@ -19887,8 +21870,10 @@ determines if a read should be globally or locally aligned, therefore particularly powerful in mapping RNA-seq reads. It supports indel detection and can map reads with both fixed and variable lengths. + edam-inputs: [] edam-operations: - Read mapping + edam-outputs: [] edam-topics: - Sequencing - Mapping @@ -19917,8 +21902,10 @@ bunya: '' description: An agile homology-based approach using a reduced SEED database to report the subsystems present in metagenomic samples and profile their abundances. + edam-inputs: [] edam-operations: - Sequence feature detection + edam-outputs: [] edam-topics: - DNA - Metagenomics @@ -19946,8 +21933,10 @@ description: This tool generates Alternative Splicing (AS) events from an annotation and calculates the PSI ("Percentage Spliced In") value for each event exploiting fast quantification of transcript abundances from multiple samples. + edam-inputs: [] edam-operations: - Splicing model analysis + edam-outputs: [] edam-topics: - Transcriptomics - RNA splicing @@ -19980,10 +21969,12 @@ from minimap2) and detects five different variant classes between the query assembly and the reference: deletions, insertions, tandem and interspersed duplications and inversions.' + edam-inputs: [] edam-operations: - Genome assembly - Variant calling - Genotyping + edam-outputs: [] edam-topics: - Sequence assembly - Genotype and phenotype @@ -20021,12 +22012,14 @@ in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.' + edam-inputs: [] edam-operations: - Haplotype mapping - Variant calling - Genotyping - Sequence assembly - Read mapping + edam-outputs: [] edam-topics: - DNA polymorphism - Sequence assembly @@ -20054,10 +22047,12 @@ bunya: '' description: Targetfinder.org provides a web based resource that allows users to find genes that have a similar expression to a query gene signature. + edam-inputs: [] edam-operations: - Gene prediction - Gene expression profiling - Gene expression analysis + edam-outputs: [] edam-topics: - Gene expression - Transcription factors and regulatory sites @@ -20086,7 +22081,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'TB Variant Filter: M. tuberculosis H37Rv VCF filter' @@ -20112,8 +22109,19 @@ records for submission to GenBank. It uses many of the same functions as Genome Workbench but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank. + edam-inputs: + - formats: + - FASTA + term: FASTA + - formats: + - Binary format + term: Binary format edam-operations: - Deposition + edam-outputs: + - formats: + - Binary format + term: Binary format edam-topics: - Data submission, annotation and curation galaxy: '' @@ -20128,47 +22136,67 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: tb-profiler + biotools: tb-profiler bunya: '' - description: '' - edam-operations: '' + description: A tool for drug resistance prediction from _M. tuberculosis_ genomic + data (sequencing reads, alignments or variants). + edam-inputs: + - formats: + - FASTQ-like format (text) + term: FASTQ-like format (text) + edam-operations: + - Antimicrobial resistance prediction + edam-outputs: [] edam-topics: '' galaxy: - description: 'TB-Profiler Profile: Infer strain types and drug resistance markers from sequences' title: TB-Profiler Profile 6.2.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbprofiler%2Ftb_profiler_profile%2F6.2.1%2Bgalaxy0 - homepage: '' + homepage: https://github.com/jodyphelan/TBProfiler id: tbprofiler - license: '' + license: GPL-3.0 name: tbprofiler nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: Rapid determination of anti-tuberculosis drug resistance from whole-genome + sequences + url: https://doi.org/10.1186/s13073-015-0164-0 resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: combat-tb_workbench + biotools: combat-tb_workbench bunya: '' - description: '' + description: The COMBAT-TB Workbench is an IRIDA based, module workbench for M. + tuberculosis bioinformatics. It is designed to be easily deployed on a single + server. + edam-inputs: '' edam-operations: '' - edam-topics: '' + edam-outputs: '' + edam-topics: + - Whole genome sequencing + - Microbiology + - Workflows + - Phylogeny galaxy: - description: 'TB Variant Report: - generate HTML report from SnpEff annotated M.tb VCF(s)' title: TB Variant Report 1.0.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbvcfreport%2Ftbvcfreport%2F1.0.1%2Bgalaxy0 - homepage: '' + homepage: https://github.com/COMBAT-TB/irida-galaxy-deploy id: tbvcfreport - license: '' + license: Apache-2.0 name: tbvcfreport nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: 10.1101/2021.09.23.21263983 + url: https://doi.org/10.1101/2021.09.23.21263983 resources: - title: .nan url: .nan @@ -20189,8 +22217,10 @@ a comprehensive, flexible ecosystem of tools, libraries and community resources that lets researchers push the state-of-the-art in ML and developers easily build and deploy ML powered applications' + edam-inputs: [] edam-operations: - Standardisation and normalisation + edam-outputs: [] edam-topics: - Machine learning - Pathology @@ -20226,8 +22256,10 @@ Note: do not move or hard link TEsorter.py alone to anywhere else, as it rely on database/ and bin/. You can add the directory to PATH or soft link TEsorter.py to PATH' + edam-inputs: [] edam-operations: - Phylogenetic tree reconstruction + edam-outputs: [] edam-topics: - Protein folds and structural domains - Phylogenetics @@ -20253,7 +22285,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'TEtranscripts: annotates reads to genes and transposable elements' @@ -20274,7 +22308,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Join: two files' @@ -20350,10 +22386,19 @@ bunya: '' description: Open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML + edam-inputs: + - formats: + - Thermo RAW + term: Thermo RAW edam-operations: - Conversion - Filtering - Peak detection + edam-outputs: + - formats: + - MGF + - mzML + term: mzML edam-topics: - Proteomics - Proteomics experiment @@ -20379,7 +22424,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'TMT Analyst: Analyze and Visualize Label-Free Proteomics output @@ -20403,9 +22450,26 @@ description: Program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. A stable SAMtools version is now packaged with the program. + edam-inputs: + - formats: [] + term: Genome identifier + - formats: + - FASTQ + - FASTA + term: FASTA edam-operations: - Splice site prediction - Read mapping + edam-outputs: + - formats: + - SAM + term: SAM + - formats: + - BED + term: BED + - formats: + - BED + term: BED edam-topics: - RNA-Seq - Mapping @@ -20437,7 +22501,9 @@ biotools: totalview bunya: '' description: TotalView is a debugger for High Performance Computing applications. + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: - Computer science galaxy: '' @@ -20462,10 +22528,12 @@ sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. + edam-inputs: [] edam-operations: - Coding region prediction - de Novo sequencing - De-novo assembly + edam-outputs: [] edam-topics: - Genomics - Gene transcripts @@ -20494,8 +22562,10 @@ description: A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. + edam-inputs: [] edam-operations: - Transposon prediction + edam-outputs: [] edam-topics: - DNA - Sequencing @@ -20533,7 +22603,9 @@ biotools: TPP_SPC bunya: '' description: Institute for Systems Biology "Trans-Proteomic Pipeline" + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: - Proteomics - Proteomics experiment @@ -20582,7 +22654,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -20601,7 +22675,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: '' @@ -20626,8 +22702,10 @@ There are no restrictions on the size of the repeats that can be detected. It determines a consensus pattern for the smallest repetitive unit in the tandem repeat. + edam-inputs: [] edam-operations: - Repeat sequence detection + edam-outputs: [] edam-topics: - Sequence analysis - Sequence composition, complexity and repeats @@ -20651,8 +22729,21 @@ bunya: '' description: Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. + edam-inputs: + - formats: [] + term: Sequence alignment edam-operations: - Multiple sequence alignment + edam-outputs: + - formats: + - ClustalW format + - PHYLIP format + - phylipnon + - FASTA + term: FASTA + - formats: + - Textual format + term: Textual format edam-topics: - Sequence analysis - Sequencing @@ -20679,10 +22770,18 @@ description: A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. + edam-inputs: + - formats: + - BAM + term: BAM edam-operations: - Sequence trimming - Primer removal - Read pre-processing + edam-outputs: + - formats: + - BAM + term: BAM edam-topics: - Sequence analysis galaxy: @@ -20705,8 +22804,26 @@ bunya: - 0.39-java-11 description: A flexible read trimming tool for Illumina NGS data + edam-inputs: + - formats: + - Binary format + - FASTQ-solexa + - FASTQ-illumina + - FASTQ-sanger + - FASTQ + term: FASTQ + - formats: + - FASTA + term: FASTA edam-operations: - Sequence trimming + edam-outputs: + - formats: + - TSV + term: TSV + - formats: + - FASTQ + term: FASTQ edam-topics: - Sequencing - Sequence analysis @@ -20739,8 +22856,10 @@ description: Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. + edam-inputs: [] edam-operations: - Transcriptome assembly + edam-outputs: [] edam-topics: - Transcriptomics - Gene expression @@ -20817,8 +22936,10 @@ description: Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. + edam-inputs: [] edam-operations: - Gene functional annotation + edam-outputs: [] edam-topics: - Gene expression - Transcriptomics @@ -20844,9 +22965,11 @@ biotools: trnascan-se bunya: '' description: A program for improved detection of transfer RNA genes in genomic sequence. + edam-inputs: [] edam-operations: - tRNA gene prediction - Sequence feature detection + edam-outputs: [] edam-topics: - RNA - Genomics @@ -20875,11 +22998,13 @@ biotools: trycycler bunya: '' description: 'Trycycler: consensus long-read assemblies for bacterial genomes' + edam-inputs: [] edam-operations: - Genome assembly - Sequence trimming - Scaffold gap completion - Sequence assembly validation + edam-outputs: [] edam-topics: - Sequence assembly - DNA @@ -20924,7 +23049,9 @@ bunya: '' description: Utilities for handling sequences and assemblies from the UCSC Genome Browser project. + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: - Sequence analysis galaxy: @@ -20962,8 +23089,10 @@ biotools: umi-tools bunya: '' description: Tools for handling Unique