asaim.yaml

---
install_repository_dependencies: true
install_resolver_dependencies: true
install_tool_dependencies: false

tools:

    # data_retrieval
  - name: 'suite_ebi_tools'
    owner: 'iuc'
    tool_panel_section_label: 'Get Data'

  - name: 'suite_enasearch'
    owner: 'iuc'
    tool_panel_section_label: 'Get Data'

  - name: 'suite_ncbi_entrez'
    owner: 'iuc'
    tool_panel_section_label: 'Get Data'

  - name: 'sra_tools'
    owner: 'iuc'
    tool_panel_section_label: 'Get Data'
   
    # quality_control
  - name: 'fastqc'
    owner: 'devteam'
    tool_panel_section_label: 'Quality Control'

  - name: 'prinseq'
    owner: 'iuc'
    tool_panel_section_label: 'Quality Control'

  - name: 'trim_galore'
    owner: 'bgruening'
    tool_panel_section_label: 'Quality Control'

  - name: 'trimmomatic'
    owner: 'pjbriggs'
    tool_panel_section_label: 'Quality Control'

  - name: 'multiqc'
    owner: 'iuc'
    tool_panel_section_label: 'Quality Control'

    # clustering
  - name: 'cdhit'
    owner: 'bebatut'
    tool_panel_section_label: 'Multiple Alignments'

  - name: 'format_cd_hit_output'
    owner: 'bebatut'
    tool_panel_section_label: 'Multiple Alignments'

    # sorting
  - name: 'sortmerna'
    owner: 'rnateam'
    tool_panel_section_label: 'Annotation'

  - name: 'data_manager_sortmerna_database_downloader'
    owner: 'rnateam'
    tool_panel_section_label: Data Managers

    # similarity_search
  - name: 'ncbi_blast_plus'
    owner: 'devteam'
    tool_panel_section_label: 'NCBI Blast'

  - name: 'diamond'
    owner: 'bgruening'
    tool_panel_section_label: 'NCBI Blast'

    # mapping
  - name: 'bwa'
    owner: 'devteam'
    tool_panel_section_label: 'Mapping'

  - name: 'bowtie2'
    owner: 'devteam'
    tool_panel_section_label: 'Mapping'

    # alignment
  - name: 'hmmer3'
    owner: 'iuc'
    tool_panel_section_label: 'Annotation'

    # metagenomics_manipulation
  - name: 'vsearch'
    owner: 'iuc'
    tool_panel_section_label: 'Metagenomic analyses'
  - name: 'nonpareil'
    owner: 'iuc'
    tool_panel_section_label: 'Metagenomic analyses'

    # assembly
  - name: 'megahit'
    owner: 'iuc'
    tool_panel_section_label: 'Assembly'

  - name: 'metaspades'
    owner: 'nml'
    tool_panel_section_label: 'Assembly'

  - name: 'quast'
    owner: 'iuc'
    tool_panel_section_label: 'Assembly'

  - name: 'valet'
    owner: 'iuc'
    tool_panel_section_label: 'Metagenomic analyses'

    # amplicon_sequence_processing
  - name: 'suite_mothur'
    owner: 'iuc'
    tool_panel_section_label: 'mothur'

  - name: 'suite_qiime'
    owner: 'iuc'
    tool_panel_section_label: 'Qiime'

  - name: 'data_manager_qiime_database_downloader'
    owner: 'iuc'
    tool_panel_section_label: Data Managers

    # wgs_taxonomic_assignations
  - name: 'suite_metaphlan2'
    owner: 'iuc'
    tool_panel_section_label: 'Metagenomic analyses'

  - name: 'format_metaphlan2_output'
    owner: 'bebatut'
    tool_panel_section_label: 'Metagenomic analyses'

  - name: 'suite_kraken_0_10_5'
    owner: 'devteam'
    tool_panel_section_label: 'Metagenomic analyses'

    # metabolism_assignation
  - name: 'suite_humann2'
    owner: 'iuc'
    tool_panel_section_label: 'Metagenomic analyses'

  - name: 'group_humann2_uniref_abundances_to_go'
    owner: 'bebatut'
    tool_panel_section_label: 'Metagenomic analyses'

  - name: 'compare_humann2_output'
    owner: 'bebatut'
    tool_panel_section_label: 'Metagenomic analyses'

  - name: 'interproscan5'
    owner: 'bgruening'
    tool_panel_section_label: 'Metagenomic analyses'

  - name: 'suite_picrust'
    owner: 'iuc'
    tool_panel_section_label: 'Annotation'

    # combination_taxo_func
  - name: 'combine_metaphlan2_humann2'
    owner: 'bebatut'
    tool_panel_section_label: 'Metagenomic analyses'

    # visualization
  - name: 'export2graphlan'
    owner: 'iuc'
    tool_panel_section_label: 'Graph/Display Data'

  - name: 'suite_graphlan'
    owner: 'iuc'
    tool_panel_section_label: 'Graph/Display Data'

  - name: 'taxonomy_krona_chart'
    owner: 'crs4'
    tool_panel_section_label: 'Graph/Display Data'