diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index 0e044170b..68fb5f6bb 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -5701,3 +5701,57 @@ Update 165 27/09/23 16:06:22 trinity False Installed iuc 8f1c3df4dd49 8f1c3df4dd Update 165 27/09/23 16:07:15 trinity_abundance_estimates_to_matrix False Installed iuc ba3720d7e68b ba3720d7e68b RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_165/install_log.txt Update 165 27/09/23 16:08:03 trinity_align_and_estimate_abundance False Installed iuc 2fb4ee002432 2fb4ee002432 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_165/install_log.txt Update 165 27/09/23 16:08:52 trinity_analyze_diff_expr False Installed iuc 9ff3765e7172 9ff3765e7172 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_165/install_log.txt +Update 166 04/10/23 11:40:36 add_value False Installed devteam 023f0a3760b3 023f0a3760b3 1/1 1/1 Text Manipulation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 11:45:28 alphafold2 False Tests failed galaxy-australia e4a053d67e24 e4a053d67e24 Staging Testing 0/4 Proteomic AI toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 11:54:23 bwa_mem2 False Tests failed iuc bfaa0d22c2e4 bfaa0d22c2e4 Staging Testing 6/7 Mapping toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 11:58:26 cat_bins False Tests failed iuc 31853794ace2 31853794ace2 Staging Testing 0/4 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 12:09:48 chipseeker False Tests failed rnateam 8bd92f2404dd 8bd92f2404dd Staging Testing 0/6 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 12:16:22 dada2_assigntaxonomyaddspecies False Tests failed iuc 7c2100246a2f 7c2100246a2f Staging Testing 2/3 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 13:24:48 deeptools_bam_compare False Installed bgruening c929a006727f c929a006727f 2/2 2/2 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 14:01:53 deeptools_bam_coverage False Installed bgruening 0e49b109abc2 0e49b109abc2 7/7 7/7 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 14:17:06 deeptools_bam_pe_fragmentsize False Installed bgruening c06951d10364 c06951d10364 2/2 2/2 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 14:37:34 deeptools_bigwig_compare False Installed bgruening 07418a30ed01 07418a30ed01 2/2 2/2 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 14:41:41 deeptools_compute_gc_bias False Tests failed bgruening 26983857c91a 26983857c91a Staging Testing 0/1 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 14:47:36 deeptools_compute_matrix False Shed-tools error bgruening a60c359ec43c a60c359ec43c Production Installation 3/3 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 14:57:22 deeptools_compute_matrix_operations False Tests failed bgruening e6d0bff01239 e6d0bff01239 Production Testing 2/2 0/2 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 15:05:04 deeptools_correct_gc_bias False Installed bgruening e479c7ca5570 e479c7ca5570 1/1 1/1 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 15:27:13 deeptools_multi_bam_summary False Installed bgruening 01fb6a7654e6 01fb6a7654e6 2/2 2/2 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 15:39:15 deeptools_multi_bigwig_summary False Installed bgruening 137c4beed34b 137c4beed34b 2/2 2/2 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 15:44:13 deeptools_plot_correlation False Tests failed bgruening bad3ca889618 bad3ca889618 Staging Testing 1/2 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 15:53:34 deeptools_plot_coverage False Installed bgruening 231994413f89 231994413f89 2/2 2/2 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 16:03:13 deeptools_plot_enrichment False Installed bgruening 4431f39ede55 4431f39ede55 1/1 1/1 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 16:17:56 deeptools_plot_fingerprint False Installed bgruening 4ed32329e0ed 4ed32329e0ed 2/2 2/2 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 16:27:32 deeptools_plot_heatmap False Installed bgruening e4c7985d4585 e4c7985d4585 2/2 2/2 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 16:42:27 deeptools_plot_pca False Installed bgruening 443d9a9d6d11 443d9a9d6d11 2/2 2/2 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 16:53:01 deeptools_plot_profile False Installed bgruening 6662b1a8d326 6662b1a8d326 2/2 2/2 DeepTools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 17:03:58 diann False Installed galaxyp ae4dc0c041f9 ae4dc0c041f9 2/2 2/2 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 17:37:42 edger False Installed iuc 0cb907a2a810 0cb907a2a810 12/12 12/12 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 17:45:47 eggnog_mapper False Tests failed galaxyp d9c3016f7283 d9c3016f7283 Staging Testing 0/11 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 17:47:53 encyclopedia_encyclopedia False Tests failed galaxyp eac99effe86f eac99effe86f Staging Testing 0/1 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 17:49:56 encyclopedia_searchtolib False Tests failed galaxyp fb192dd6658a fb192dd6658a Staging Testing 0/2 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 17:51:58 encyclopedia_walnut False Tests failed galaxyp 0d2e93e01e68 0d2e93e01e68 Staging Testing 0/1 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 18:00:45 featurecounts False Tests failed iuc f9d49f5cb597 f9d49f5cb597 Staging Testing 6/7 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 18:15:14 humann False Tests failed iuc fc6c328c292f fc6c328c292f Staging Testing 2/8 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 18:21:16 humann_regroup_table False Tests failed iuc e88b731dad59 e88b731dad59 Staging Testing 2/3 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 18:41:15 humann_rename_table False Tests failed iuc 094ad9c068af 094ad9c068af Staging Testing 1/3 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 18:42:14 keras_model_builder False Installed bgruening 66d7efc06000 66d7efc06000 Machine Learning toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 18:43:01 keras_model_config False Installed bgruening f22a9297440f f22a9297440f Machine Learning toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 18:43:49 keras_train_and_eval False Installed bgruening 818f9b69d8a0 818f9b69d8a0 Machine Learning toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 19:10:01 kraken2tax False Tests failed devteam 50bd98b3ae5a 50bd98b3ae5a Staging Testing 0/1 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 19:25:30 merqury False Tests failed iuc 09c589057ee8 09c589057ee8 Staging Testing 3/6 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 19:26:34 ml_visualization_ex False Installed bgruening 1588f9076e32 1588f9076e32 Machine Learning toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 19:27:31 model_prediction False Installed bgruening 9991c4ddde14 9991c4ddde14 Machine Learning toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 19:32:38 openms_decoydatabase False Tests failed galaxyp 25529df60a81 25529df60a81 Staging Testing 0/4 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 19:35:14 openms_targetedfileconverter False Tests failed galaxyp 9c70a651a53e 9c70a651a53e Staging Testing 0/20 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 19:37:23 openms_xmlvalidator False Tests failed galaxyp f036e8cf1a55 f036e8cf1a55 Staging Testing 0/1 Proteomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 19:56:11 rgrnastar False Tests failed iuc 79de45b5069b 79de45b5069b Staging Testing 14/18 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 20:37:03 rna_starsolo False Tests failed iuc 5ef7ec16b04f 5ef7ec16b04f Staging Testing 12/13 Mapping toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 20:38:02 sklearn_build_pipeline False Installed bgruening 7442b94d6a1e 7442b94d6a1e Statistics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 20:38:51 sklearn_ensemble False Installed bgruening f3dfa4bdf87e f3dfa4bdf87e Machine Learning toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 20:39:42 sklearn_estimator_attributes False Installed bgruening 9fda0b82f419 9fda0b82f419 Statistics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 20:40:27 sklearn_generalized_linear False Installed bgruening 927586a18553 927586a18553 Machine Learning toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 20:41:19 sklearn_nn_classifier False Installed bgruening 7ae443e6217d 7ae443e6217d Statistics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 20:42:07 sklearn_numeric_clustering False Installed bgruening bb9fc9d46ea4 bb9fc9d46ea4 Statistics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 20:42:58 sklearn_searchcv False Installed bgruening 36e8d6d5d01b 36e8d6d5d01b Machine Learning toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 20:43:44 sklearn_svm_classifier False Installed bgruening 0630258dcf35 0630258dcf35 Machine Learning toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt +Update 166 04/10/23 20:44:28 sklearn_to_categorical False Installed bgruening 61634a87efc7 61634a87efc7 Machine Learning toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_166/install_log.txt diff --git a/staging.usegalaxy.org.au/annotation.yml b/staging.usegalaxy.org.au/annotation.yml index 9694d25b7..4612c6519 100644 --- a/staging.usegalaxy.org.au/annotation.yml +++ b/staging.usegalaxy.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 78c75f134c16 - - 3f3e247c053d - - 6e9aea89e388 - 4efdca267d51 + - 78c75f134c16 - c2ef298da409 + - 6e9aea89e388 + - 3f3e247c053d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -36,38 +36,38 @@ tools: - name: annotatemyids owner: iuc revisions: - - fe3ca740a485 - 44018dd6b447 - f29602ae449e - 133f36c29579 - - 1aae04680c4b - 4f2967b27e67 - - cd2480f35935 - - 3e1f6f6d557e - b5d8e5475247 + - 3e1f6f6d557e + - 1aae04680c4b + - cd2480f35935 + - fe3ca740a485 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - e78e25d3b4bd - bc88856eddab + - e78e25d3b4bd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: + - 6519ebe25019 - 7be22100e5e1 - dc027fa56d55 - - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 09855551d713 - ca6d970d931c - 28433faa6e42 + - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -79,9 +79,9 @@ tools: - name: barrnap owner: iuc revisions: - - 7355bbf5e05f - - fe48aa4ccd5e - 8fd427007e93 + - fe48aa4ccd5e + - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: chipseeker @@ -118,41 +118,41 @@ tools: - name: funannotate_annotate owner: iuc revisions: + - 9f2455341fac - 14f588312c56 - 582fd74dc2a1 - - 9f2455341fac tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: + - 30fb23d4c31c - 73428a792541 - a230ea445788 - - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - 563a19373357 - - 494f0bb4a993 - 30f08d74024f + - 494f0bb4a993 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - f31125bb85ea - 2bba2ff070d9 - 7abc5f6dd595 + - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: + - 52af33194019 - d3af38b9c7e1 - b3cf4684e9c7 - - 52af33194019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -164,9 +164,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 2aea122fbd25 - - 07d7991bf205 - 79261884facd + - 07d7991bf205 + - 2aea122fbd25 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -178,9 +178,9 @@ tools: - name: goseq owner: iuc revisions: + - 8b3e3657034e - ef2ad746b589 - 602de62d995b - - 8b3e3657034e - 43798b4caee0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -206,8 +206,8 @@ tools: - name: interproscan owner: bgruening revisions: - - 74810db257cc - 98cafcbd2578 + - 74810db257cc - c55643c3d813 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -234,15 +234,15 @@ tools: owner: iuc revisions: - d46d803ca6cc - - 3c1a01127868 - 370c210d9541 + - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 624606f7c996 - 033755194fe9 + - 624606f7c996 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -266,11 +266,11 @@ tools: - name: prokka owner: crs4 revisions: - - d643e3b03500 - - bf68eb663bc3 - 8a22554cdde2 - - a17498c603ec + - bf68eb663bc3 + - d643e3b03500 - eaee459f3d69 + - a17498c603ec tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -289,8 +289,8 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: rgi @@ -309,19 +309,19 @@ tools: owner: iuc revisions: - 8f92c2b26e6d - - 68693743661e + - cfcf33df7fc0 - 268d162b9c49 - - 5a29ab10dba6 - 5b80f544c67f - 5c7b70713fb5 - - cfcf33df7fc0 + - 5a29ab10dba6 + - 68693743661e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 5fab4f81391d - 2b3e65a4252f + - 5fab4f81391d - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -346,15 +346,15 @@ tools: - name: tbprofiler owner: iuc revisions: - - 45083d070fb8 + - 2c68b0c38785 - e1a9d6fd258d - - 200c378d85f3 - - ba6f87115e13 - ac8250086ac3 + - 45083d070fb8 + - ba6f87115e13 - 37213cf56392 - - 037a11682176 - - 2c68b0c38785 - 809dfc93d593 + - 200c378d85f3 + - 037a11682176 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/staging.usegalaxy.org.au/assembly.yml b/staging.usegalaxy.org.au/assembly.yml index dcc483282..4edd9f7f5 100644 --- a/staging.usegalaxy.org.au/assembly.yml +++ b/staging.usegalaxy.org.au/assembly.yml @@ -2,42 +2,42 @@ tools: - name: abyss owner: iuc revisions: + - a929ce596a34 - 8f1b150a2487 - - fa5259cc561b - - 890b794c997d - - 553bfe8bd0b5 - - 841084c5fc46 - 0e93176640ac - - a929ce596a34 + - 841084c5fc46 + - 890b794c997d + - fa5259cc561b - 7547fcab5d19 + - 553bfe8bd0b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - b2860df42e16 - - b9e31c5c01c7 - 067592b6b312 + - b2860df42e16 - 94fe43e75ddc - - 21e491ad532a - ddddce450736 + - 21e491ad532a + - b9e31c5c01c7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 25ca5d73aedf - 321347bd0494 + - 25ca5d73aedf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - 5258e18bbe23 - 22286dab5aa1 + - a7f16f24e9a1 - 3371c5bdc17a + - 5258e18bbe23 - faee8629b460 - - a7f16f24e9a1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -49,29 +49,29 @@ tools: - name: busco owner: iuc revisions: + - 46ae58b1d792 + - e824f5d958d0 - 2dd755c1c6ff - - bb935709506a + - f18f0b887c31 - cf13a1e03e5b + - 602fb8e63aa7 - 0d243f458b53 - - 94170eee0ad8 - - 1e62c28ba91d - - f18f0b887c31 - - 41030a6c03b7 + - e4bd1e99bacf - 4048d82f0c88 - - e824f5d958d0 - 1440ae06552f + - 94170eee0ad8 + - 1e62c28ba91d + - bb935709506a - 5ecdeca79a0d - - e4bd1e99bacf - - 46ae58b1d792 - - 602fb8e63aa7 + - 41030a6c03b7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - 5732f959936a - 86f150c8019d - c5b7390290b1 - - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -83,37 +83,37 @@ tools: - name: flye owner: bgruening revisions: - - e27815e82dd4 - 276f5d8712d5 - 8d4f03b5fe9d - 3ee0ef312022 - 1ce9b1d72ec3 + - e27815e82dd4 - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - b2f674562a18 - 01210c4e9144 - 3169a38c2656 + - b2f674562a18 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: + - 611219887a48 - 8b330a577046 - 06bcf65179fb - - 611219887a48 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 690c2caa367e - - 3ef480892a9f - - 3fba9c77550a - 5127a713de83 + - 3fba9c77550a + - 3ef480892a9f + - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -125,18 +125,18 @@ tools: - name: hifiasm owner: bgruening revisions: - - da9d8bf98802 - ec9e21e9c71b - - 5bec28269d95 - - 6505bd37670d - - 5f625c63b8bc + - f3c89da3af16 + - 71740308d412 - 045c7c3d8e59 + - 366a11d316a7 + - 5bec28269d95 - 9ef6920c3089 + - da9d8bf98802 + - 6505bd37670d - 2061fb3b81b4 - - f3c89da3af16 - - 71740308d412 + - 5f625c63b8bc - 3f7be05a1597 - - 366a11d316a7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -162,29 +162,29 @@ tools: - name: merqury owner: iuc revisions: - - f8113c25bc6b - 39edec572bae - 9d79beb19ac3 + - f8113c25bc6b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - eadfd71dde37 - 29dabd8db6f2 + - eadfd71dde37 - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - e731ea24e48d - eb7a370f6588 - - 3ca2d2a9068c - - 2ecf5a570907 + - e731ea24e48d - fd128c111ab0 - 606b09cc9860 - f338e9942b27 + - 2ecf5a570907 + - 3ca2d2a9068c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -196,11 +196,11 @@ tools: - name: miniasm owner: iuc revisions: - - 8dee0218ac7d - - a7b889b90140 + - 8b6d0d85252b - 73a3846701e1 - 80d1250bd5fd - - 8b6d0d85252b + - 8dee0218ac7d + - a7b889b90140 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -212,9 +212,9 @@ tools: - name: novoplasty owner: iuc revisions: + - 15200570e926 - 7c2f5268d01c - 64a1c751d99b - - 15200570e926 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -226,74 +226,74 @@ tools: - name: pretext_map owner: iuc revisions: + - d256a51a656b + - 8fef980d48b5 - 02831bf9e95f + - 2b16ba799da9 - bbe19ef04a74 - dfb8a4497339 - - d256a51a656b - - 2b16ba799da9 - - 8fef980d48b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - 76d4cbefff85 - - a315c25dc813 - e9bd16ba5ebd + - a315c25dc813 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - ebb0dcdb621a - - 72472698a2df - - 875d0f36d66f - - 675488238c96 - 3061c8b029e5 - - 59db8ea8c845 + - 675488238c96 - 6fcbee531de6 - 342a1d1fed7b + - 59db8ea8c845 + - 72472698a2df - 7594365c546b + - ebb0dcdb621a + - 875d0f36d66f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - a199cd7ac344 - 936f0b5e7fcc - d865b62f501c - 39bed8de8017 - - cd06929b224b - aa39b19ca11e + - cd06929b224b + - a199cd7ac344 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: + - 33b7d8481a76 + - 3edba9afc9bc - f8564b2d7f63 - 2b2a352488fa - f11b994b7eb2 - - 3edba9afc9bc - - 33b7d8481a76 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: + - ef69617ecb42 + - e122f9101584 - 378e55aeeb25 - - 53c2bc8c2ae3 - 1d06c8b38e77 - - e122f9101584 - - ef69617ecb42 + - 53c2bc8c2ae3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - - 9a22227bb6d0 - f77f7a7f3b83 - - ba7b0f11e470 + - 9a22227bb6d0 - ab5b7f6b7198 + - ba7b0f11e470 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -305,151 +305,151 @@ tools: - name: shovill owner: iuc revisions: - - d9f6a00b6db7 - - ad80238462c1 - - f698c7604b3b - 865119fcb694 + - d9f6a00b6db7 - 83ead2be47b2 + - f698c7604b3b + - ad80238462c1 - 196a599ec43d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 5e0825476fb7 - 5a0ddb4dc3a4 + - 5e0825476fb7 - 24e471d13fe9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 904bf932cf78 - - 7490b213baa9 - - 1bb12736175c - - 1fc82fe7ebef - 051fd2db8a27 + - 1fc82fe7ebef + - 1bb12736175c + - 7490b213baa9 + - 904bf932cf78 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - ad8b536d1caa - 34305b013402 - - 808b3a0a6716 + - ad8b536d1caa - fee85957cebe + - 808b3a0a6716 - d6e617c4e338 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 8d4b90bf9caf - 6b5a5842531e - - b8002c3f7141 + - 8d4b90bf9caf - 21da31ed41a1 + - b8002c3f7141 - e5a3b75a271f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 9de69775f512 - 2a10645aeadd - - 328aa71f0f3c - 86f66ab58e14 + - 328aa71f0f3c + - 9de69775f512 - f1532cb33c75 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 6aad515a5270 - - 340bc17f49cf - 1708851f8804 - 85fb02c43042 - e41dcb0e913b + - 6aad515a5270 + - 340bc17f49cf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - d159735a6a9f - 249f6a28c751 - - d5fb354f745d - b65a43f70b99 - b3490b036c5a + - d5fb354f745d + - d159735a6a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 33368fec3b70 - - 9006e5836729 - - d2d1df21dfb9 + - 7897763d14ec - dd7ad84f3943 - b7829778729f - - 7897763d14ec + - 9006e5836729 + - 33368fec3b70 + - d2d1df21dfb9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 8f631679571f - - 6f4c8ad6ea01 + - ced385aa976d - 189e837009c9 + - 6f4c8ad6ea01 + - 8f631679571f - 505a9833ab5d - - ced385aa976d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - 19bdfd1e6fe3 + - d40ed4eb0c0e + - e59bee4565b3 - 9ded6109434a - 356afed970b4 - - e59bee4565b3 - - d40ed4eb0c0e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: + - b23249f81bc4 + - 4688ae3b49b5 - 80a17897564d - ebd801e712bc - - 4688ae3b49b5 - 6dd935e4984b - - b23249f81bc4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - b64696992ee9 + - b5e35a2ca4f3 - 937ea677d437 + - b64696992ee9 - 59bd28f6265d - - b5e35a2ca4f3 - cb1e3db43020 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 2628f6790eda - - 383bb5ad32e2 - cb4768eeca3b - - 6015aa0303f2 - 05bd7504fdb2 + - 383bb5ad32e2 + - 6015aa0303f2 + - 2628f6790eda tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 6e26c9afd301 + - d10bdad2fd17 - e92675014ac9 - - 0a3a602cd1e3 + - 6e26c9afd301 - 9e3e80cc4ad4 - - d10bdad2fd17 + - 0a3a602cd1e3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet @@ -464,10 +464,10 @@ tools: - name: velvetoptimiser owner: simon-gladman revisions: + - 0e2b4e3f9ca1 - d81360ea69d8 - 4a53b89fa703 - 37d88f41c810 - - 0e2b4e3f9ca1 - 82398ba86ba7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/bacterial_typing.yml b/staging.usegalaxy.org.au/bacterial_typing.yml index d41135905..373bc4f76 100644 --- a/staging.usegalaxy.org.au/bacterial_typing.yml +++ b/staging.usegalaxy.org.au/bacterial_typing.yml @@ -2,8 +2,8 @@ tools: - name: integron_finder owner: iuc revisions: - - 4768f7f8e93f - 1ae00120dd24 + - 4768f7f8e93f tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -15,17 +15,17 @@ tools: - name: mlst owner: iuc revisions: + - 31812e7a1315 - 1f5641a52664 - ded48b36f3b7 - 8e8dc9a1e3e5 - - 31812e7a1315 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: + - 24a7a95867b0 - 5c8ff92e38a9 - 17fcac7ddf54 - - 24a7a95867b0 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/bb_tools.yml b/staging.usegalaxy.org.au/bb_tools.yml index 05eb64807..93b7c3d31 100644 --- a/staging.usegalaxy.org.au/bb_tools.yml +++ b/staging.usegalaxy.org.au/bb_tools.yml @@ -2,8 +2,8 @@ tools: - name: bbtools_bbduk owner: iuc revisions: + - a9c9d768b751 - 159b04e36791 - 204a131e47db - - a9c9d768b751 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/bed.yml b/staging.usegalaxy.org.au/bed.yml index 7776f9344..d9680f6f9 100644 --- a/staging.usegalaxy.org.au/bed.yml +++ b/staging.usegalaxy.