Molecular Identifiers in NGS data sets. + edam-inputs: [] edam-operations: - Sequencing quality control + edam-outputs: [] edam-topics: - NGS - Sequence sites, features and motifs @@ -21003,9 +23132,18 @@ bunya: '' description: A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. + edam-inputs: + - formats: + - Raw sequence format + term: Raw sequence format edam-operations: - Genome assembly - Aggregation + edam-outputs: + - formats: + - Graph format + - FASTA + term: FASTA edam-topics: - Microbiology - Genomics @@ -21033,9 +23171,17 @@ biotools: unipept bunya: '' description: Metaproteomics data analysis with a focus on interactive data visualizations. + edam-inputs: + - formats: [] + term: Protein sequence edam-operations: - Prediction and recognition - Visualisation + edam-outputs: + - formats: [] + term: Sequence set + - formats: [] + term: Phylogenetic tree edam-topics: - Proteomics - Proteogenomics @@ -21061,45 +23207,135 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' +- biocontainers: uniprot + biotools: uniprot bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + description: 'The universal protein knowledgebase in 2021. + + + You are using a version of browser that may not display all the features of this + website.' + edam-inputs: [] + edam-operations: + - Text annotation + - Data retrieval + - Database search + - Deposition + edam-outputs: [] + edam-topics: + - Proteomics + - Sequence analysis + - Literature and language + - Model organisms + - Proteomics experiment galaxy: - description: 'UniProt: download proteome as XML or fasta' title: UniProt 2.4.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Funiprotxml_downloader%2Funiprotxml_downloader%2F2.4.0 - homepage: '' + homepage: https://www.uniprot.org/ id: UniProt_Downloader - license: '' + license: CC-BY-4.0 name: UniProt_Downloader nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-operations: '' - edam-topics: '' + publications: + - title: 'UniProt: the universal protein knowledgebase in 2021' + url: https://doi.org/10.1093/NAR/GKAA1100 + - title: Reorganizing the protein space at the Universal Protein Resource (UniProt) + url: https://doi.org/10.1093/nar/gkr981 + - title: The Universal Protein resource (UniProt) 2009 + url: https://doi.org/10.1093/nar/gkn664 + - title: The universal protein resource (UniProt) in 2010 + url: https://doi.org/10.1093/nar/gkp846 + - title: The Universal Protein Resource (UniProt) + url: https://doi.org/10.1093/nar/gki070 + - title: The Universal Protein Resource (UniProt) + url: https://doi.org/10.1093/nar/gkl929 + - title: 'The Universal Protein Resource (UniProt): an expanding universe of protein + information.' + url: https://doi.org/10.1093/nar/gkj161 + - title: The Universal Protein resource (UniProt) + url: https://doi.org/10.1093/nar/gkm895 + - title: 'UniProt Knowledgebase: A hub of integrated protein data' + url: https://doi.org/10.1093/database/bar009 + - title: 'UniProt: A worldwide hub of protein knowledge' + url: https://doi.org/10.1093/nar/gky1049 + - title: 10.1093/nar/gkh131 + url: https://doi.org/10.1093/nar/gkh131 + - title: 'UniProt: The universal protein knowledgebase' + url: https://doi.org/10.1093/nar/gkw1099 + - title: 'Erratum: UniProt: The universal protein knowledgebase (Nucleic Acids Research + (2017) 45 (D158-D169) DOI: 10.1093/nar/gkw1099)' + url: https://doi.org/10.1093/nar/gky092 + - title: Update on activities at the Universal Protein Resource (UniProt) in 2013 + url: https://doi.org/10.1093/nar/gks1068 + resources: + - title: .nan + url: .nan +- biocontainers: uniprot + biotools: uniprot + bunya: '' + description: 'The universal protein knowledgebase in 2021. + + + You are using a version of browser that may not display all the features of this + website.' + edam-inputs: [] + edam-operations: + - Text annotation + - Data retrieval + - Database search + - Deposition + edam-outputs: [] + edam-topics: + - Proteomics + - Sequence analysis + - Literature and language + - Model organisms + - Proteomics experiment galaxy: - description: 'UniProt: ID mapping and retrieval' title: UniProt 0.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Funiprot_rest_interface%2Funiprot%2F0.4 - homepage: '' + homepage: https://www.uniprot.org/ id: uniprot_rest_interface - license: '' + license: CC-BY-4.0 name: uniprot_rest_interface nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: 'UniProt: the universal protein knowledgebase in 2021' + url: https://doi.org/10.1093/NAR/GKAA1100 + - title: Reorganizing the protein space at the Universal Protein Resource (UniProt) + url: https://doi.org/10.1093/nar/gkr981 + - title: The Universal Protein resource (UniProt) 2009 + url: https://doi.org/10.1093/nar/gkn664 + - title: The universal protein resource (UniProt) in 2010 + url: https://doi.org/10.1093/nar/gkp846 + - title: The Universal Protein Resource (UniProt) + url: https://doi.org/10.1093/nar/gki070 + - title: The Universal Protein Resource (UniProt) + url: https://doi.org/10.1093/nar/gkl929 + - title: 'The Universal Protein Resource (UniProt): an expanding universe of protein + information.' + url: https://doi.org/10.1093/nar/gkj161 + - title: The Universal Protein resource (UniProt) + url: https://doi.org/10.1093/nar/gkm895 + - title: 'UniProt Knowledgebase: A hub of integrated protein data' + url: https://doi.org/10.1093/database/bar009 + - title: 'UniProt: A worldwide hub of protein knowledge' + url: https://doi.org/10.1093/nar/gky1049 + - title: 10.1093/nar/gkh131 + url: https://doi.org/10.1093/nar/gkh131 + - title: 'UniProt: The universal protein knowledgebase' + url: https://doi.org/10.1093/nar/gkw1099 + - title: 'Erratum: UniProt: The universal protein knowledgebase (Nucleic Acids Research + (2017) 45 (D158-D169) DOI: 10.1093/nar/gkw1099)' + url: https://doi.org/10.1093/nar/gky092 + - title: Update on activities at the Universal Protein Resource (UniProt) in 2013 + url: https://doi.org/10.1093/nar/gks1068 resources: - title: .nan url: .nan @@ -21110,7 +23346,9 @@ - 6.0-gcccore-11.3.0 - 6.0-gcccore-12.3.0 (D) description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Unzip: Unzip a file' @@ -21135,9 +23373,11 @@ with genome annotation (via GFF). This includes vertebrates and also plants, fungi, protists, metazoa and bacteria. There is a web and a REST API version but the most powerful is the Perl script version. See McLaren et al., 2016, Genome Biology + edam-inputs: [] edam-operations: - SNP annotation - Genetic variation analysis + edam-outputs: [] edam-topics: - Genetic variation - Genomics @@ -21160,8 +23400,10 @@ bunya: '' description: VarScan, an open source tool for variant detection that is compatible with several short read align-ers. + edam-inputs: [] edam-operations: - Variant calling + edam-outputs: [] edam-topics: - Sequencing - DNA polymorphism @@ -21202,8 +23444,10 @@ bunya: - 1.0.3-foss-2021a-r-4.1.0 description: API and command line utilities for the manipulation of VCF files. + edam-inputs: [] edam-operations: - Data handling + edam-outputs: [] edam-topics: - Genomics - Data management @@ -21308,10 +23552,12 @@ - 0.1.16-gcc-11.3.0 (D) description: Provide easily accessible methods for working with complex genetic variation data in the form of VCF files. + edam-inputs: [] edam-operations: - Data handling - Variant filtering - Genetic variation analysis + edam-outputs: [] edam-topics: - Genetic variation galaxy: @@ -21341,8 +23587,20 @@ bunya: '' description: A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. + edam-inputs: + - formats: + - BAM + - SAM + - FASTQ + - FASTA + term: FASTA edam-operations: - Formatting + edam-outputs: + - formats: [] + term: Sequence + - formats: [] + term: Resource metadata edam-topics: - Sequence assembly galaxy: @@ -21374,7 +23632,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://github.com/marbl/verkko @@ -21393,7 +23653,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://wci.llnl.gov/simulation/computer-codes/visit/ @@ -21416,9 +23678,17 @@ dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. + edam-inputs: + - formats: [] + term: Nucleic acid sequence edam-operations: - DNA mapping - Chimera detection + edam-outputs: + - formats: [] + term: Sequence similarity score + - formats: [] + term: Sequence alignment edam-topics: - Metagenomics - Sequence analysis @@ -21464,7 +23734,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'Sequence Logo: generator for fasta (eg Clustal alignments)' @@ -21487,8 +23759,10 @@ description: Software for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. It is especially suitable for long reads, but works also well with short reads. + edam-inputs: [] edam-operations: - Genotyping + edam-outputs: [] edam-topics: - DNA polymorphism - Sequence assembly @@ -21515,9 +23789,11 @@ bunya: '' description: windowmasker identifies and masks highly repetitive DNA sequences in a genome, using only the sequence of the genome itself. + edam-inputs: [] edam-operations: - Repeat sequence detection - Repeat sequence analysis + edam-outputs: [] edam-topics: - Sequencing galaxy: @@ -21546,8 +23822,10 @@ and PacBio reads to repetitive reference sequences. Winnowmap development began on top of minimap2 codebase, and since then we have incorporated the following two ideas to improve mapping accuracy within repeats + edam-inputs: [] edam-operations: - Sequence alignment + edam-outputs: [] edam-topics: - Mapping galaxy: '' @@ -21573,6 +23851,15 @@ description: First fully open-source and collaborative online platform for computational metabolomics. It includes preprocessing, normalization, quality control, statistical analysis of LC/MS, FIA-MS, GC/MS and NMR data. + edam-inputs: + - formats: [] + term: NMR spectrum + - formats: + - netCDF + - mzXML + - mzData + - mzML + term: mzML edam-operations: - Visualisation - Statistical calculation @@ -21581,6 +23868,7 @@ - Annotation - Mass spectrum visualisation - Enrichment analysis + edam-outputs: [] edam-topics: - Systems biology - Metabolomics @@ -21679,8 +23967,15 @@ is led by Paul Sternberg of CalTech, Paul Kersey of the EBI, Matt Berriman of the Wellcome Trust Sanger Institute, and Lincoln Stein of the Ontario Institute for Cancer Research. + edam-inputs: + - formats: [] + term: Gene symbol edam-operations: - Query and retrieval + edam-outputs: + - formats: + - HTML + term: HTML edam-topics: - Model organisms galaxy: @@ -21704,7 +23999,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: - description: 'NetCDF xarray Metadata Info: summarize content of a Netcdf file' @@ -21732,6 +24029,17 @@ and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling. + edam-inputs: + - formats: + - netCDF + - mzML + - mzXML + term: mzXML + - formats: + - netCDF + - mzML + - mzXML + term: mzXML edam-operations: - Mass spectrum visualisation - Label-free quantification @@ -21740,6 +24048,11 @@ - Chromatographic alignment - Peak detection - Chromatogram visualisation + edam-outputs: + - formats: + - netCDF + - mzQuantML + term: mzQuantML edam-topics: - Biological imaging - Data visualisation @@ -21791,7 +24104,9 @@ biotools: '' bunya: '' description: '' + edam-inputs: '' edam-operations: '' + edam-outputs: '' edam-topics: '' galaxy: '' homepage: https://github.com/AustralianBioCommons/xml4ena @@ -21815,10 +24130,12 @@ Python package for detection of differential RNA modifications from direct RNA sequencing.' + edam-inputs: [] edam-operations: - Quantification - Expression analysis - DMR identification + edam-outputs: [] edam-topics: - RNA-Seq - RNA @@ -21843,12 +24160,30 @@ biotools: xtandem bunya: '' description: Matches tandem mass spectra with peptide sequences. + edam-inputs: + - formats: + - dta + - pkl + - mzXML + - mzData + - MGF + - X!Tandem XML + - mzML + term: mzML + - formats: + - FASTA + term: FASTA edam-operations: - Blind peptide database search - PTM identification - Peptide identification - Peptide database search - Protein identification + edam-outputs: + - formats: + - X!Tandem XML + - mzIdentML + term: mzIdentML edam-topics: - Proteomics - Proteomics experiment @@ -21878,10 +24213,12 @@ description: YaHS is scaffolding tool using Hi-C data. It relies on a new algorithm for contig joining detection which considers the topological distribution of Hi-C signals aiming to distinguish real interaction signals from mapping noises. + edam-inputs: [] edam-operations: - Scaffolding - Genome assembly - De-novo assembly + edam-outputs: [] edam-topics: - Sequence assembly - DNA binding sites @@ -21908,11 +24245,23 @@ bunya: '' description: Search and retrieve S. cerevisiae data, populated by SGD and powered by InterMine + edam-inputs: + - formats: [] + term: Sequence features + - formats: [] + term: Ontology data edam-operations: - Data retrieval - Visualisation - Gene-set enrichment analysis - Query and retrieval + edam-outputs: + - formats: [] + term: Over-representation data + - formats: [] + term: Query script + - formats: [] + term: Sequence features edam-topics: - Data management - Genomics @@ -21942,11 +24291,23 @@ \ integrates biological data sets from multiple sources.\r\nIt currently includes\ \ updates of data from ZFIN, the zebrafish model organism database. There is also\ \ data from the Panther database." + edam-inputs: + - formats: [] + term: Sequence features + - formats: [] + term: Ontology data edam-operations: - Data retrieval - Visualisation - Gene-set enrichment analysis - Query and retrieval + edam-outputs: + - formats: [] + term: Over-representation data + - formats: [] + term: Query script + - formats: [] + term: Sequence features edam-topics: - Data management - Genomics From 90dbe855340c7626f138d2df7eaa9ac5a6017daf Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 25 Jun 2024 22:57:19 +0000 Subject: [PATCH 3/5] Updated the data.yml sourced from australianbiocommons.github.io --- _data/data.yaml | 360 ++++++++++++++++++++++++++++++------------------ 1 file changed, 224 insertions(+), 136 deletions(-) diff --git a/_data/data.yaml b/_data/data.yaml index cbf538b..5dbac09 100644 --- a/_data/data.yaml +++ b/_data/data.yaml @@ -7155,190 +7155,190 @@ - description: 'LAV to BED: Converts a LAV formatted file to BED format' title: LAV to BED 1.0.0 url: https://usegalaxy.org.au/root?tool_id=lav_to_bed1 - - description: 'Convert FASTA to Tabular: ' - title: Convert FASTA to Tabular 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular - - description: 'Convert XTC, DCD, and TRR: ' - title: Convert XTC, DCD, and TRR 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert - - description: 'Convert uncompressed file to compressed: ' - title: Convert uncompressed file to compressed 1.16+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz - - description: 'Convert BED to Feature Location Index: ' - title: Convert BED to Feature Location Index 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0 - - description: 'Convert Genomic Intervals To Strict BED6: ' - title: Convert Genomic Intervals To Strict BED6 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 - - description: 'Convert FASTA to len file: ' - title: Convert FASTA to len file 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len + - description: 'Convert BAM to coordinate-sorted BAM: ' + title: Convert BAM to coordinate-sorted BAM 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam + - description: 'Convert CML to SMILES: ' + title: Convert CML to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles - description: 'OpenBabel converter for molecular formats: ' title: OpenBabel converter for molecular formats 2.4.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules - - description: 'Convert FASTA to Bowtie color space Index: ' - title: Convert FASTA to Bowtie color space Index 1.2.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index - description: 'Convert compressed file to uncompressed.: ' title: Convert compressed file to uncompressed. 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed - - description: 'Convert BAM to BigWig: ' - title: Convert BAM to BigWig 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0 + - description: 'Convert plink pbed to ld reduced format: ' + title: Convert plink pbed to ld reduced format 0.02 + url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert - description: 'Convert Interval to BGZIP: ' title: Convert Interval to BGZIP 1.0.3 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0 - - description: 'Convert FASTQ files to seek locations: ' - title: Convert FASTQ files to seek locations 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0 - - description: 'Convert BED to GFF: ' - title: Convert BED to GFF 2.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0 - - description: 'Convert tabular to dbnsfp: ' - title: Convert tabular to dbnsfp 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp - - description: 'Convert Wiggle to Interval: ' - title: Convert Wiggle to Interval 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 - - description: 'Convert neostore.zip files to neostore: ' - title: Convert neostore.zip files to neostore 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore - - description: 'Convert GFF to Interval Index: ' - title: Convert GFF to Interval Index 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0 + - description: 'Convert compressed and uncompressed BCF files: ' + title: Convert compressed and uncompressed BCF files 0.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf + - description: 'Convert uncompressed file to compressed: ' + title: Convert uncompressed file to compressed 1.16+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz - description: 'Convert tar to directory: ' title: Convert tar to directory 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory - - description: 'Convert Interval to tabix: ' - title: Convert Interval to tabix 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0 - - description: 'Convert Len file to Linecount: ' - title: Convert Len file to Linecount 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount + - description: 'Convert FASTA to len file: ' + title: Convert FASTA to len file 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len + - description: 'Convert Genomic Intervals To BED: ' + title: Convert Genomic Intervals To BED 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0 + - description: 'Convert FASTQ files to seek locations: ' + title: Convert FASTQ files to seek locations 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0 + - description: 'Convert SMILES to MOL: ' + title: Convert SMILES to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL - description: 'Convert Genomic Intervals To Strict BED12: ' title: Convert Genomic Intervals To Strict BED12 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0 - - description: 'Convert Biom datasets: ' - title: Convert Biom datasets 2.1.5 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom + - description: 'Convert InChI to MOL: ' + title: Convert InChI to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol + - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence + taxonomy file to a 2 column mothur taxonomy_outline format' + title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony - description: 'Convert BAM to queryname-sorted BAM: ' title: Convert BAM to queryname-sorted BAM 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam - - description: 'Convert compressed file to uncompressed.: ' - title: Convert compressed file to uncompressed. 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed + - description: 'Convert BigWig to Wiggle: Convert bigWig to wig' + title: Convert BigWig to Wiggle 377+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=bigwigtowig - description: 'Convert FASTA to Bowtie base space Index: ' title: Convert FASTA to Bowtie base space Index 1.3.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index + - description: 'Convert Interval to tabix: ' + title: Convert Interval to tabix 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0 + - description: 'Convert tabular to CSV: ' + title: Convert tabular to CSV 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv - description: 'Convert FASTA to fai file: ' title: Convert FASTA to fai file 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai + - description: 'Convert XTC, DCD, and TRR: ' + title: Convert XTC, DCD, and TRR 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert + - description: 'Convert Wiggle to Interval: ' + title: Convert Wiggle to Interval 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 + - description: 'Convert compressed file to uncompressed.: ' + title: Convert compressed file to uncompressed. 