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: - - ce3c7f062223 - - 87ee588b3d45 - - a8eabd2838f6 - - 589e7e57fd6d - - 07e8b80f278c - - b28e0cfa7ba1 - a1a923cd89e8 - - 0a5c785ac6db + - 589e7e57fd6d - a68aa6c1204a - - e19bebe96cd2 - dde39ba9c031 + - a8eabd2838f6 + - 87ee588b3d45 + - e19bebe96cd2 + - ce3c7f062223 + - 0a5c785ac6db + - 07e8b80f278c + - b28e0cfa7ba1 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/blast.yml b/staging.usegalaxy.org.au/blast.yml index 5fc5e07c1..bf2ebd13a 100644 --- a/staging.usegalaxy.org.au/blast.yml +++ b/staging.usegalaxy.org.au/blast.yml @@ -8,10 +8,10 @@ tools: - name: diamond owner: bgruening revisions: - - 54f751e413f4 - 62c9df8382c2 - - 1e3323a44643 - f921014aba5a + - 1e3323a44643 + - 54f751e413f4 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,12 +23,12 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - 2889433c7ae1 - - 0e3cf9594bb7 - - acf4e47b734c - 6f386c5dc4fb - 5edc472ec434 + - 0e3cf9594bb7 + - 2889433c7ae1 - e25d3acf6e68 + - acf4e47b734c tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus diff --git a/staging.usegalaxy.org.au/chemicaltoolbox.yml b/staging.usegalaxy.org.au/chemicaltoolbox.yml index 77adbbca7..dbb1c5ec1 100644 --- a/staging.usegalaxy.org.au/chemicaltoolbox.yml +++ b/staging.usegalaxy.org.au/chemicaltoolbox.yml @@ -2,13 +2,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: + - f4230f116196 + - da6bd1975a71 + - c8cdde00b105 + - 6ca543ec1bf8 - 095ad4d096d1 - 710301bc46fa - 27ee142314a9 - - 6ca543ec1bf8 - - c8cdde00b105 - - f4230f116196 - - da6bd1975a71 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -81,8 +81,8 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - 67ee76f0e497 - 2a868592ebcb + - 67ee76f0e497 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -100,9 +100,9 @@ tools: - name: gmx_editconf owner: chemteam revisions: + - 0fac8e2afc13 - 88076940fa94 - bfb65cb551d8 - - 0fac8e2afc13 - 3b8a9d5ced85 - 79cfd9ead848 tool_panel_section_label: ChemicalToolBox @@ -110,81 +110,81 @@ tools: - name: gmx_em owner: chemteam revisions: - - f5d979cb4b54 - - eb6564a60136 - b46d4b4d995c - - 715cd0e87781 - d532b7e5f64b - 55918daa5651 + - eb6564a60136 + - f5d979cb4b54 + - 715cd0e87781 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: + - 5579659312e6 - d2f955aea23a + - fdf2cc80adb5 - 97872d87ba80 - f26afd1b7104 - - fdf2cc80adb5 - - 5579659312e6 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - 319a28774da9 - d1d0efda35c0 - bc31d02be922 + - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - ed736e6eee39 - - 4da9ee404eab - - cac1886249a2 - - 070e3ecc3fda - 2c349b027a01 + - 070e3ecc3fda + - cac1886249a2 + - 4da9ee404eab tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: + - 2e219a2d9327 + - 73008ef1f487 - 525ca7c8065f + - da8753545526 + - 807aa4c9293d - d1f803b5943c - - 73008ef1f487 - - c0c9a5024177 - f197e34c33a9 - - 807aa4c9293d - - 2e219a2d9327 - - da8753545526 + - c0c9a5024177 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 2c8ed1b52bf7 - - 7568ae18908a - - c4fbab8e03c5 + - 61094e01eff9 - 1809414a9454 - 27ea4e1a3f95 - - 61094e01eff9 + - 2c8ed1b52bf7 + - c4fbab8e03c5 + - 7568ae18908a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: - - 79e8ab8f1e81 - ccfbd956a2d3 + - 730ef07b90ae - ba83f0923369 + - 79e8ab8f1e81 - d7ec25187599 - - 730ef07b90ae tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 48d6a6eb438b - 9a3a1f698fc6 + - 48d6a6eb438b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: natural_product_likeness @@ -196,8 +196,8 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - b59c91adeac1 - e6011617c748 + - b59c91adeac1 - 1400d1977e7b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/chip_seq.yml b/staging.usegalaxy.org.au/chip_seq.yml index 3228d6ca2..0775c4b51 100644 --- a/staging.usegalaxy.org.au/chip_seq.yml +++ b/staging.usegalaxy.org.au/chip_seq.yml @@ -3,8 +3,8 @@ tools: owner: bgruening revisions: - 163688bb8f73 - - fa56d93f7980 - c97a786e8fb5 + - fa56d93f7980 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -29,10 +29,10 @@ tools: - name: macs2 owner: iuc revisions: - - 640d3af5d833 - f5d67c722d67 - - 495a4173006f + - 640d3af5d833 - 424aefbd7777 + - 495a4173006f tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -44,16 +44,16 @@ tools: - name: rnachipintegrator owner: pjbriggs revisions: - - 087d9872fb0d - b695071de766 + - 087d9872fb0d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer owner: devteam revisions: + - 4a14714649b4 - 74c9214cc8e6 - 5c2cc3b58c7d - - 4a14714649b4 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/staging.usegalaxy.org.au/collection_operations.yml b/staging.usegalaxy.org.au/collection_operations.yml index c28bd6ed7..e0f203214 100644 --- a/staging.usegalaxy.org.au/collection_operations.yml +++ b/staging.usegalaxy.org.au/collection_operations.yml @@ -9,9 +9,9 @@ tools: - name: collapse_collections owner: nml revisions: - - 33151a38533a - - 830961c48e42 - 90981f86000f + - 830961c48e42 + - 33151a38533a - 25136a2b0cfe tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/convert_formats.yml b/staging.usegalaxy.org.au/convert_formats.yml index 60fa53db7..1f6fb638d 100644 --- a/staging.usegalaxy.org.au/convert_formats.yml +++ b/staging.usegalaxy.org.au/convert_formats.yml @@ -8,35 +8,35 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 4a6ee918c13a + - 6ef0b5664c69 - a3b86937ead6 - - 0b3c3ad92827 + - f3a19509108a + - 4a6ee918c13a + - 5e1240a87bcb - e3cbd2287f63 - 367b1ed91207 - - 5e1240a87bcb - - f3a19509108a - - 6ef0b5664c69 + - 0b3c3ad92827 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 33c99804a32f - - 1b5fc03380d4 - - 54ccb7e1f49a - - bd46669113b9 - - 501c21cce614 - - e177a8ea0bf1 - - e525f9ffb9ac - 72ed72122deb + - e525f9ffb9ac + - e177a8ea0bf1 + - bd46669113b9 + - 1b5fc03380d4 - 584008e574b2 + - 33c99804a32f + - 501c21cce614 + - 54ccb7e1f49a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 owner: iuc revisions: - - a0d092f27fdf - 11c3eb512633 + - a0d092f27fdf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: compress_file @@ -48,23 +48,23 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - 7e801ab2b70e - e7ed3c310b74 + - 7e801ab2b70e tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: - - 8979c288aefb - - 186b8d913e6c - 77b41c89d856 + - 186b8d913e6c + - 8979c288aefb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - 4b347702c4aa + - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fml_gff3togtf @@ -115,25 +115,25 @@ tools: - name: tabular_to_fasta owner: devteam revisions: - - 0a7799698fe5 - 0b4e36026794 + - 0a7799698fe5 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq owner: devteam revisions: - - 68f57cc8fad0 - 2dcfbbf9071a + - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: + - 26c6706bfb07 + - b9b385097f13 - 19e45916daf9 - 63769c4217a7 - 92ac8e086317 - - b9b385097f13 - - 26c6706bfb07 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/staging.usegalaxy.org.au/deeptools.yml b/staging.usegalaxy.org.au/deeptools.yml index 5f4ee00ac..f0937bce3 100644 --- a/staging.usegalaxy.org.au/deeptools.yml +++ b/staging.usegalaxy.org.au/deeptools.yml @@ -4,42 +4,46 @@ tools: revisions: - 29451af70c52 - de72ba3ed6f2 - - e821645ef8fc - a1ca9bccc7f2 + - e821645ef8fc - 268e91e540ee - 5f6d123679f4 + - c929a006727f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: + - 0e143b4c3987 + - 12af64f93288 - 5d11599b8a7d + - 0e49b109abc2 - 7a7fd0f5f15d - - 2d2cf5c1ea8a - bb1e4f63e0e6 - - 0e143b4c3987 - - 12af64f93288 + - 2d2cf5c1ea8a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: + - 1d848bc4585f - dc059492a995 + - c06951d10364 - 195e98217334 - 7c1beb6d6eca - - 1d848bc4585f - 81b1e3e1fc6c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: + - 07418a30ed01 - 71aa86af6762 - - a67ac707496a - 3d211717a775 - - 26e7304d6737 - bfff7454b59a + - a67ac707496a - 93eb012d9eed + - 26e7304d6737 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias @@ -47,143 +51,153 @@ tools: revisions: - b8858746dc1f - 56d5b797ce84 - - 29fcfd36e90a + - dd0b7398bb96 - 2bc10a9ca58b + - 29fcfd36e90a - 5be24eba848d - - dd0b7398bb96 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - 7ef978dc1b8a - - ee3a1b0f45f1 - c3e012dfe21f - 72bfafe3330b - - 9384cd033f30 + - ee3a1b0f45f1 - 7e6bcd2e5128 + - 9384cd033f30 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - fd1275e01605 + - fb9cf9c97ec4 + - a60c359ec43c - b73e213add0c - - 514fa53b5efb + - fd1275e01605 - 9470f29702f8 - d9a637e83828 - 167788df3b46 - - fb9cf9c97ec4 + - 514fa53b5efb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - ca0616bb2cdf - - 2c37ce318bc3 - 86febdcc4283 - - c34d11ea4ba6 - a02cfa31e9cb + - ca0616bb2cdf + - e479c7ca5570 + - 2c37ce318bc3 - 5bffaa8354a1 + - c34d11ea4ba6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 69a8621ca2f0 - - 2d466b530754 - - 004aea905d4d - 1fcb7adc39b8 - - 78f405266706 + - 004aea905d4d + - 2d466b530754 + - 01fb6a7654e6 - 192ef85c0b0b + - 69a8621ca2f0 + - 78f405266706 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 3c9f0c486cca - - d580d6acd1df + - db940c262830 - d9ce4897dbb2 - - 2f9e4843f480 + - d580d6acd1df - 9ecba5e225a6 + - 137c4beed34b - 459cfa861f0b - - db940c262830 + - 3c9f0c486cca + - 2f9e4843f480 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - f264afa9fa6f - - fbe773640707 - 2c66e43f1c86 + - f264afa9fa6f + - 32e451def88c - fd408d755394 - bd7db9e2f2cb - - 32e451def88c + - fbe773640707 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: + - 231994413f89 - 7fda5607e777 - - 9368fbc49c8b - 4e12ea27f788 - - 56bce3c82278 - - 3b9d990a0a0e + - 9368fbc49c8b - 7e361d147872 + - 3b9d990a0a0e + - 56bce3c82278 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - e65d16fb2724 - - c03c3384cd81 - - b1779366c8e9 - - ce4ce3316f74 + - 4431f39ede55 - 94ca68515826 + - b1779366c8e9 - d9114ef1c8a5 + - ce4ce3316f74 + - c03c3384cd81 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - 4ed32329e0ed + - f8fc4e5aff9d - 2da482e408b8 + - b88ebb3672a1 - 793665fff0f8 - d57251071381 - - f8fc4e5aff9d - - b88ebb3672a1 - 23f7c5f1fdaf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - 512155688d98 - - a7849312d328 - - a4dfb122e52b + - c60570fa602f - 010e58e9d822 + - a7849312d328 + - 512155688d98 - ba6efa77fb79 + - e4c7985d4585 + - a4dfb122e52b - 25d830337d31 - - c60570fa602f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 00d869ea03a1 + - 443d9a9d6d11 + - 4d678170d29b - c899e0ccff8c - - 38e3f226248b - 69264da0ce77 - - 4d678170d29b - aa200e4f3939 + - 00d869ea03a1 + - 38e3f226248b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: + - d806504e96d9 - a2d70c4fd406 - - c361b12d207a - - 10301d137111 - aac8444d6681 - - d806504e96d9 + - 10301d137111 + - 6662b1a8d326 + - c361b12d207a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/dna_metabarcoding.yml b/staging.usegalaxy.org.au/dna_metabarcoding.yml index 1c0d5f7e0..f3b3d8064 100644 --- a/staging.usegalaxy.org.au/dna_metabarcoding.yml +++ b/staging.usegalaxy.org.au/dna_metabarcoding.yml @@ -9,8 +9,8 @@ tools: - name: obi_clean owner: iuc revisions: - - 12baadec7809 - 7d16de45c021 + - 12baadec7809 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -23,8 +23,8 @@ tools: - name: obi_grep owner: iuc revisions: - - e9e49cf06b42 - fe7ec8a3d35e + - e9e49cf06b42 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend @@ -51,21 +51,21 @@ tools: - name: obi_stat owner: iuc revisions: - - 39320fee9d70 - 723a93febe89 + - 39320fee9d70 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab owner: iuc revisions: - - 5f7003111e32 - 3299c7d5268f + - 5f7003111e32 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq owner: iuc revisions: - - c0f7b58b4ce4 - ec215ed98831 + - c0f7b58b4ce4 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/emboss.yml b/staging.usegalaxy.org.au/emboss.yml index b265e8fe5..2bdbfb936 100644 --- a/staging.usegalaxy.org.au/emboss.yml +++ b/staging.usegalaxy.org.au/emboss.yml @@ -4,7 +4,7 @@ tools: revisions: - dba489bfcd62 - 832c20329690 - - 63dd26468588 - ce385837c160 + - 63dd26468588 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/epigenetics.yml b/staging.usegalaxy.org.au/epigenetics.yml index 35a842c4d..c8668c907 100644 --- a/staging.usegalaxy.org.au/epigenetics.yml +++ b/staging.usegalaxy.org.au/epigenetics.yml @@ -2,9 +2,9 @@ tools: - name: bwameth owner: iuc revisions: + - d82648ad25a3 - 6da3972210ee - 62f5fab76dfb - - d82648ad25a3 - 29bdbc353f20 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/fastafastq.yml b/staging.usegalaxy.org.au/fastafastq.yml index 7cbceb6f9..930ea1282 100644 --- a/staging.usegalaxy.org.au/fastafastq.yml +++ b/staging.usegalaxy.org.au/fastafastq.yml @@ -8,22 +8,22 @@ tools: - name: cutadapt owner: lparsons revisions: - - 5915ea1ec9b1 - - c4b82dce8335 - - 288f97432497 - - 8c0175e03cee + - c053d4cad713 + - 4e5056fefd88 + - 660cffd8d92a - 135b80fb1ac2 - de6cebe3c043 - - 44e2cc14f75b - - 660cffd8d92a - - c053d4cad713 - - 8665bcc8b847 + - 288f97432497 - 093678460093 - - c5e2e5902201 + - 44e2cc14f75b + - c4b82dce8335 - 49370cb85f0f + - 8c0175e03cee + - c5e2e5902201 - e4691e1589d3 + - 5915ea1ec9b1 - 48f587c13075 - - 4e5056fefd88 + - 8665bcc8b847 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -56,8 +56,8 @@ tools: - name: fasta_concatenate_by_species owner: devteam revisions: - - 717aee069681 - 25b8736c627a + - 717aee069681 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_extract @@ -69,16 +69,16 @@ tools: - name: fasta_filter_by_length owner: devteam revisions: - - e626b3ff9922 - 8cacfcf96a52 + - e626b3ff9922 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: - - 859422bcb689 - - 516b97a23d7e - 9457a20156db + - 516b97a23d7e + - 859422bcb689 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -97,9 +97,9 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - f773e98b26cf - - ec0b5076173a - f81d4362b6c1 + - ec0b5076173a + - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -127,8 +127,8 @@ tools: owner: iuc revisions: - 65b93b623c77 - - 1d8fe9bc4cb0 - dbf9c561ef29 + - 1d8fe9bc4cb0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -140,22 +140,22 @@ tools: - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - f1dc2a761c30 + - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: - - 10b75444feae - 81a9090d6df3 + - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer owner: devteam revisions: - - 47e5dbc3e790 - 8611b80a14d6 + - 47e5dbc3e790 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation @@ -175,8 +175,8 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - 03d57fea6482 - f3936d0632cb + - 03d57fea6482 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -189,16 +189,16 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: - - c885369b207b - 09a2199cd356 + - c885369b207b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - - 35e38452bb3f - - e39cc71d3ed6 - 249c8393f2d4 + - e39cc71d3ed6 + - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -211,8 +211,8 @@ tools: owner: devteam revisions: - 045f0e1043f7 - - 74db4cffab1f - 54053ea6c77e + - 74db4cffab1f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -244,10 +244,10 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 529bccd5e4a1 + - 09070cacefd8 - 567d5b3c52b1 - d5e9e83cd3d8 - - 09070cacefd8 + - 529bccd5e4a1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter @@ -260,8 +260,8 @@ tools: owner: devteam revisions: - 8abdedf55101 - - 0b7ec11b3c7c - 4bedca26c133 + - 0b7ec11b3c7c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -273,10 +273,10 @@ tools: - name: fastx_clipper owner: devteam revisions: - - bdf1ce174e39 + - 736b8f6ee456 - cb1e251cac37 + - bdf1ce174e39 - 90858c306551 - - 736b8f6ee456 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -302,10 +302,10 @@ tools: - name: fastx_renamer owner: devteam revisions: + - b29d37ca9e41 + - f984bb114520 - 02f8a17a4ebd - 3599f5451ee2 - - f984bb114520 - - b29d37ca9e41 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -317,10 +317,10 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: + - 177f0621c266 - 0c2907307ba4 - 6027ef51ef91 - e246088b6e34 - - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -332,10 +332,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: - - 73194cdd4f57 - - 61b4cedc8934 - 547e8d00f11c - 377ac2829eac + - 61b4cedc8934 + - 73194cdd4f57 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -372,8 +372,8 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 3b0a14722175 - 8e1a90917fa7 + - 3b0a14722175 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -398,8 +398,8 @@ tools: - name: ucsc_fasplit owner: iuc revisions: - - bf04bd405d5b - 71f649c23021 + - bf04bd405d5b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -411,11 +411,11 @@ tools: - name: umi_tools_count owner: iuc revisions: + - e654095ab143 - 24013bf85a6f - - 8250ea3a1501 - a535cf1e5da4 - - e654095ab143 - b557acca0b56 + - 8250ea3a1501 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -433,12 +433,12 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 828dba98cdb4 + - 9fa7803d1c51 - 27ac32a22ad2 - - 6a675c3aa610 - - 7accf7407811 - f3759eec3018 - - 9fa7803d1c51 + - 7accf7407811 + - 6a675c3aa610 + - 828dba98cdb4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract diff --git a/staging.usegalaxy.org.au/fastq_quality_control.yml b/staging.usegalaxy.org.au/fastq_quality_control.yml index c13d9b89d..bf67bce85 100644 --- a/staging.usegalaxy.org.au/fastq_quality_control.yml +++ b/staging.usegalaxy.org.au/fastq_quality_control.yml @@ -2,8 +2,8 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 7b4468117008 - ce9cd02d5b88 + - 7b4468117008 - 64e9a6afdd0c - e41385662e5e tool_panel_section_label: FASTQ Quality Control @@ -18,13 +18,13 @@ tools: - name: fastqc owner: devteam revisions: - - e7b2202befea - 3d0c7bdf12f5 + - 2b0c9d9fc6ca + - e7b2202befea - ff9530579d1f - f2e8552cf1d0 - - 2b0c9d9fc6ca - - 5ec9f6bceaee - 9da02be9c6cc + - 5ec9f6bceaee tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -45,31 +45,31 @@ tools: - name: fastx_quality_statistics owner: devteam revisions: - - 7306ec78632a - - cc0fd298cc17 - 59003d0543cd + - cc0fd298cc17 + - 7306ec78632a tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: + - 8880fb74ef56 - 41b2ad601cf0 - a72af9de6bf5 - - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 9a913cdee30e - - abfd8a6544d7 - bf675f34b056 - b2f1f75d49c4 - f7985e0479b9 + - 3d93dd18d9f8 + - 9a913cdee30e - 1c2db0054039 + - abfd8a6544d7 - 5e33b465d8d5 - 75c93c70d094 - - 3d93dd18d9f8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore diff --git a/staging.usegalaxy.org.au/filter_and_sort.yml b/staging.usegalaxy.org.au/filter_and_sort.yml index 5b44a1c25..7946b577d 100644 --- a/staging.usegalaxy.org.au/filter_and_sort.yml +++ b/staging.usegalaxy.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs diff --git a/staging.usegalaxy.org.au/gemini_tools.yml b/staging.usegalaxy.org.au/gemini_tools.yml index 1b2990d06..4b788c79f 100644 --- a/staging.usegalaxy.org.au/gemini_tools.yml +++ b/staging.usegalaxy.org.au/gemini_tools.yml @@ -2,8 +2,8 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 3630a6e624d4 - 142d95ab942e + - 3630a6e624d4 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend @@ -24,29 +24,29 @@ tools: - name: gemini_burden owner: iuc revisions: - - 1a4c5adcd587 - df57188562f0 + - 1a4c5adcd587 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets owner: iuc revisions: - - 7cf9bc210044 - 62647e2637f6 + - 7cf9bc210044 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info owner: iuc revisions: - - 7d75673f4d6f - 4c5f4e9b1931 + - 7d75673f4d6f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo owner: iuc revisions: - - d5b01cc263be - 9db3e299b1c8 + - d5b01cc263be tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -59,15 +59,15 @@ tools: - name: gemini_fusions owner: iuc revisions: - - 8151a5a0e4f6 - 91d53f89ca54 + - 8151a5a0e4f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -87,8 +87,8 @@ tools: owner: iuc revisions: - b2c25142267e - - 45296e47d565 - cf61daf064fe + - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -108,8 +108,8 @@ tools: - name: gemini_pathways owner: iuc revisions: - - 6b09debcfc49 - 9199331c3421 + - 6b09debcfc49 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -122,9 +122,9 @@ tools: - name: gemini_query owner: iuc revisions: - - 666f60a9331a - 840fb4850be3 - da74170c55c7 + - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -137,8 +137,8 @@ tools: - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh @@ -151,8 +151,8 @@ tools: - name: gemini_set_somatic owner: iuc revisions: - - ef9991a4a9a7 - e4e2128460e3 + - ef9991a4a9a7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats diff --git a/staging.usegalaxy.org.au/genome_editing.yml b/staging.usegalaxy.org.au/genome_editing.yml index 451dd80c8..0fe27413f 100644 --- a/staging.usegalaxy.org.au/genome_editing.yml +++ b/staging.usegalaxy.org.au/genome_editing.yml @@ -2,8 +2,8 @@ tools: - name: mageck_count owner: iuc revisions: - - e329d44424d7 - 3edbd1ff5602 + - e329d44424d7 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea @@ -16,21 +16,21 @@ tools: - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway owner: iuc revisions: - - 9744e1124d0f - 39a996d44e16 + - 9744e1124d0f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test owner: iuc revisions: - - 9b4f4533c9ee - 688a8eccea71 + - 9b4f4533c9ee tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/get_data.yml b/staging.usegalaxy.org.au/get_data.yml index e72003d8a..7c535b884 100644 --- a/staging.usegalaxy.org.au/get_data.yml +++ b/staging.usegalaxy.org.au/get_data.yml @@ -2,54 +2,54 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - c1b437242fee - b39347891609 - - 983bf725dfc2 - e9df53a75f3c + - c1b437242fee + - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download owner: iuc revisions: - - e063168e0a81 - 1c58de56d587 - 28587613264f + - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 734abc7ac21d + - 7068f48d0ef9 + - 653e89d73fc4 + - 1790dcf3c32d - 5e6237d58b0c + - c441583adae5 - 4df8de2d0e48 - - 653e89d73fc4 - - 69ebb7f46e45 - - 7068f48d0ef9 + - 4317d3cb6cba + - f5ea3ce9b9b0 + - 9a776b080193 - 6ea73833cf67 - e08a7ad4378b - - aad3885b3216 - - 1790dcf3c32d - 83c7d564b128 - - f5ea3ce9b9b0 - - 9a776b080193 - - 4317d3cb6cba - - c441583adae5 + - aad3885b3216 + - 734abc7ac21d + - 69ebb7f46e45 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 7863f1abcdda - - 75b3b3d0adbf - 34758ab8aaa4 - 9aaa46d45472 + - 7863f1abcdda + - 75b3b3d0adbf tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - bfdc6a7ffd3a - - 054483e27a35 - af5eccf83605 + - 054483e27a35 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/graphdisplay_data.yml b/staging.usegalaxy.org.au/graphdisplay_data.yml index de556baa8..5010b8141 100644 --- a/staging.usegalaxy.org.au/graphdisplay_data.yml +++ b/staging.usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - a64dc31ab7f2 - - 4b519282a05b - - ae9994cf526f - - 740057a5126d - - df7356989ac1 - - 290a11559985 - c4bde687c846 + - 740057a5126d - fd59d783248a + - 290a11559985 - 7f13dc906cb9 + - ae9994cf526f + - 4b519282a05b + - a64dc31ab7f2 + - df7356989ac1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -34,16 +34,16 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 7cf5b1d072b5 - f95284aa2946 - 867ab348287d + - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap2 owner: iuc revisions: - - '566197475670' - 53460afd5115 + - '566197475670' - ca7cb0eaad62 - 3b37b1b1c3a7 tool_panel_section_label: Graph/Display Data @@ -51,11 +51,11 @@ tools: - name: ggplot2_heatmap owner: iuc revisions: - - da4c086cff5b + - d3a9e32672ec - 3d059e9c2fba - 10515715c940 - - d3a9e32672ec - 391a4cc45fea + - da4c086cff5b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point @@ -63,9 +63,9 @@ tools: revisions: - 5fe1dc76176e - e3a675da7fd0 - - 299307abd804 - d0fc8b746d57 - 1acf88921176 + - 299307abd804 - 3b12bf9b4b87 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -78,8 +78,8 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - cf1df6b2220a - 5d6f8f0bef7c + - cf1df6b2220a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan @@ -92,24 +92,24 @@ tools: - name: histogram owner: devteam revisions: - - 6f134426c2b0 - cdb9e89e2970 + - 6f134426c2b0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: jbrowse owner: iuc revisions: - - 1cfc579079a6 - - a6e57ff585c0 - - 2bb2e07a7a21 + - fd5dbf0f732e + - 17359b808b01 - ca2def38369c - - 836d1aa3e89a + - 112eb40ba6cf - 6cd09d7b5f37 - - 17359b808b01 - - fd5dbf0f732e - - 4542035c1075 + - a6e57ff585c0 - 667e17248bfe - - 112eb40ba6cf + - 4542035c1075 + - 2bb2e07a7a21 + - 1cfc579079a6 + - 836d1aa3e89a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -127,8 +127,8 @@ tools: - name: pathview owner: iuc revisions: - - f1691de443a7 - fe154a7af404 + - f1691de443a7 - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -141,8 +141,8 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 62e3a4e8c54c - 85da91bbdbfb + - 62e3a4e8c54c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -161,8 +161,8 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 44c66e8d21e6 - 7c9417381ad5 + - 44c66e8d21e6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -174,22 +174,22 @@ tools: - name: pygenometracks owner: iuc revisions: + - 14e7c35f3d00 - a1abfa420d9d - - 7dd841a32245 - - 2824d77cd8f8 + - 326a3db8d9d1 - 360df4999907 + - 2824d77cd8f8 - 59fd173ac850 - - 14e7c35f3d00 - - 326a3db8d9d1 + - 7dd841a32245 - 4ac4e7083b7e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 83c573f2e73c - 44608d0193ed - 73b8cb5bddcd + - 83c573f2e73c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/staging.usegalaxy.org.au/hca_single_cell.yml b/staging.usegalaxy.org.au/hca_single_cell.yml index 650427647..8869d2223 100644 --- a/staging.usegalaxy.org.au/hca_single_cell.yml +++ b/staging.usegalaxy.org.au/hca_single_cell.yml @@ -173,8 +173,8 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - 767a675b5254 - 0f98603d0116 + - 767a675b5254 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data diff --git a/staging.usegalaxy.org.au/hicexplorer.yml b/staging.usegalaxy.org.au/hicexplorer.yml index 28826c830..3c358c31f 100644 --- a/staging.usegalaxy.org.au/hicexplorer.yml +++ b/staging.usegalaxy.org.au/hicexplorer.yml @@ -18,9 +18,9 @@ tools: - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 03dd3c16ae4e - 9e357a8b2ec3 - 4d511437b1e5 + - 03dd3c16ae4e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca diff --git a/staging.usegalaxy.org.au/imaging.yml b/staging.usegalaxy.org.au/imaging.yml index 9af6bccc9..89b30b86d 100644 --- a/staging.usegalaxy.org.au/imaging.yml +++ b/staging.usegalaxy.org.au/imaging.yml @@ -2,8 +2,8 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 0c777d708acc - 81f0cbca04a7 + - 0c777d708acc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction @@ -34,8 +34,8 @@ tools: owner: imgteam revisions: - f3360fbeda64 - - b07f4839ca77 - 10eed33aa9b2 + - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -81,8 +81,8 @@ tools: - name: cp_display_data_on_image owner: bgruening revisions: - - 6a7da2e5f696 - 2484086dee41 + - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features @@ -95,8 +95,8 @@ tools: - name: cp_export_to_spreadsheet owner: bgruening revisions: - - d0178bdcd00e - f8fa0f6718a3 + - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color @@ -123,29 +123,29 @@ tools: - name: cp_mask_image owner: bgruening revisions: - - b178453ea8d1 - 3a05117669cf + - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - a1a961c46d4b - ac5bea85a391 + - a1a961c46d4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 20dbb1f7ec7b - 91e03287f285 + - 20dbb1f7ec7b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - 5499dc6f8ac1 - 8536b1ae0254 + - 5499dc6f8ac1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality @@ -158,22 +158,22 @@ tools: - name: cp_measure_object_intensity owner: bgruening revisions: - - 407925835dd9 - 980aed9e8fd5 + - 407925835dd9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - acf3aa487283 - 79e10d12d90a + - acf3aa487283 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - 035a58c7f54a - 80b200ae516b + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -192,8 +192,8 @@ tools: - name: cp_save_images owner: bgruening revisions: - - 33f4fa1413fb - 4ecf93628f97 + - 33f4fa1413fb tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -217,7 +217,7 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 8ad39f493587 - 22e573b7dcb1 + - 8ad39f493587 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/ivar.yml b/staging.usegalaxy.org.au/ivar.yml index 4df7a7355..ec8c09568 100644 --- a/staging.usegalaxy.org.au/ivar.yml +++ b/staging.usegalaxy.org.au/ivar.yml @@ -3,70 +3,70 @@ tools: owner: iuc revisions: - e4ee04da1c19 - - d6e72da3ec35 - e319b5b65879 - - 17f911830a8c - f362150bef41 - - 78bbd17d0703 + - d6e72da3ec35 - 3e4f434a69c6 + - 17f911830a8c - a38934e303b9 + - 78bbd17d0703 - 1069f6db0a0e tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 72ddd32392cd - - 7fe36019c073 - 8f8df367470d + - 72ddd32392cd + - c88553ec696e - f91cfb73d369 + - 0135f1d487a0 + - 9537184d421f - 2b95d5c04908 - 1ef5b6e3e09d - - c88553ec696e - - 9537184d421f - - 0135f1d487a0 + - 7fe36019c073 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - 2cf4a1cafc16 - fafb3d685fa9 - ad0dc9f4c9e2 + - 2cf4a1cafc16 - d7e79eb3bcb3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 43aac8d29685 - - 8c05afb547fa + - 6a1515bb0687 + - 94df24c6bc00 - 3d18f8c3c0f6 + - 43aac8d29685 - bd2a7d1316b9 - - 69797fa273c3 - - ee2beb764a7b - - 94df24c6bc00 - - 7f1cfa4c0e32 - ee29337f905c - - 8d36959b000d - 28a6f1908fcc + - ee2beb764a7b + - 8c05afb547fa - 9eaadf03e0df - - 6a1515bb0687 + - 8d36959b000d + - 7f1cfa4c0e32 + - 69797fa273c3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - db536ad45f28 - c092052ed673 - - 8858fa037a15 - 5d6ed46cc101 + - 364f4ffec275 - cb903c9dc33d + - 0893a1dbb807 + - 9f978da6528a - d37ede8589b2 - e3bb03cf207a - - 364f4ffec275 - - 9f978da6528a - - 0893a1dbb807 + - 8858fa037a15 + - db536ad45f28 - bcaa0d571ce2 - 5671e1d3d5ee tool_panel_section_label: iVar @@ -74,16 +74,16 @@ tools: - name: ivar_variants owner: iuc revisions: + - f95f403841ad + - 12d66d0d05ac - ed28dd32141c + - e1a015876aa9 - 49236b03e4fd - - 38b91a3190cd - - 584beffa972b - - 12d66d0d05ac - - 3b6a16d82c1b - c5c9f02b6167 - - e1a015876aa9 - 230b05597996 + - 38b91a3190cd - 045d6d00f606 - - f95f403841ad + - 584beffa972b + - 3b6a16d82c1b tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/join_subtract_and_group.yml b/staging.usegalaxy.org.au/join_subtract_and_group.yml index c821a9ba4..1ea917f35 100644 --- a/staging.usegalaxy.org.au/join_subtract_and_group.yml +++ b/staging.usegalaxy.org.au/join_subtract_and_group.yml @@ -4,16 +4,16 @@ tools: revisions: - b8a457820315 - f198773344e4 - - 0f1724dd59d2 - 17e3b698dd52 + - 0f1724dd59d2 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - ac092723240d - 22c2a1ac7ae3 - - 374cb875d38a - ba0c40780ecf + - ac092723240d + - 374cb875d38a tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/machine_learning.yml b/staging.usegalaxy.org.au/machine_learning.yml index a5366e7a8..21b328027 100644 --- a/staging.usegalaxy.org.au/machine_learning.yml +++ b/staging.usegalaxy.org.au/machine_learning.yml @@ -2,46 +2,46 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - f7ecdde4b201 - - 20cd4269deb2 - 772e0e89fc68 + - 20cd4269deb2 + - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - b9906ce4756c - 8a794e6d3388 - - 61a6132df9e0 + - f22a9297440f + - b9906ce4756c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: + - e1317b5502fa - b6ef6d0cb6b7 - f1b9a42d6809 - - 0af678661e20 - - e1317b5502fa - e29894cdea47 + - 818f9b69d8a0 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - 6fabdcde0214 - - 05143043ca13 - - 947c2eacccb8 - - a536d2736c2d - c80db5d6fd8c + - 947c2eacccb8 + - 05143043ca13 + - 1588f9076e32 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 83228baae3c5 - - 1552b8cb4a94 + - 9991c4ddde14 - 948eca2af157 - - 980bf31faa05 + - 1552b8cb4a94 + - 83228baae3c5 - 29e4122c90de tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -49,52 +49,52 @@ tools: owner: bgruening revisions: - 841a6cc5fc58 - - 1682df52c084 - - 1a53edc4b438 + - f3dfa4bdf87e - 315f01a9d2c2 - - 53616c8b0865 - a07ab242b0b5 + - 1a53edc4b438 + - 53616c8b0865 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 14f0ccc85505 + - 2fc89dcd41c8 - 40f4447733b2 + - 927586a18553 - dc4b5fd604a6 - - c648d0716fb0 - 91c4e3331208 - - 2fc89dcd41c8 + - c648d0716fb0 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: + - 1ddf415cb349 - e5a5ad882f1f - 301e07345c93 - 25ab6b4e376e - - d37a7f17e35d + - 36e8d6d5d01b - c6ae57f774c6 - - 1ddf415cb349 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - b7c3e9a3b954 - - fa9d6a4d95ad - f9639b488779 - 4ed102b922cb + - 0630258dcf35 - 02d2be90dedb - - 6d23883e0b94 + - fa9d6a4d95ad + - b7c3e9a3b954 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - ec69cbe34b73 - - 2d53571c2f00 - 14180f9c831e + - ec69cbe34b73 - a4f18bbb4eca + - 61634a87efc7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/mapping.yml b/staging.usegalaxy.org.au/mapping.yml