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed + - description: 'Convert GFF to Interval Index: ' + title: Convert GFF to Interval Index 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0 + - description: 'Convert BGZ VCF to tabix: ' + title: Convert BGZ VCF to tabix 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 + - description: 'Convert plink pbed to linkage lped: ' + title: Convert plink pbed to linkage lped 0.02 + url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert + - description: 'Convert neostore.zip files to neostore: ' + title: Convert neostore.zip files to neostore 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore - description: 'Convert BED, GFF, or VCF to BigWig: ' title: Convert BED, GFF, or VCF to BigWig 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0 - - description: 'Convert tabular to CSV: ' - title: Convert tabular to CSV 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv - - description: 'Convert compressed and uncompressed BCF files: ' - title: Convert compressed and uncompressed BCF files 0.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf + - description: 'Convert FASTA to Bowtie color space Index: ' + title: Convert FASTA to Bowtie color space Index 1.2.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index - description: 'Convert MAF to Fasta: ' title: Convert MAF to Fasta 1.0.2 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_fasta_0 - - description: 'Convert BGZ VCF to tabix: ' - title: Convert BGZ VCF to tabix 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 - - description: 'Convert PDB to GRO: ' - title: Convert PDB to GRO 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0 - - description: 'Convert SMILES to MOL: ' - title: Convert SMILES to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL - - description: 'Convert BAM to coordinate-sorted BAM: ' - title: Convert BAM to coordinate-sorted BAM 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam - - description: 'Convert FASTA to 2bit: ' - title: Convert FASTA to 2bit 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit - - description: 'Convert Parquet to csv: ' - title: Convert Parquet to csv 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv - - description: 'Convert BedGraph to BigWig: ' - title: Convert BedGraph to BigWig 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig + - description: 'Convert BAM to BigWig: ' + title: Convert BAM to BigWig 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0 + - description: 'Convert SAM to BigWig: ' + title: Convert SAM to BigWig 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 + - description: 'Convert Genomic Intervals To Strict BED6: ' + title: Convert Genomic Intervals To Strict BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 + - description: 'Convert GFF to BED: ' + title: Convert GFF to BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0 + - description: 'Convert CRAM to BAM: ' + title: Convert CRAM to BAM 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 - description: 'Convert GFF to Feature Location Index: ' title: Convert GFF to Feature Location Index 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0 - - description: 'Convert lped to plink pbed: ' - title: Convert lped to plink pbed 0.02 - url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert + - description: 'SMILES to SMILES: ' + title: SMILES to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles + - description: 'Convert FASTA to 2bit: ' + title: Convert FASTA to 2bit 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit + - description: 'Convert BED to Feature Location Index: ' + title: Convert BED to Feature Location Index 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0 + - description: 'Convert Genomic Intervals To Strict BED: ' + title: Convert Genomic Intervals To Strict BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 - description: 'Convert CSV to tabular: ' title: Convert CSV to tabular 1.0.0 url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular + - description: 'Convert Parquet to csv: ' + title: Convert Parquet to csv 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv + - description: 'Convert PDB to GRO: ' + title: Convert PDB to GRO 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0 - description: 'Convert Bam to Bai: ' title: Convert Bam to Bai 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0 - - description: 'Convert MAF to Genomic Intervals: ' - title: Convert MAF to Genomic Intervals 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0 - - description: 'Convert Genomic Intervals To BED: ' - title: Convert Genomic Intervals To BED 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0 - - description: 'Convert MOL2 to MOL: ' - title: Convert MOL2 to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol - - description: 'Convert SAM to BAM without sorting: ' - title: Convert SAM to BAM without sorting 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam - - description: 'Convert BigWig to Wiggle: Convert bigWig to wig' - title: Convert BigWig to Wiggle 377+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=bigwigtowig - - description: 'Convert plink pbed to linkage lped: ' - title: Convert plink pbed to linkage lped 0.02 - url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert - - description: 'Convert GRO to PDB: ' - title: Convert GRO to PDB 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0 + - description: 'Convert Biom datasets: ' + title: Convert Biom datasets 2.1.5 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom + - description: 'Convert tabular to dbnsfp: ' + title: Convert tabular to dbnsfp 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp + - description: 'Convert BED to GFF: ' + title: Convert BED to GFF 2.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0 + - description: 'Convert BedGraph to BigWig: ' + title: Convert BedGraph to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig - description: 'Convert Genomic Intervals To Coverage: ' title: Convert Genomic Intervals To Coverage 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0 - - description: 'Convert CML to SMILES: ' - title: Convert CML to SMILES 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles - - description: 'Convert Genomic Intervals To Strict BED: ' - title: Convert Genomic Intervals To Strict BED 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 - - description: 'Convert SAM to BigWig: ' - title: Convert SAM to BigWig 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 - description: 'Convert lped to fped: ' title: Convert lped to fped 0.02 url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert - - description: 'Convert plink pbed to ld reduced format: ' - title: Convert plink pbed to ld reduced format 0.02 - url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert - - description: 'Convert InChI to MOL: ' - title: Convert InChI to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol - - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence - taxonomy file to a 2 column mothur taxonomy_outline format' - title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony - - description: 'Convert Wiggle to BigWig: ' - title: Convert Wiggle to BigWig 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig - - description: 'SMILES to SMILES: ' - title: SMILES to SMILES 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles + - description: 'Convert SAM to BAM without sorting: ' + title: Convert SAM to BAM without sorting 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam + - description: 'Convert MAF to Genomic Intervals: ' + title: Convert MAF to Genomic Intervals 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0 + - description: 'Convert MOL2 to MOL: ' + title: Convert MOL2 to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol - description: 'Convert Picard Interval List to BED6: converter' title: Convert Picard Interval List to BED6 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 - - description: 'Convert GFF to BED: ' - title: Convert GFF to BED 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0 - - description: 'Convert CRAM to BAM: ' - title: Convert CRAM to BAM 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 + - description: 'Convert Wiggle to BigWig: ' + title: Convert Wiggle to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig + - description: 'Convert GRO to PDB: ' + title: Convert GRO to PDB 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0 + - description: 'Convert Len file to Linecount: ' + title: Convert Len file to Linecount 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount + - description: 'Convert FASTA to Tabular: ' + title: Convert FASTA to Tabular 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular + - description: 'Convert lped to plink pbed: ' + title: Convert lped to plink pbed 0.02 + url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert homepage: '' id: Galaxy CONVERTER license: '' @@ -7551,6 +7551,9 @@ edam-outputs: '' edam-topics: '' galaxy: + - description: 'Intersect: the intervals of two datasets' + title: Intersect 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fintersect%2Fgops_intersect_1%2F1.0.0 - description: 'Gene BED To Exon/Intron/Codon BED: expander' title: Gene BED To Exon/Intron/Codon BED 1.0.0 url: https://usegalaxy.org.au/root?tool_id=gene2exon1 @@ -11974,6 +11977,30 @@ resources: - title: .nan url: .nan +- biocontainers: '' + biotools: '' + bunya: '' + description: '' + edam-inputs: '' + edam-operations: '' + edam-outputs: '' + edam-topics: '' + galaxy: + - description: 'Manipulate Expression Set Object: Manipulate ExpressionSet objects + by a variety of attributes' + title: Manipulate Expression Set Object 0.1.1+galaxy4 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fmusic_manipulate_eset%2Fmusic_manipulate_eset%2F0.1.1%2Bgalaxy4 + homepage: '' + id: music_manipulate_eset + license: '' + name: Manipulate Expression Set Object + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: '' + resources: + - title: .nan + url: .nan - biocontainers: mash biotools: mash bunya: @@ -14597,6 +14624,63 @@ resources: - title: .nan url: .nan +- biocontainers: popmusic + biotools: popmusic + bunya: '' + description: "MuSiC is a suite of programs that evaluate the biophysical effects\ + \ of amino acid mutations in proteins. They request the experimental or modeled\ + \ 3-dimensional protein structure as input, and predict the impact of specific\ + \ single-site mutations requested by the user or of all possible single-site mutations.\n\ + \nPoPMuSiC and HoTMuSiC predict the changes in thermodynamic and thermal stability,\ + \ respectively, upon mutation. They are helpful for the rational design of modified\ + \ proteins with controlled stability properties. \n\nSNPMuSiC predicts whether\ + \ protein variants are deleterious or benign due to stability issues, thus providing\ + \ a molecular-level interpretation of disease phenotype." + edam-inputs: [] + edam-operations: + - Variant effect prediction + - Design + - Protein property calculation + edam-outputs: [] + edam-topics: + - Protein folding, stability and design + - Genetic variation + - Computational biology + - Bioengineering + - Protein properties + galaxy: + - description: 'MuSiC Compare: estimate and compare cell type proportions in multiple + sets of bulk RNA-seq data' + title: MuSiC Compare 0.1.1+galaxy4 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fmusic_compare%2Fmusic_compare%2F0.1.1%2Bgalaxy4 + homepage: http://dezyme.com/ + id: music_compare + license: '' + name: MuSiC Compare + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: + - title: 'Fast and accurate predictions of protein stability changes upon mutations + using statistical potentials and neural networks: PoPMuSiC-2.0' + url: http://www.ncbi.nlm.nih.gov/pubmed/19654118 + - title: 'PoPMuSiC 2.1: A web server for the estimation of protein stability changes + upon mutation and sequence optimality' + url: http://www.ncbi.nlm.nih.gov/pubmed/21569468 + - title: Quantification of biases in predictions of protein stability changes upon + mutations + url: http://www.ncbi.nlm.nih.gov/pubmed/29718106 + - title: 'Predicting protein thermal stability changes upon point mutations using + statistical potentials: Introducing HoTMuSiC' + url: http://www.ncbi.nlm.nih.gov/pubmed/26988870 + - title: Protein Thermal Stability Engineering Using HoTMuSiC + url: http://www.ncbi.nlm.nih.gov/pubmed/32006278 + - title: Prediction and interpretation of deleterious coding variants in terms of + protein structural stability + url: http://www.ncbi.nlm.nih.gov/pubmed/29540703 + resources: + - title: .nan + url: .nan - biocontainers: '' biotools: '' bunya: '' @@ -21742,6 +21826,10 @@ - RNA-Seq - Transcriptomics galaxy: + - description: 'RNA STARSolo: mapping, demultiplexing and gene quantification for + single cell RNA-seq' + title: RNA STARSolo 2.7.11a+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Frna_starsolo%2Frna_starsolo%2F2.7.11a%2Bgalaxy0 - description: 'RNA STAR: Gapped-read mapper for RNA-seq data' title: RNA STAR 2.7.11a+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Frgrnastar%2Frna_star%2F2.7.11a%2Bgalaxy0 From b523912d8bd32dac6c26fc4afde856f1a84494e3 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 3 Jul 2024 07:13:51 +0000 Subject: [PATCH 4/5] Updated the data.yml sourced from australianbiocommons.github.io --- _data/data.yaml | 734 ++++++++++++++++++++++++++++-------------------- 1 file changed, 427 insertions(+), 307 deletions(-) diff --git a/_data/data.yaml b/_data/data.yaml index 5dbac09..fa2441c 100644 --- a/_data/data.yaml +++ b/_data/data.yaml @@ -115,6 +115,34 @@ resources: - title: .nan url: .nan +- biocontainers: AGAT + biotools: AGAT + bunya: '' + description: 'Another Gff Analysis Toolkit (AGAT) + + Suite of tools to handle gene annotations in any GTF/GFF format.' + edam-inputs: [] + edam-operations: + - Data handling + - Genome annotation + edam-outputs: [] + edam-topics: + - Genomics + galaxy: '' + homepage: https://github.com/NBISweden/AGAT + id: agat + license: GPL-3.0 + name: AGAT + nci-gadi: '' + nci-if89: + - 1.4.0 + pawsey: '' + publications: + - title: 10.5281/zenodo.3552717 + url: https://doi.org/10.5281/zenodo.3552717 + resources: + - title: .nan + url: .nan - biocontainers: amber biotools: amber bunya: '' @@ -2236,6 +2264,36 @@ resources: - title: .nan url: .nan +- biocontainers: bracken + biotools: bracken + bunya: '' + description: Statistical method that computes the abundance of species in DNA sequences + from a metagenomics sample. + edam-inputs: [] + edam-operations: + - Statistical calculation + edam-outputs: [] + edam-topics: + - Metagenomics + - Microbial ecology + galaxy: + - description: 'Bracken: to re-estimate abundance at a taxonomic level from kraken + output' + title: Bracken 2.9+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbracken%2Fest_abundance%2F2.9%2Bgalaxy0 + homepage: https://ccb.jhu.edu/software/bracken/ + id: bracken + license: GPL-3.0 + name: Bracken + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: + - title: 'Bracken: Estimating species abundance in metagenomics data' + url: https://doi.org/10.7717/peerj-cs.104 + resources: + - title: .nan + url: .nan - biocontainers: braker1 biotools: braker1 bunya: @@ -3799,7 +3857,7 @@ homepage: '' id: compose_text_param license: '' - name: compose_text_param + name: Compose text parameter value nci-gadi: '' nci-if89: '' pawsey: '' @@ -3930,7 +3988,7 @@ homepage: https://github.com/NordicESMhub/ctsm/tree/fates_emerald_api id: ctsm_fates license: '' - name: ctsm_fates + name: CTSM/FATES-EMERALD nci-gadi: '' nci-if89: '' pawsey: '' @@ -5843,7 +5901,7 @@ homepage: '' id: ethercalc license: '' - name: ethercalc + name: EtherCalc nci-gadi: '' nci-if89: '' pawsey: '' @@ -6494,6 +6552,35 @@ resources: - title: .nan url: .nan +- biocontainers: feelnc + biotools: feelnc + bunya: '' + description: A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. + edam-inputs: [] + edam-operations: + - Annotation + edam-outputs: [] + edam-topics: + - RNA-seq + - Functional, regulatory and non-coding RNA + galaxy: + - description: 'FEELnc: FlExible Extraction of LncRNA' + title: FEELnc 0.2.1+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeelnc%2Ffeelnc%2F0.2.1%2Bgalaxy0 + homepage: https://github.com/tderrien/FEELnc + id: feelnc + license: GPL-3.0 + name: FEELnc + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: + - title: 'FEELnc: A tool for long non-coding RNA annotation and its application + to the dog transcriptome' + url: https://doi.org/10.1093/nar/gkw1306 + resources: + - title: .nan + url: .nan - biocontainers: '' biotools: '' bunya: @@ -6515,6 +6602,54 @@ resources: - title: .nan url: .nan +- biocontainers: featurecounts + biotools: featurecounts + bunya: '' + description: featureCounts is a very efficient read quantifier. It can be used to + summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such + as genes, exons, promoters, gene bodies and genomic bins. It is included in the + Bioconductor Rsubread package and also in the SourceForge Subread package. + edam-inputs: + - formats: + - GFF + term: GFF + - formats: + - GTF + term: GTF + - formats: + - BAM + term: BAM + - formats: + - SAM + term: SAM + edam-operations: + - Read summarisation + - RNA-Seq quantification + edam-outputs: + - formats: + - DSV + term: DSV + edam-topics: + - RNA-Seq + galaxy: + - description: 'featureCounts: Measure gene expression in RNA-Seq experiments from + SAM or BAM files' + title: featureCounts 2.0.3+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts%2F2.0.3%2Bgalaxy2 + homepage: http://bioconductor.org/packages/release/bioc/html/Rsubread.html + id: featurecounts + license: GPL-3.0 + name: FeatureCounts + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: + - title: 'FeatureCounts: An efficient general purpose program for assigning sequence + reads to genomic features' + url: http://www.ncbi.nlm.nih.gov/pubmed/24227677 + resources: + - title: .nan + url: .nan - biocontainers: fgenesh biotools: fgenesh bunya: '' @@ -6588,7 +6723,7 @@ homepage: '' id: filter_transcripts_via_tracking license: '' - name: filter_transcripts_via_tracking + name: Filter Combined Transcripts nci-gadi: '' nci-if89: '' pawsey: '' @@ -7155,190 +7290,190 @@ - description: 'LAV to BED: Converts a LAV formatted file to BED format' title: LAV to BED 1.0.0 url: https://usegalaxy.org.au/root?tool_id=lav_to_bed1 - - description: 'Convert BAM to coordinate-sorted BAM: ' - title: Convert BAM to coordinate-sorted BAM 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam - - description: 'Convert CML to SMILES: ' - title: Convert CML to SMILES 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles - - description: 'OpenBabel converter for molecular formats: ' - title: OpenBabel converter for molecular formats 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules - - description: 'Convert compressed file to uncompressed.: ' - title: Convert compressed file to uncompressed. 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed - description: 'Convert plink pbed to ld reduced format: ' title: Convert plink pbed to ld reduced format 0.02 url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert - - description: 'Convert Interval to BGZIP: ' - title: Convert Interval to BGZIP 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0 - - description: 'Convert compressed and uncompressed BCF files: ' - title: Convert compressed and uncompressed BCF files 0.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf - - description: 'Convert uncompressed file to compressed: ' - title: Convert uncompressed file to compressed 1.16+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz - - description: 'Convert tar to directory: ' - title: Convert tar to directory 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory - - description: 'Convert FASTA to len file: ' - title: Convert FASTA to len file 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len - - description: 'Convert Genomic Intervals To BED: ' - title: Convert Genomic Intervals To BED 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0 - - description: 'Convert FASTQ files to seek locations: ' - title: Convert FASTQ files to seek locations 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0 + - description: 'Convert Biom datasets: ' + title: Convert Biom datasets 2.1.5 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom + - description: 'OpenBabel converter for molecular formats: ' + title: OpenBabel converter for molecular formats 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules + - description: 'Convert BedGraph to BigWig: ' + title: Convert BedGraph to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig + - description: 'Convert Interval to tabix: ' + title: Convert Interval to tabix 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0 + - description: 'Convert Genomic Intervals To Strict BED: ' + title: Convert Genomic Intervals To Strict BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 + - description: 'Convert CRAM to BAM: ' + title: Convert CRAM to BAM 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 - description: 'Convert SMILES to MOL: ' title: Convert SMILES to MOL 2.4.