index 834412417..f5f6b4bd0 100644 --- a/staging.usegalaxy.org.au/mapping.yml +++ b/staging.usegalaxy.org.au/mapping.yml @@ -2,15 +2,15 @@ tools: - name: bowtie2 owner: devteam revisions: - - 03e9b2fbc005 - - cd659e8cc5fa + - f6877ad76b00 + - 937aa69e715f + - 017aba02828d - 749c918495f7 - - 17062a0decb7 - a6d65b0c67af - - 937aa69e715f + - cd659e8cc5fa + - 17062a0decb7 + - 03e9b2fbc005 - 3ba8d4563129 - - 017aba02828d - - f6877ad76b00 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -28,10 +28,10 @@ tools: - name: bwa owner: devteam revisions: - - 53646aaaafef + - e188dc7a68e6 - 64f11cf59c6e - 3fe632431b68 - - e188dc7a68e6 + - 53646aaaafef - dfd8b7f78c37 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -44,41 +44,41 @@ tools: - name: lastz owner: devteam revisions: + - 2ff111fac1d7 - 3e1ea2facca6 - 60afcc2c1d05 - 37b497aa133f - - 2ff111fac1d7 - e7f19d6a9af8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 09b53c1d4ab1 - - 11a0d50a54e6 - - b3eab4b67562 - - 3f4d6399997b - - 8c6cd2650d1f - - 037c6e54df11 - - 77b2770508f6 - 6b1e195506a3 - - f54f5baedfdd + - 037c6e54df11 + - b3eab4b67562 - 53c0b7a1a0c3 - be1d967337e4 - c0c2d0941de8 + - 8c6cd2650d1f + - f54f5baedfdd + - 3f4d6399997b + - 77b2770508f6 + - 09b53c1d4ab1 + - 11a0d50a54e6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 79b885ce78d7 - - e403d27e8f24 + - 00fbfac99d39 + - 9ee34ba73ebf - 13022c3d3076 + - e403d27e8f24 + - 79b885ce78d7 - 178bdbdb6d24 - b8f5f6e87f5c - ec9cbd6b9a49 - - 9ee34ba73ebf - - 00fbfac99d39 - 1cd2511a396e tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/metagenomic_analysis.yml b/staging.usegalaxy.org.au/metagenomic_analysis.yml index 55797def1..04594e0dc 100644 --- a/staging.usegalaxy.org.au/metagenomic_analysis.yml +++ b/staging.usegalaxy.org.au/metagenomic_analysis.yml @@ -2,8 +2,8 @@ tools: - name: cat_bins owner: iuc revisions: - - 18676df0cb3a - 0094893f5001 + - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -34,89 +34,89 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 76d3d2b10738 - 63f86089423e - 5b5a7af9fbb4 + - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - 1c35dadbe76f - - 18a502a9d287 - 84fd33a60b35 - 96336c6a2bb7 + - 18a502a9d287 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - a9f4a217dcd6 + - addaf9d22850 - f732237754fc - 34e55239e68b - - addaf9d22850 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 75403243703a - - 8c202e741d68 - 0776d824d896 + - 75403243703a - 04c15826a0b8 + - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 1c9b3bcd4261 - - e96bbb9e24ea - 43c99742158b + - e96bbb9e24ea + - 1c9b3bcd4261 - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: + - 5c865a382933 - 84743da21318 - - 306a40d4bb8f - 1d75bd0595e2 - - 5c865a382933 + - 306a40d4bb8f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: + - 78faebd0879c - ac72310b038a - - 8daf4564ccda - 555ccac8a4c5 - - 78faebd0879c + - 8daf4564ccda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: + - a58e4a43f49c - d60df8727f59 - 7b8cb2b02978 - - a58e4a43f49c - f947b4bb5107 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 1bc3657cd694 - - 7f3b59dee073 - 04144473e59e + - 7f3b59dee073 + - 1bc3657cd694 - 7136e9ab70db tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 19299bb1c6af - d943081510da - 0a1224c4b781 + - 19299bb1c6af - 9058d8943303 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -130,8 +130,8 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - 6501b5b33988 - c4db8c4de66f + - 6501b5b33988 - dbf1798c0dcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -145,9 +145,9 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: + - 6d364c65c946 - 6c84982ee6f7 - 654548ae1357 - - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -160,23 +160,23 @@ tools: owner: iuc revisions: - e66ab198ec15 - - bd7a9c6efb10 - 6aad8ca3918b + - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - b084117133af - - d77397f09da1 - c6676a890f50 + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - 9704f1a3b32d - 7f208f1eb64f + - 9704f1a3b32d - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -189,17 +189,17 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - 31c6d107e7a5 - c409a495841f - 79706f10d680 + - 31c6d107e7a5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 71ea608ddfa3 - 172920f67a84 - 714d5a28cc5c + - 71ea608ddfa3 - d24841f5c3d2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -207,39 +207,39 @@ tools: owner: iuc revisions: - a293a742194f + - 4137b492233e + - 12fb63b5f63f - a4d7148ccee4 - d7e9a3c41657 - - 12fb63b5f63f - - 4137b492233e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: - - 97f7bb0851e7 - 6fcb8ac37a3e - - cf87759761eb - 75bedfb2078b - - 64bc7acc22a9 - e2c71b852aba + - 97f7bb0851e7 + - 64bc7acc22a9 + - cf87759761eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: + - 4033827c76b8 - 5e5a999ffaa9 - - 080ea153677c - c82508e76ad1 - - 4033827c76b8 - 2d35528d2141 + - 080ea153677c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: + - 6b7622dda516 - 95bf7479d53c - 2cd76b089570 - - 6b7622dda516 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -305,8 +305,8 @@ tools: - name: kraken2 owner: iuc revisions: - - e674066930b2 - 4a9da2b6c2e3 + - e674066930b2 - 328c607150ff tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -319,15 +319,15 @@ tools: - name: kraken_filter owner: devteam revisions: - - 3d6570bffdb1 - 5bee9adae474 + - 3d6570bffdb1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 1902d3de4a4f - 6c09bed3444f + - 1902d3de4a4f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -339,8 +339,8 @@ tools: - name: kraken owner: devteam revisions: - - aec58624706f - 8ba2174315aa + - aec58624706f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2krona @@ -371,18 +371,18 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 2cff76cf35c6 - 4fd3b5d8706b - 0270541aaf46 - - e073891b2afc + - 2cff76cf35c6 - 27250f92a01a + - e073891b2afc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 708abf08a626 - 76bc4efa1aeb + - 708abf08a626 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -448,20 +448,20 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - ebb74774457e - fdbd63e92b01 + - ebb74774457e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - 2131d7dca455 - - b89b0765695d - - ff8f55893e7d - - 6dee4abadccb - a16313517e55 + - 2131d7dca455 - a92a632c4d9b + - b89b0765695d - 1a6cdf55390f + - 6dee4abadccb + - ff8f55893e7d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -533,8 +533,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 9168545e09df - 0ba7dfaa941d + - 9168545e09df tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -583,13 +583,13 @@ tools: - name: staramr owner: nml revisions: + - be818ae858e4 + - 4b9a8031ab74 + - 141afacabcfa - 3b22de20bd4b - - 2fd4d4c9c5c2 - aeaa20b96ef2 - 4d83eccf5f81 - - be818ae858e4 - - 141afacabcfa - - 4b9a8031ab74 + - 2fd4d4c9c5c2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus diff --git a/staging.usegalaxy.org.au/mothur.yml b/staging.usegalaxy.org.au/mothur.yml index 1aef0a352..3a4bc2787 100644 --- a/staging.usegalaxy.org.au/mothur.yml +++ b/staging.usegalaxy.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - de3cfb122105 - 12e856482d26 + - de3cfb122105 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - ab12df91b47f - 4e9136c2c4c3 + - ab12df91b47f tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - f4d7d5755f01 - 63b74bfc8052 + - f4d7d5755f01 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - 67cb43432196 - e866e31f6da3 + - 67cb43432196 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual diff --git a/staging.usegalaxy.org.au/multiple_alignments.yml b/staging.usegalaxy.org.au/multiple_alignments.yml index 26e7f16a3..2bdecc9da 100644 --- a/staging.usegalaxy.org.au/multiple_alignments.yml +++ b/staging.usegalaxy.org.au/multiple_alignments.yml @@ -2,37 +2,37 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - a74dbfee5a86 - - 9baa871cb1d1 - - cd07731e4434 - - 9422c5a87ee2 - 9eeb13a92d79 + - 80f03df2e2ce - 94b8c6013083 + - 9baa871cb1d1 + - 48c13389050d + - cd07731e4434 - 2263989660f5 - - 80f03df2e2ce - 6ae5a7b5a0a2 - - bdfbaf0c10aa - - 48c13389050d - 8b67dd48fec1 + - 9422c5a87ee2 + - bdfbaf0c10aa + - a74dbfee5a86 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - fc2e49f91e52 - c18157c68134 + - fc2e49f91e52 + - f0af8936ed41 + - 4a60927aaca5 + - '764845535798' - 5abf2c2249aa - - d390fe1567dc + - f14193ec1f50 - d7ce0ec78e51 + - 3ff17bad4006 + - aaa0d6a8b808 + - d390fe1567dc + - bc3831dd65c1 - 2e093badc689 - be78f13134e2 - - f0af8936ed41 - - bc3831dd65c1 - - aaa0d6a8b808 - - f14193ec1f50 - - '764845535798' - - 4a60927aaca5 - - 3ff17bad4006 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -44,8 +44,8 @@ tools: - name: chromeister owner: iuc revisions: - - e483be1014b6 - b768cc4cca40 + - e483be1014b6 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -64,18 +64,18 @@ tools: - name: mafft owner: rnateam revisions: - - f0d493f8f84f + - 15974dd17515 - f1a5908ea2cb + - f0d493f8f84f - c5908940967d - a65296ffb4a0 - - 15974dd17515 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - b3acbb3a6af0 - fbca557a4847 + - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff @@ -88,8 +88,8 @@ tools: - name: mummer_mummer owner: iuc revisions: - - bcd65de9725b - 48823c9635a4 + - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot @@ -102,14 +102,14 @@ tools: - name: mummer_nucmer owner: iuc revisions: - - e18267f90096 - 636b049e6141 + - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - 959c1f8dae95 - b4124df98b26 + - 959c1f8dae95 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/nanopore.yml b/staging.usegalaxy.org.au/nanopore.yml index d6a92a0b5..4d08626c6 100644 --- a/staging.usegalaxy.org.au/nanopore.yml +++ b/staging.usegalaxy.org.au/nanopore.yml @@ -8,10 +8,10 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - a7228a7ea146 - - 72b5e9dda577 - fc8804320156 - 79e9a869f40e + - 72b5e9dda577 + - a7228a7ea146 - cb34f00cc10f - 0e9e7fcdd543 tool_panel_section_label: Nanopore @@ -19,25 +19,25 @@ tools: - name: medaka_consensus owner: iuc revisions: - - db25ec99c3ea - - fa11aa8103b2 + - 682d1e2c8be4 - d6cddc06aeae + - fa11aa8103b2 - 18505fe2bdb1 - - 682d1e2c8be4 + - db25ec99c3ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: - - eb746fa6f514 + - 222669c4afb6 - 2bf63b38ee9b + - ec699520444c + - eb746fa6f514 + - edf6d4003fad + - 0f5f4a208660 - 43815fa60f3a - 19f3b583a9b3 - - 222669c4afb6 - cc36773a3681 - - ec699520444c - - 0f5f4a208660 - - edf6d4003fad tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -56,31 +56,31 @@ tools: - name: nanoplot owner: iuc revisions: - - a3c4fe6f49ab - - 645159bcee2d - edbb6c5028f5 - 0f1c34698076 + - 645159bcee2d + - a3c4fe6f49ab tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 85a394edc247 - d219b6d8158a + - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - be95355fef8d - a8d4be409446 + - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 449e9aeded2d - d376944466bf + - 