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL - - description: 'Convert Genomic Intervals To Strict BED12: ' - title: Convert Genomic Intervals To Strict BED12 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0 - - description: 'Convert InChI to MOL: ' - title: Convert InChI to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol - - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence - taxonomy file to a 2 column mothur taxonomy_outline format' - title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony - - description: 'Convert BAM to queryname-sorted BAM: ' - title: Convert BAM to queryname-sorted BAM 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam - description: 'Convert BigWig to Wiggle: Convert bigWig to wig' title: Convert BigWig to Wiggle 377+galaxy0 url: https://usegalaxy.org.au/root?tool_id=bigwigtowig - description: 'Convert FASTA to Bowtie base space Index: ' title: Convert FASTA to Bowtie base space Index 1.3.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index - - description: 'Convert Interval to tabix: ' - title: Convert Interval to tabix 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0 - - description: 'Convert tabular to CSV: ' - title: Convert tabular to CSV 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv + - description: 'Convert FASTQ files to seek locations: ' + title: Convert FASTQ files to seek locations 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0 - description: 'Convert FASTA to fai file: ' title: Convert FASTA to fai file 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai - - description: 'Convert XTC, DCD, and TRR: ' - title: Convert XTC, DCD, and TRR 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert - - description: 'Convert Wiggle to Interval: ' - title: Convert Wiggle to Interval 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 - - description: 'Convert compressed file to uncompressed.: ' - title: Convert compressed file to uncompressed. 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed + - description: 'Convert Genomic Intervals To Coverage: ' + title: Convert Genomic Intervals To Coverage 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0 + - description: 'Convert PDB to GRO: ' + title: Convert PDB to GRO 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0 + - description: 'Convert BAM to queryname-sorted BAM: ' + title: Convert BAM to queryname-sorted BAM 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam + - description: 'Convert FASTA to Tabular: ' + title: Convert FASTA to Tabular 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular + - description: 'Convert CML to SMILES: ' + title: Convert CML to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles + - description: 'Convert Bam to Bai: ' + title: Convert Bam to Bai 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0 + - description: 'Convert tabular to CSV: ' + title: Convert tabular to CSV 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv + - description: 'Convert lped to plink pbed: ' + title: Convert lped to plink pbed 0.02 + url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert + - description: 'Convert BED to Feature Location Index: ' + title: Convert BED to Feature Location Index 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0 - description: 'Convert GFF to Interval Index: ' title: Convert GFF to Interval Index 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0 - - description: 'Convert BGZ VCF to tabix: ' - title: Convert BGZ VCF to tabix 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 - - description: 'Convert plink pbed to linkage lped: ' - title: Convert plink pbed to linkage lped 0.02 - url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert + - description: 'Convert GFF to Feature Location Index: ' + title: Convert GFF to Feature Location Index 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0 + - description: 'Convert Interval to BGZIP: ' + title: Convert Interval to BGZIP 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0 + - description: 'Convert MOL2 to MOL: ' + title: Convert MOL2 to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol + - description: 'Convert Genomic Intervals To Strict BED12: ' + title: Convert Genomic Intervals To Strict BED12 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0 + - description: 'Convert MAF to Genomic Intervals: ' + title: Convert MAF to Genomic Intervals 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0 + - description: 'Convert BAM to coordinate-sorted BAM: ' + title: Convert BAM to coordinate-sorted BAM 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam + - description: 'Convert InChI to MOL: ' + title: Convert InChI to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol + - description: 'Convert FASTA to len file: ' + title: Convert FASTA to len file 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len + - description: 'Convert SAM to BAM without sorting: ' + title: Convert SAM to BAM without sorting 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam + - description: 'Convert compressed file to uncompressed.: ' + title: Convert compressed file to uncompressed. 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed + - description: 'Convert lped to fped: ' + title: Convert lped to fped 0.02 + url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert - description: 'Convert neostore.zip files to neostore: ' title: Convert neostore.zip files to neostore 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore - description: 'Convert BED, GFF, or VCF to BigWig: ' title: Convert BED, GFF, or VCF to BigWig 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0 - - description: 'Convert FASTA to Bowtie color space Index: ' - title: Convert FASTA to Bowtie color space Index 1.2.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index - - description: 'Convert MAF to Fasta: ' - title: Convert MAF to Fasta 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_fasta_0 + - description: 'Convert uncompressed file to compressed: ' + title: Convert uncompressed file to compressed 1.16+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz + - description: 'Convert GFF to BED: ' + title: Convert GFF to BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0 + - description: 'Convert plink pbed to linkage lped: ' + title: Convert plink pbed to linkage lped 0.02 + url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert + - description: 'Convert XTC, DCD, and TRR: ' + title: Convert XTC, DCD, and TRR 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert - description: 'Convert BAM to BigWig: ' title: Convert BAM to BigWig 1.0.2 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0 - - description: 'Convert SAM to BigWig: ' - title: Convert SAM to BigWig 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 - description: 'Convert Genomic Intervals To Strict BED6: ' title: Convert Genomic Intervals To Strict BED6 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 - - description: 'Convert GFF to BED: ' - title: Convert GFF to BED 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0 - - description: 'Convert CRAM to BAM: ' - title: Convert CRAM to BAM 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 - - description: 'Convert GFF to Feature Location Index: ' - title: Convert GFF to Feature Location Index 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0 - - description: 'SMILES to SMILES: ' - title: SMILES to SMILES 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles - - description: 'Convert FASTA to 2bit: ' - title: Convert FASTA to 2bit 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit - - description: 'Convert BED to Feature Location Index: ' - title: Convert BED to Feature Location Index 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0 - - description: 'Convert Genomic Intervals To Strict BED: ' - title: Convert Genomic Intervals To Strict BED 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 - - description: 'Convert CSV to tabular: ' - title: Convert CSV to tabular 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular - - description: 'Convert Parquet to csv: ' - title: Convert Parquet to csv 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv - - description: 'Convert PDB to GRO: ' - title: Convert PDB to GRO 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0 - - description: 'Convert Bam to Bai: ' - title: Convert Bam to Bai 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0 - - description: 'Convert Biom datasets: ' - title: Convert Biom datasets 2.1.5 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom - - description: 'Convert tabular to dbnsfp: ' - title: Convert tabular to dbnsfp 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp - - description: 'Convert BED to GFF: ' - title: Convert BED to GFF 2.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0 - - description: 'Convert BedGraph to BigWig: ' - title: Convert BedGraph to BigWig 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig - - description: 'Convert Genomic Intervals To Coverage: ' - title: Convert Genomic Intervals To Coverage 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0 - - description: 'Convert lped to fped: ' - title: Convert lped to fped 0.02 - url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert - - description: 'Convert SAM to BAM without sorting: ' - title: Convert SAM to BAM without sorting 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam - - description: 'Convert MAF to Genomic Intervals: ' - title: Convert MAF to Genomic Intervals 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0 - - description: 'Convert MOL2 to MOL: ' - title: Convert MOL2 to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol - - description: 'Convert Picard Interval List to BED6: converter' - title: Convert Picard Interval List to BED6 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 - - description: 'Convert Wiggle to BigWig: ' - title: Convert Wiggle to BigWig 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig + - description: 'Convert BGZ VCF to tabix: ' + title: Convert BGZ VCF to tabix 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 + - description: 'Convert CSV to tabular: ' + title: Convert CSV to tabular 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular + - description: 'Convert Wiggle to Interval: ' + title: Convert Wiggle to Interval 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 + - description: 'Convert Parquet to csv: ' + title: Convert Parquet to csv 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv + - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence + taxonomy file to a 2 column mothur taxonomy_outline format' + title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony + - description: 'Convert FASTA to 2bit: ' + title: Convert FASTA to 2bit 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit + - description: 'Convert tar to directory: ' + title: Convert tar to directory 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory + - description: 'Convert SAM to BigWig: ' + title: Convert SAM to BigWig 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 - description: 'Convert GRO to PDB: ' title: Convert GRO to PDB 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0 + - description: 'Convert compressed file to uncompressed.: ' + title: Convert compressed file to uncompressed. 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed + - description: 'Convert tabular to dbnsfp: ' + title: Convert tabular to dbnsfp 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp - description: 'Convert Len file to Linecount: ' title: Convert Len file to Linecount 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount - - description: 'Convert FASTA to Tabular: ' - title: Convert FASTA to Tabular 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular - - description: 'Convert lped to plink pbed: ' - title: Convert lped to plink pbed 0.02 - url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert + - description: 'Convert Genomic Intervals To BED: ' + title: Convert Genomic Intervals To BED 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0 + - description: 'Convert Wiggle to BigWig: ' + title: Convert Wiggle to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig + - description: 'Convert Picard Interval List to BED6: converter' + title: Convert Picard Interval List to BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 + - description: 'Convert MAF to Fasta: ' + title: Convert MAF to Fasta 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_fasta_0 + - description: 'Convert compressed and uncompressed BCF files: ' + title: Convert compressed and uncompressed BCF files 0.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf + - description: 'Convert FASTA to Bowtie color space Index: ' + title: Convert FASTA to Bowtie color space Index 1.2.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index + - description: 'Convert BED to GFF: ' + title: Convert BED to GFF 2.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0 + - description: 'SMILES to SMILES: ' + title: SMILES to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles homepage: '' id: Galaxy CONVERTER license: '' @@ -7383,6 +7518,13 @@ - description: 'modENCODE worm: server' title: modENCODE worm 1.0.1 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=modENCODEworm + - description: 'metabolicMine: server' + title: metabolicMine 1.0.0 + url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=metabolicmine + - description: 'EBI SCXA Data Retrieval: Retrieves expression matrixes and metadata + from EBI Single Cell Expression Atlas (SCXA)' + title: EBI SCXA Data Retrieval v0.0.2+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fretrieve_scxa%2Fretrieve_scxa%2Fv0.0.2%2Bgalaxy2 homepage: '' id: galaxy_data_sources license: '' @@ -7403,6 +7545,9 @@ edam-outputs: '' edam-topics: '' galaxy: + - description: 'Filter sequences by ID: from a tabular file' + title: Filter sequences by ID 0.2.9 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpeterjc%2Fseq_filter_by_id%2Fseq_filter_by_id%2F0.2.9 - description: 'Filter FASTA: on the headers and/or the sequences' title: Filter FASTA 2.3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxyp%2Ffilter_by_fasta_ids%2Ffilter_by_fasta_ids%2F2.3 @@ -7459,6 +7604,16 @@ - description: 'Histogram: of a numeric column' title: Histogram 1.0.4 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fhistogram%2Fhistogram_rpy%2F1.0.4 + - description: 'Plot confusion matrix, precision, recall and ROC and AUC curves: + of tabular data' + title: Plot confusion matrix, precision, recall and ROC and AUC curves 0.3 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_ml_performance_plots%2Fplotly_ml_performance_plots%2F0.3 + - description: 'Parallel Coordinates Plot: of tabular data' + title: Parallel Coordinates Plot 0.2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_parallel_coordinates_plot%2Fplotly_parallel_coordinates_plot%2F0.2 + - description: 'Plot actual vs predicted curves and residual plots: of tabular data' + title: Plot actual vs predicted curves and residual plots 0.1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_regression_performance_plots%2Fplotly_regression_performance_plots%2F0.1 - description: 'proportional venn: from 2-3 sets' title: proportional venn 0.5 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fidot%2Fprop_venn%2Fprop_venn%2F0.5 @@ -7613,6 +7768,9 @@ edam-outputs: '' edam-topics: '' galaxy: + - description: 'Filter Tabular: ' + title: Filter Tabular 3.3.1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffilter_tabular%2Ffilter_tabular%2F3.3.1 - description: 'Number lines: ' title: Number lines 9.3+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftext_processing%2Fnl%2F9.3%2Bgalaxy1 @@ -7646,9 +7804,6 @@ - description: 'cut_francais: keep or remove selected column' title: cut_francais 1.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fr-lannes%2Fcut_include_exclude%2Fcut_fr%2F1.0 - - description: 'Filter Tabular: ' - title: Filter Tabular 3.3.0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffilter_tabular%2Ffilter_tabular%2F3.3.0 - description: 'Join two files: on column allowing a small difference' title: Join two files 1.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fjoin_files_on_column_fuzzy%2Fjoin_files_on_column_fuzzy%2F1.0.1 @@ -7709,6 +7864,13 @@ - description: 'Secure Hash / Message Digest: on a dataset' title: Secure Hash / Message Digest 0.0.2 url: https://usegalaxy.org.au/root?tool_id=secure_hash_message_digest + - description: 'Add line to file: writes a line of text at the begining or end of + a text file.' + title: Add line to file 0.1.0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fadd_line_to_file%2Fadd_line_to_file%2F0.1.0 + - description: 'Remove columns: by heading' + title: Remove columns 1.0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fcolumn_remove_by_header%2Fcolumn_remove_by_header%2F1.0 - description: 'Pick parameter value: ' title: Pick parameter value 0.2.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpick_value%2Fpick_value%2F0.2.0 @@ -8390,6 +8552,9 @@ - description: 'Get organelle from reads: ' title: Get organelle from reads 1.7.7.1+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgetorganelle%2Fget_organelle_from_reads%2F1.7.7.1%2Bgalaxy0 + - description: 'Get annotated regions from genbank files (getorganelle): ' + title: Get annotated regions from genbank files (getorganelle) 0.1.0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgetorganelle%2Fget_annotated_regions_from_gb%2F0.1.0 homepage: https://github.com/Kinggerm/GetOrganelle id: getorganelle license: GPL-3.0 @@ -10541,26 +10706,26 @@ - Evolutionary biology - Sequencing galaxy: - - description: 'ivar consensus: Call consensus from aligned BAM file' - title: ivar consensus 1.4.2+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_consensus%2Fivar_consensus%2F1.4.2%2Bgalaxy0 + - description: 'ivar variants: Call variants from aligned BAM file' + title: ivar variants 1.4.3+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_variants%2Fivar_variants%2F1.4.3%2Bgalaxy1 - description: 'ivar filtervariants: Filter variants across replicates or multiple samples aligned using the same reference' - title: ivar filtervariants 1.4.2+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_filtervariants%2Fivar_filtervariants%2F1.4.2%2Bgalaxy0 + title: ivar filtervariants 1.4.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_filtervariants%2Fivar_filtervariants%2F1.4.3%2Bgalaxy0 + - description: 'ivar consensus: Call consensus from aligned BAM file' + title: ivar consensus 1.4.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_consensus%2Fivar_consensus%2F1.4.3%2Bgalaxy0 - description: 'ivar getmasked: Detect primer mismatches and get primer indices for the amplicon to be masked' title: ivar getmasked 1.2.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_getmasked%2Fivar_getmasked%2F1.2.2%2Bgalaxy0 - description: 'ivar removereads: Remove reads from trimmed BAM file' - title: ivar removereads 1.4.2+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_removereads%2Fivar_removereads%2F1.4.2%2Bgalaxy0 + title: ivar removereads 1.4.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_removereads%2Fivar_removereads%2F1.4.3%2Bgalaxy0 - description: 'ivar trim: Trim reads in aligned BAM' title: ivar trim 1.4.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_trim%2Fivar_trim%2F1.4.2%2Bgalaxy0 - - description: 'ivar variants: Call variants from aligned BAM file' - title: ivar variants 1.4.2+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_variants%2Fivar_variants%2F1.4.2%2Bgalaxy1 homepage: https://github.com/CGR-UNIMORE/iVar id: ivar license: AGPL-3.0 @@ -12016,65 +12181,25 @@ - Statistics and probability - Sequence analysis - DNA mutation - galaxy: '' - homepage: https://github.com/marbl/mash - id: mash - license: CC-BY-4.0 - name: mash - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: - - title: 10.1186/s13059-016-0997-x - url: https://doi.org/10.1186/s13059-016-0997-x - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-inputs: '' - edam-operations: '' - edam-outputs: '' - edam-topics: '' galaxy: - description: 'mash screen: determines how well query sequences are contained within a pool of sequences' title: mash screen 2.3+galaxy3 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmash%2Fmash_screen%2F2.3%2Bgalaxy3 - homepage: '' - id: mash_screen - license: '' - name: mash_screen - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-inputs: '' - edam-operations: '' - edam-outputs: '' - edam-topics: '' - galaxy: - description: 'mash sketch: Create a reduced representation of a sequence or set of sequences, based on min-hashes' title: mash sketch 2.3+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmash_sketch%2Fmash_sketch%2F2.3%2Bgalaxy0 - homepage: '' - id: mash_sketch - license: '' - name: mash_sketch + homepage: https://github.com/marbl/mash + id: mash + license: CC-BY-4.0 + name: mash nci-gadi: '' nci-if89: '' pawsey: '' - publications: '' + publications: + - title: 10.1186/s13059-016-0997-x + url: https://doi.org/10.1186/s13059-016-0997-x resources: - title: .nan url: .nan @@ -12511,7 +12636,7 @@ homepage: '' id: merge_cols license: '' - name: merge_cols + name: ' Merge Columns' nci-gadi: '' nci-if89: '' pawsey: '' @@ -12645,29 +12770,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-inputs: '' - edam-operations: '' - edam-outputs: '' - edam-topics: '' - galaxy: - - description: 'metabolicMine: server' - title: metabolicMine 1.0.0 - url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=metabolicmine - homepage: '' - id: metabolicmine - license: '' - name: metabolicmine - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: MetaDEGalaxy biotools: MetaDEGalaxy bunya: '' @@ -13286,6 +13388,27 @@ resources: - title: .nan url: .nan +- biocontainers: '' + biotools: '' + bunya: '' + description: '' + edam-inputs: '' + edam-operations: '' + edam-outputs: '' + edam-topics: '' + galaxy: '' + homepage: '' + id: minigraph + license: '' + name: minigraph + nci-gadi: '' + nci-if89: + - '0.20' + pawsey: '' + publications: '' + resources: + - title: .nan + url: .nan - biocontainers: minimap2 biotools: minimap2 bunya: @@ -13391,7 +13514,7 @@ homepage: https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts id: mircounts license: '' - name: mircounts + name: miRcounts nci-gadi: '' nci-if89: '' pawsey: '' @@ -13449,7 +13572,7 @@ homepage: '' id: mitobim license: '' - name: mitobim + name: MITObim nci-gadi: '' nci-if89: '' pawsey: '' @@ -13758,6 +13881,35 @@ resources: - title: .nan url: .nan +- biocontainers: mosdepth + biotools: mosdepth + bunya: '' + description: Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. + edam-inputs: [] + edam-operations: + - Nucleic acid sequence analysis + - Read depth analysis + edam-outputs: [] + edam-topics: + - Statistics and probability + - Data quality management + galaxy: + - description: 'mosdepth: - fast and flexible depth coverage calculation' + title: mosdepth 0.3.8+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmosdepth%2Fmosdepth%2F0.3.8%2Bgalaxy0 + homepage: https://github.com/brentp/mosdepth + id: mosdepth + license: MIT + name: mosdepth + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: + - title: 'Mosdepth: Quick coverage calculation for genomes and exomes' + url: https://doi.org/10.1093/bioinformatics/btx699 + resources: + - title: .nan + url: .nan - biocontainers: mothur biotools: mothur bunya: '' @@ -14971,7 +15123,7 @@ homepage: '' id: natural_product_likeness_scorer license: '' - name: natural_product_likeness_scorer + name: Natural-Product-Likeness Scorer nci-gadi: '' nci-if89: '' pawsey: '' @@ -15539,7 +15691,7 @@ homepage: '' id: nvc license: '' - name: nvc + name: Naive Variant Caller (NVC) nci-gadi: '' nci-if89: '' pawsey: '' @@ -16070,7 +16222,7 @@ homepage: '' id: param_value_from_file license: '' - name: param_value_from_file + name: Parse parameter value nci-gadi: '' nci-if89: '' pawsey: '' @@ -16131,7 +16283,7 @@ homepage: '' id: parse_mito_blast license: '' - name: parse_mito_blast + name: Parse mitochondrial blast nci-gadi: '' nci-if89: '' pawsey: '' @@ -16446,7 +16598,7 @@ homepage: '' id: peptide_genomic_coordinate license: '' - name: peptide_genomic_coordinate + name: ' Peptide Genomic Coordinate' nci-gadi: '' nci-if89: '' pawsey: '' @@ -16978,7 +17130,7 @@ homepage: '' id: pileup_interval license: '' - name: pileup_interval + name: Pileup-to-Interval nci-gadi: '' nci-if89: '' pawsey: '' @@ -17001,7 +17153,7 @@ homepage: '' id: pileup_parser license: '' - name: pileup_parser + name: ' Filter pileup ' nci-gadi: '' nci-if89: '' pawsey: '' @@ -17137,36 +17289,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-inputs: '' - edam-operations: '' - edam-outputs: '' - edam-topics: '' - galaxy: - - description: 'Plot confusion matrix, precision, recall and ROC and AUC curves: - of tabular data' - title: Plot confusion matrix, precision, recall and ROC and AUC curves 0.3 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_ml_performance_plots%2Fplotly_ml_performance_plots%2F0.3 - - description: 'Parallel Coordinates Plot: of tabular data' - title: Parallel Coordinates Plot 0.2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_parallel_coordinates_plot%2Fplotly_parallel_coordinates_plot%2F0.2 - - description: 'Plot actual vs predicted curves and residual plots: of tabular data' - title: Plot actual vs predicted curves and residual plots 0.1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_regression_performance_plots%2Fplotly_regression_performance_plots%2F0.1 - homepage: '' - id: plotly - license: '' - name: plotly - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: pnetcdf biotools: pnetcdf bunya: '' @@ -17207,7 +17329,7 @@ homepage: '' id: poisson2test license: '' - name: poisson2test + name: Poisson two-sample test nci-gadi: '' nci-if89: '' pawsey: '' @@ -17345,7 +17467,7 @@ homepage: '' id: pretext_map license: '' - name: pretext_map + name: PretextMap nci-gadi: '' nci-if89: '' pawsey: '' @@ -19176,7 +19298,7 @@ homepage: '' id: repenrich license: '' - name: repenrich + name: RepEnrich nci-gadi: '' nci-if89: '' pawsey: '' @@ -19671,7 +19793,7 @@ homepage: '' id: salmon_kallisto_mtx_to_10x license: '' - name: salmon_kallisto_mtx_to_10x + name: ' salmonKallistoMtxTo10x' nci-gadi: '' nci-if89: '' pawsey: '' @@ -19732,7 +19854,7 @@ homepage: '' id: sam_bitwise_flag_filter license: '' - name: sam_bitwise_flag_filter + name: Filter SAM nci-gadi: '' nci-if89: '' pawsey: '' @@ -20329,7 +20451,7 @@ homepage: '' id: sdf_to_tab license: '' - name: sdf_to_tab + name: Extract values from an SD-file nci-gadi: '' nci-if89: '' pawsey: '' @@ -20392,29 +20514,6 @@ resources: - title: .nan url: .nan -- biocontainers: '' - biotools: '' - bunya: '' - description: '' - edam-inputs: '' - edam-operations: '' - edam-outputs: '' - edam-topics: '' - galaxy: - - description: 'Filter sequences by ID: from a tabular file' - title: Filter sequences by ID 0.2.9 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fpeterjc%2Fseq_filter_by_id%2Fseq_filter_by_id%2F0.2.9 - homepage: '' - id: seq_filter_by_id - license: '' - name: seq_filter_by_id - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - resources: - - title: .nan - url: .nan - biocontainers: '' biotools: '' bunya: '' @@ -22240,8 +22339,8 @@ galaxy: - description: 'TB-Profiler Profile: Infer strain types and drug resistance markers from sequences' - title: TB-Profiler Profile 6.2.1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbprofiler%2Ftb_profiler_profile%2F6.2.1%2Bgalaxy0 + title: TB-Profiler Profile 6.2.1+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbprofiler%2Ftb_profiler_profile%2F6.2.1%2Bgalaxy1 homepage: https://github.com/jodyphelan/TBProfiler id: tbprofiler license: GPL-3.0 @@ -22812,6 +22911,27 @@ resources: - title: .nan url: .nan +- biocontainers: '' + biotools: '' + bunya: '' + description: '' + edam-inputs: '' + edam-operations: '' + edam-outputs: '' + edam-topics: '' + galaxy: '' + homepage: '' + id: trf-mod + license: '' + name: TRF-mod + nci-gadi: '' + nci-if89: + - 4.10.0 + pawsey: '' + publications: '' + resources: + - title: .nan + url: .nan - biocontainers: trimal biotools: trimal bunya: '' @@ -22837,7 +22957,7 @@ - Sequencing - Sequence sites, features and motifs galaxy: '' - homepage: http://trimal.cgenomics.org + homepage: https://trimal.readthedocs.io id: trimal license: '' name: trimAl From bb0340c44f9c03ecb6ba8e8e528b506d27b6c3d0 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 3 Jul 2024 07:37:23 +0000 Subject: [PATCH 5/5] Updated the data.yml sourced from australianbiocommons.github.io --- _data/data.yaml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/_data/data.yaml b/_data/data.yaml index fa2441c..00bb706 100644 --- a/_data/data.yaml +++ b/_data/data.yaml @@ -9592,13 +9592,16 @@ - ChIP-seq - Epigenetics galaxy: + - description: 'hicFindTADs: identify TAD boundaries by computing the degree of + separation of each Hi-C matrix bin' + title: hicFindTADs 3.7.5+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicfindtads%2Fhicexplorer_hicfindtads%2F3.7.5%2Bgalaxy0 + - description: 'hicBuildMatrix: create a contact matrix' + title: hicBuildMatrix 3.7.5+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicbuildmatrix%2Fhicexplorer_hicbuildmatrix%2F3.7.5%2Bgalaxy0 - description: 'hicPCA: compute the principal components for A / B compartment analysis' title: hicPCA 3.7.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicpca%2Fhicexplorer_hicpca%2F3.7.2%2Bgalaxy0 - - description: 'hicFindTADs: identify TAD boundaries by computing the degree of - separation of each Hi-C matrix bin' - title: hicFindTADs 3.7.2+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicfindtads%2Fhicexplorer_hicfindtads%2F3.7.2%2Bgalaxy0 - description: 'hicPlotMatrix: plot a Hi-C contact matrix heatmap' title: hicPlotMatrix 3.7.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicplotmatrix%2Fhicexplorer_hicplotmatrix%2F3.7.2%2Bgalaxy0 @@ -9606,9 +9609,6 @@ to reduce its resolution' title: hicMergeMatrixBins 3.7.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicmergematrixbins%2Fhicexplorer_hicmergematrixbins%2F3.7.2%2Bgalaxy0 - - description: 'hicBuildMatrix: create a contact matrix' - title: hicBuildMatrix 3.7.2+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicbuildmatrix%2Fhicexplorer_hicbuildmatrix%2F3.7.2%2Bgalaxy0 homepage: https://hicexplorer.usegalaxy.eu id: hicexplorer license: '' @@ -12636,7 +12636,7 @@ homepage: '' id: merge_cols license: '' - name: ' Merge Columns' + name: Merge Columns nci-gadi: '' nci-if89: '' pawsey: '' @@ -16598,7 +16598,7 @@ homepage: '' id: peptide_genomic_coordinate license: '' - name: ' Peptide Genomic Coordinate' + name: Peptide Genomic Coordinate nci-gadi: '' nci-if89: '' pawsey: '' @@ -17153,7 +17153,7 @@ homepage: '' id: pileup_parser license: '' - name: ' Filter pileup ' + name: Filter pileup nci-gadi: '' nci-if89: '' pawsey: '' @@ -19793,7 +19793,7 @@ homepage: '' id: salmon_kallisto_mtx_to_10x license: '' - name: ' salmonKallistoMtxTo10x' + name: salmonKallistoMtxTo10x nci-gadi: '' nci-if89: '' pawsey: ''