449e9aeded2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants @@ -94,8 +94,8 @@ tools: owner: iuc revisions: - 5f76b20953e5 - - 543cbeef3949 - 93d623d9979c + - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events @@ -127,8 +127,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 336791b5665f - 338d15b8d6fb + - 336791b5665f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -140,15 +140,15 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 4fe6b96aff72 - 2e22ebec211a + - 4fe6b96aff72 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle owner: iuc revisions: - - ce8af9373061 - 34553d0caa5e + - ce8af9373061 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/staging.usegalaxy.org.au/none.yml b/staging.usegalaxy.org.au/none.yml index 015ddfeb8..a7aac49ac 100644 --- a/staging.usegalaxy.org.au/none.yml +++ b/staging.usegalaxy.org.au/none.yml @@ -53,16 +53,16 @@ tools: owner: iuc revisions: - d74850cf4e42 - - 3e73c97f025d - adfd6bf710bd + - 3e73c97f025d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: + - 83da94c0e4a6 - 9dd107db92c2 - 1586b111d2a3 - - 83da94c0e4a6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -143,16 +143,16 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 6287d0ee459e - 9a40272f56d0 + - 6287d0ee459e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 5bcf0e24f42c - b4b2b284230a - 172815da3d41 + - 5bcf0e24f42c - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -165,8 +165,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d74c740bdb25 - d210e1f185bd + - d74c740bdb25 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -178,9 +178,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - fea85c467896 - - 87febc68b45b - 19bbd19b74b3 + - 87febc68b45b + - fea85c467896 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -211,9 +211,9 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 4ba60cb14cb0 - - 5fe20c915fa6 - 9c43baa60906 + - 5fe20c915fa6 + - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -225,26 +225,26 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: + - 0db22932bc39 - aec831b54a5b - 9d09724f2bf1 - - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - df30a2f1db55 - - ed7a967cb11b - 6e24e79d3d69 + - ed7a967cb11b + - df30a2f1db55 - 29c738066906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - ad90c2da4f38 - - 3e4d45aca422 - 1865e693d8b2 + - 3e4d45aca422 + - ad90c2da4f38 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff @@ -263,17 +263,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - c520a52b5174 - d63c1442407f - 64deddb6a8ec + - c520a52b5174 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - 9946bc39c834 - - 625fd9476402 - 94a50db37d1a + - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1031,9 +1031,9 @@ tools: - name: rdock_rbdock owner: bgruening revisions: + - a22969b08177 - e4b7d1507a75 - c362398df83b - - a22969b08177 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes diff --git a/staging.usegalaxy.org.au/phylogenetics.yml b/staging.usegalaxy.org.au/phylogenetics.yml index 62e1b3b99..e2c1c9201 100644 --- a/staging.usegalaxy.org.au/phylogenetics.yml +++ b/staging.usegalaxy.org.au/phylogenetics.yml @@ -33,44 +33,44 @@ tools: - name: hyphy_absrel owner: iuc revisions: + - 8834daeb9892 + - f04a1264e2a2 + - 5a7c56a5cc08 + - a6619171428e + - cce7b18495e4 + - d7c7ef3353fe - d033ffc1c161 - - 3f59ebfbfe3d - - '841557158611' - 26de3a7b1cb9 - - 5a7c56a5cc08 - - 81e66674859e - 3b8b5bde0bd9 - - b89cac5156ec - - cce7b18495e4 - - f73435dc282b + - 81e66674859e - 107d3ba7024a - - d7c7ef3353fe - - a6619171428e - - f04a1264e2a2 + - 3f59ebfbfe3d - 6a457678efcb - - 8834daeb9892 + - f73435dc282b + - b89cac5156ec - c78f3d7dd1db + - '841557158611' tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 659517798cc4 - - 88c4aa435ded - - df47d4845b62 - - 5b777002c2de - - aa8cc71438cf + - 3b96e92e8ec3 - 6223845127ea - - 02b8758214b0 - - 4755f52427c4 - - 6a726db04d4b - - 7a2092844346 + - df47d4845b62 - 5fcd1ece3a6e - e75442c7f4da - - b0af57c1a968 + - 4755f52427c4 - a185b079b095 - - 3b96e92e8ec3 + - 7a2092844346 + - 5b777002c2de + - 88c4aa435ded + - b0af57c1a968 + - aa8cc71438cf - 6283babe736e + - 659517798cc4 + - 02b8758214b0 + - 6a726db04d4b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree @@ -79,41 +79,41 @@ tools: - 524d31add34a - f97743d52b87 - b8476e82ac20 - - 9b892d7f82cc - d1c340a5664b + - 9b892d7f82cc tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - 128ba8da994f + - daddf188c13f - feb40665d7cd - 9e10ba792be2 - - daddf188c13f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - 81804a978fc0 - - 03ed9524dcd1 - - 2fa9d4f1b48f - - b6abccb1f25b - - ca0d8cf80567 + - ca337cce3888 + - 5f8727ff21e7 - 437e28791761 - 9d61d3fa046c - - 83a69484cb87 + - 36912871ccdc - 7bb8726be37c - - a2099fb98cdb - - 2f1019071464 - - 5f8727ff21e7 - 14ae456b8cc5 - - 36912871ccdc - - 3a43c3982401 - - ca337cce3888 - - b7e297c2ede6 - abf6dbe8c9d7 + - ca0d8cf80567 + - 81804a978fc0 + - 3a43c3982401 + - 83a69484cb87 + - a2099fb98cdb + - 2f1019071464 - 42a174224817 + - b6abccb1f25b + - b7e297c2ede6 + - 2fa9d4f1b48f + - 03ed9524dcd1 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -125,21 +125,21 @@ tools: - name: raxml owner: iuc revisions: - - 73a469f7dc96 - ea30d3089354 - - a4b71be30c3c - - 29ff6a849eac - ba29b5e2a4be + - 29ff6a849eac + - a4b71be30c3c + - 73a469f7dc96 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - e88a7de55d6e - - 15ac71df11a0 - - f1ccc8a6eb05 + - dbe2b2204555 - 91887494eb97 + - f1ccc8a6eb05 + - e88a7de55d6e - 809e42326fc2 - - dbe2b2204555 + - 15ac71df11a0 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/picard.yml b/staging.usegalaxy.org.au/picard.yml index 848e76a6f..4de5a9bfb 100644 --- a/staging.usegalaxy.org.au/picard.yml +++ b/staging.usegalaxy.org.au/picard.yml @@ -2,13 +2,13 @@ tools: - name: picard owner: devteam revisions: - - a1f0b3f4b781 - fc288950c3b7 - - f9242e01365a - - f6ced08779c4 - 7d34178f2812 - b502c227b5e6 - 881d7645d1bf + - f6ced08779c4 - 1aac2a13842a + - a1f0b3f4b781 + - f9242e01365a tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/proteomic_ai.yml b/staging.usegalaxy.org.au/proteomic_ai.yml index 29c8c8198..c634228c2 100644 --- a/staging.usegalaxy.org.au/proteomic_ai.yml +++ b/staging.usegalaxy.org.au/proteomic_ai.yml @@ -2,13 +2,13 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - c0e71cb2bd1b - - 7fbec959cf2b - - 3bd420ec162d - eb085b3dbaf8 - - d00e15139065 - - ca90d17ff51b - a58f7eb0df2c + - d00e15139065 + - 3bd420ec162d + - 7fbec959cf2b - 5b85006245f3 + - c0e71cb2bd1b + - ca90d17ff51b tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/proteomics.yml b/staging.usegalaxy.org.au/proteomics.yml index 2090ab662..aa995dc64 100644 --- a/staging.usegalaxy.org.au/proteomics.yml +++ b/staging.usegalaxy.org.au/proteomics.yml @@ -2,21 +2,21 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - b574b84afc4d - f28ad96b76dc - - b18329a8ac14 - ece627528a78 - - 277dc652246e - 0a18ac48ac53 + - 277dc652246e + - b574b84afc4d + - b18329a8ac14 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - e988563cc6e5 - - 525f201b86c1 - - e215f71d7983 - bf06d196e23d + - e215f71d7983 + - 525f201b86c1 - b41107d8fe89 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -24,8 +24,8 @@ tools: owner: galaxyp revisions: - 8da3511c9467 - - bb6397b94018 - 4fbffddde8cd + - bb6397b94018 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering @@ -33,28 +33,28 @@ tools: revisions: - f23d67e28cc8 - b8c79e70516d - - a8157342d9a3 - 528fb09022be + - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - 80600735685d - - a69865da6f80 - - 25b83cbd596a - a95a82eb4d50 - 59e85306eae5 + - a69865da6f80 + - 25b83cbd596a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 798da6bdff3d - ed9ed1e6cca2 - - e0669b1854b1 - - 611d80c0e29d - f1897eb07081 + - 611d80c0e29d + - 798da6bdff3d + - e0669b1854b1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report @@ -69,18 +69,18 @@ tools: owner: galaxyp revisions: - cc430977c8ff - - df2187f9013b - 82f6c2f4332d + - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - c5aa9fca18c6 - - 043f9c91f686 - - 10566783d718 - 1693b2126f30 - d2483487e077 + - 10566783d718 + - 043f9c91f686 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -98,6 +98,7 @@ tools: - name: diann owner: galaxyp revisions: + - ae4dc0c041f9 - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -117,9 +118,9 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: + - 4081e4faa4ab - 0fa397f4f40b - 1c5cbf8f79ce - - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -131,8 +132,8 @@ tools: - name: encyclopedia_walnut owner: galaxyp revisions: - - d6a4dfdad269 - ce1a157a41bd + - d6a4dfdad269 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -144,8 +145,8 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - e66f552a3c47 - d286ff4600dd + - e66f552a3c47 - 160538a890a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -159,48 +160,48 @@ tools: - name: maxquant_mqpar owner: galaxyp revisions: - - 9cb7dcc07dae - 3fc2116ac6d9 + - 9cb7dcc07dae tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - f522c08e900c + - 97a7f34fcb6a + - 4d17fcdeb8ff - 8934bc76bb52 - 1f39c833f65f - - 4d17fcdeb8ff - - 37d669de2828 - - 2133b0be850a - - 97a7f34fcb6a - e42225f8a659 - - 7f432d87c82c - 837224ad1694 + - 2133b0be850a + - 7f432d87c82c + - 37d669de2828 + - f522c08e900c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - - 0ed07016d668 - - a72ac2c7cc5b - 85b8866f06d7 - '860429737408' + - a72ac2c7cc5b + - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: + - 352b37c66d97 - 1974224d63c2 - 990b4560ead7 - 4187b6df1a40 - - 352b37c66d97 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - a1daafbf5233 - deaf035bbe9f + - a1daafbf5233 - 99450519d727 - 4f359549383c tool_panel_section_label: Proteomics @@ -208,27 +209,27 @@ tools: - name: metaquantome_sample owner: galaxyp revisions: + - 40ca115438d2 - e79958768a2c - c1343e3389ca - c7745841de24 - - 40ca115438d2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: + - da986f83631b - b648e45fd3cf - d2eac53666f0 - - da986f83631b - d46d64e7964d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 1199751329b0 - 9bf325045235 - eb811f3018ea + - 1199751329b0 - 944b43462104 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -247,10 +248,10 @@ tools: - name: msstats owner: galaxyp revisions: - - 593839e1f2c3 - - 28434abe6c5c - - 8212e342e482 - b7034eff0db1 + - 8212e342e482 + - 28434abe6c5c + - 593839e1f2c3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -277,42 +278,42 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 9cdf15d3cfc8 - f7fef900f5b2 - - c9eff69a7c62 - 518b1730cf2a + - 9cdf15d3cfc8 + - c9eff69a7c62 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - ca88bd28f116 - - 5e948629bc73 - dff6c756eee5 + - 5e948629bc73 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 41859bbdc16e - 890025d6e426 + - 41859bbdc16e - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 5ad0b5bf1deb - 6634cad7d797 - 9b7977080f6d + - 5ad0b5bf1deb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: + - d6878d27f051 - 05d5e1ddc985 - 0bb5056cb775 - - d6878d27f051 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo @@ -326,16 +327,16 @@ tools: - name: openms_filemerger owner: galaxyp revisions: - - 39e8fde08881 - 27cba4c5fc42 + - 39e8fde08881 - 92352a475eed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 0efbc235f314 - 9e26f5c770f8 + - 0efbc235f314 - d413dc49d650 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -350,17 +351,17 @@ tools: - name: openms_idfilter owner: galaxyp revisions: - - 382cde407f81 - - c55dddc5844a - c427a8628cbe + - 382cde407f81 - ca799a7246e7 + - c55dddc5844a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - 39caaa778d2e - 8ddb7bab1138 + - 39caaa778d2e - b5d0905419da tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -368,17 +369,17 @@ tools: owner: galaxyp revisions: - 1c5f31b8d632 - - 18f93351f8b6 - f817513840a9 - 8d4db262964c + - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - c69f69d7867a - - 5d9f175dff81 - 111c3a00136d + - 5d9f175dff81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher @@ -392,8 +393,8 @@ tools: - name: openms_msfraggeradapter owner: galaxyp revisions: - - e133b5c8878f - 9866e1170611 + - e133b5c8878f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter @@ -422,8 +423,8 @@ tools: - name: openms_openswathanalyzer owner: galaxyp revisions: - - 0ced5bc9f4dd - a2a6e9551046 + - 0ced5bc9f4dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator @@ -450,8 +451,8 @@ tools: - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - 0bddef8d144e - d4396637b9f5 + - 0bddef8d144e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter @@ -464,15 +465,15 @@ tools: - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - f9ed7e074900 - 05ec9fb05ed1 + - f9ed7e074900 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 6e8cc5ed2a9b - 18826fb8e5db + - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow @@ -485,18 +486,18 @@ tools: - name: openms_peakpickerhires owner: galaxyp revisions: + - 5ae104d0da6e - 3d8d4ada5405 - decc397c3b7e - - 5ae104d0da6e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - e039cc5c7aed - 539a3a4dcc9e - - 5182338d5e7c - dd173849c3d8 + - e039cc5c7aed + - 5182338d5e7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier @@ -529,15 +530,15 @@ tools: owner: galaxyp revisions: - fb52e95a370c - - c8b225c69a7f - 7f6a1f27553e + - c8b225c69a7f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - a6282baa8c6f - 073a2965e3b2 + - a6282baa8c6f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptide_genomic_coordinate @@ -550,14 +551,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - 1beff3ddce58 - - 943a34df6047 - - 7fdd9119cc4f - - 3634c90301af - 3ec27b4cee7c + - 3634c90301af + - 1beff3ddce58 - 07ff622ec007 - a72c48001f7c - da885ca16cb2 + - 943a34df6047 + - 7fdd9119cc4f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -611,10 +612,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 1a5690a5eedc - - 12692567c7f9 - 265c35540faa - a371252a2cf6 + - 12692567c7f9 + - 1a5690a5eedc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/staging.usegalaxy.org.au/rad_seq.yml b/staging.usegalaxy.org.au/rad_seq.yml index 853b41d93..abc2efe8e 100644 --- a/staging.usegalaxy.org.au/rad_seq.yml +++ b/staging.usegalaxy.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: + - 110a346daf36 + - 42201b90e3f4 - 289b7d6b69a4 - e345aadf914f - - 2f1d464ebfd2 - cd5f98911089 - - 110a346daf36 - - 42201b90e3f4 + - 2f1d464ebfd2 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -19,12 +19,12 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - 0345dbaaa79b - - fcce77c09289 - - 42d9087b4789 - 0cd2df8af811 - c207119ba5f6 + - 42d9087b4789 - 8501601a118d + - fcce77c09289 + - 0345dbaaa79b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: - - ad5ab22ffe24 - - 33486216eec0 - - 405a212b32ab - - 04db7fd6b238 - 89eb29319bf4 - 421c33b8bf17 + - 405a212b32ab + - 33486216eec0 + - 04db7fd6b238 + - ad5ab22ffe24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -53,12 +53,12 @@ tools: - name: stacks2_gstacks owner: iuc revisions: - - fa51dc5e8386 - - 7370bb65bad4 - - 7b72fde3d27e - - f6e91108b7b1 - 1d839ead7ad3 + - f6e91108b7b1 - eb784fa07f80 + - 7370bb65bad4 + - 7b72fde3d27e + - fa51dc5e8386 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -70,12 +70,12 @@ tools: - name: stacks2_kmerfilter owner: iuc revisions: + - 8a55d29c8fcf - d30e36c48c93 - - a3e86cd9cac7 - 1544278c272e + - a3e86cd9cac7 - c9b77ced9a78 - 3d70c2996730 - - 8a55d29c8fcf tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -87,12 +87,12 @@ tools: - name: stacks2_populations owner: iuc revisions: - - 7b881f5f5ad5 - - 564c33e5c3e3 - a5969aa9347e - 887cf585cafc - - b242deb58952 - e2db212d64ad + - b242deb58952 + - 564c33e5c3e3 + - 7b881f5f5ad5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -105,10 +105,10 @@ tools: owner: iuc revisions: - e897c74a48bb - - bd5ff77e2036 - b4bab607eb05 - - 8cff84759bf6 - 9a171f9a450b + - bd5ff77e2036 + - 8cff84759bf6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: + - 6dafad990086 - 5e10f396979e - - adc7a7610d4f - 4f65e343ecdf - - 887e0991eb24 - 33f0793edf93 - - 6dafad990086 + - adc7a7610d4f + - 887e0991eb24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -139,10 +139,10 @@ tools: revisions: - 4e280b27a831 - 97575d01f06b - - 17d39bf0a63a - - c5d7050e4ad7 - c287418eb288 + - 17d39bf0a63a - 43e3eeb2e0ec + - c5d7050e4ad7 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,12 +154,12 @@ tools: - name: stacks2_sstacks owner: iuc revisions: - - a819ec3b362d - - 0b8c84a7fdb5 - - 9586f08634c0 - - cd034465d4a4 - 09b8edb56d80 + - 9586f08634c0 - d9bf483266a1 + - 0b8c84a7fdb5 + - cd034465d4a4 + - a819ec3b362d tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -171,12 +171,12 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: - - a4b4bd84f69e - 2645575d1bf2 + - a9c34a289493 - 69842dd5aa48 - - 95351dd0fd3f + - a4b4bd84f69e - bf0e43ab0416 - - a9c34a289493 + - 95351dd0fd3f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -189,11 +189,11 @@ tools: owner: iuc revisions: - cfb504394ae1 + - 912f904a6e1e - 8a35a3bc6752 + - bb0475c884ff - d033e1ccb386 - - 912f904a6e1e - d1fda11e602f - - bb0475c884ff tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks diff --git a/staging.usegalaxy.org.au/rna_seq.yml b/staging.usegalaxy.org.au/rna_seq.yml index 6ab90ffb1..c84eb94c7 100644 --- a/staging.usegalaxy.org.au/rna_seq.yml +++ b/staging.usegalaxy.org.au/rna_seq.yml @@ -2,15 +2,15 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 31f8063eedea - 2d4e3aff9dc7 + - 31f8063eedea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 125d20cb23d7 - 32e542c2a773 + - 125d20cb23d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -46,23 +46,23 @@ tools: - name: cuffcompare owner: devteam revisions: - - e66b9b5b8580 - f648e5180e40 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: - - d080005cffe1 - e04dbae2abe0 + - d080005cffe1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - - cf747d1bd79a - 6a6717a5f421 - 86285ddd4512 + - cf747d1bd79a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -100,9 +100,9 @@ tools: owner: iuc revisions: - 8f0181aacb7a - - 0693ccd171c4 - - e3b16fd7dd08 - 3b36efd62b3e + - e3b16fd7dd08 + - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -114,13 +114,13 @@ tools: - name: deseq2 owner: iuc revisions: - - 9a882d108833 - - 8fe98f7094de - d027d1f4984e - - 6a3a025714d3 - cd9874cb9019 + - 6a3a025714d3 - 24a09ca67621 - 0696db066a5b + - 9a882d108833 + - 8fe98f7094de tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -133,9 +133,9 @@ tools: owner: iuc revisions: - b47c006d90c5 + - 62adf13b86ea - df929f257179 - 2872c633f07e - - 62adf13b86ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -147,20 +147,21 @@ tools: - name: edger owner: iuc revisions: - - a8305cf0c951 - - df0c8d0a5992 + - 3d89af8a44f0 + - 0cb907a2a810 + - 9bdff28ae1b1 - 6e53e565fc6a - 555659de7321 - - 334ce9b1bac5 - - 9bdff28ae1b1 - - 3d89af8a44f0 - f2843df56434 + - df0c8d0a5992 + - a8305cf0c951 + - 334ce9b1bac5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - a8305cf0c951 + - 0cb907a2a810 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -185,16 +186,16 @@ tools: - name: featurecounts owner: iuc revisions: - - 6f66ae7c5f7a - - f3a5f075498f - - 90d16db017d7 + - e6a2a912677a - a37612abf7f9 + - f3a5f075498f + - a56fbe2d6ba7 + - 6f66ae7c5f7a - 38b6d12edc68 - af814359d244 - - a56fbe2d6ba7 - - 7db9d3ea71c9 - ea04b737afa0 - - e6a2a912677a + - 7db9d3ea71c9 + - 90d16db017d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -238,12 +239,12 @@ tools: - name: hisat2 owner: iuc revisions: - - d4b55e2beb12 - - 6c19daec423d - - 3fb01a8c902d - 6ab42baa56e9 + - d4b55e2beb12 - f4af63aaf57a - 26371a1df031 + - 3fb01a8c902d + - 6c19daec423d - a86e80d3c09c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -281,10 +282,10 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 87c11c05d238 - ce5d418183c5 - 01247aaf0a10 - 1c75aa5de15e + - 87c11c05d238 - 5ae5c312d718 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -298,8 +299,8 @@ tools: owner: iuc revisions: - c971db6f0fe5 - - 10c98fab6c5a - 40985510cd98 + - 10c98fab6c5a - 4f9c4e6566e5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -312,13 +313,13 @@ tools: - name: limma_voom owner: iuc revisions: - - 32511f586472 + - 0921444c832d + - 708348a17fa1 - d6f5fa4ee473 - 58c35179ebf0 - - 0921444c832d - 97e06a4c7c75 + - 32511f586472 - e827f9aae031 - - 708348a17fa1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -336,8 +337,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_mapper @@ -379,18 +380,18 @@ tools: - name: rgrnastar owner: iuc revisions: - - 99b17b74a8cd - - c7c55b694974 - - 7ed2edc1337f - - 4074fc1940e2 - 0a563fd2f22e - - 5ec75f5dae3c - - 3ea5a2a63fa2 - - c772497b2c32 - - e132e7d02a3e - - b9e04854e2bb - 980d2a2e1180 - 4df95e2d7f61 + - c772497b2c32 + - 3ea5a2a63fa2 + - b9e04854e2bb + - e132e7d02a3e + - 5ec75f5dae3c + - 7ed2edc1337f + - c7c55b694974 + - 99b17b74a8cd + - 4074fc1940e2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -414,13 +415,13 @@ tools: - name: salmon owner: bgruening revisions: - - e3d32471da11 - - 53e9709776a0 - - 49121db48873 - - 2c0ca397d302 - cc05793bb896 - ebab418107f5 + - 53e9709776a0 - 15cd64d7c58b + - 2c0ca397d302 + - 49121db48873 + - e3d32471da11 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -433,21 +434,21 @@ tools: owner: iuc revisions: - 8c28affc7c48 + - c0fd285eb553 - 56242ff81c84 - fab6ff46e019 - - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: + - 1ebd14235b92 + - 258d696dbd7e + - 914cfcba0ec8 - ae618321f34a - 76d290331481 - - cef79931dda5 - - 914cfcba0ec8 - dd4df992d93d - - 1ebd14235b92 - - 258d696dbd7e + - cef79931dda5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -477,10 +478,10 @@ tools: - name: transdecoder owner: iuc revisions: - - 0db979fead3a - - ffd1300599a1 - c6334cb383ff - d0d4cef4f967 + - 0db979fead3a + - ffd1300599a1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -493,8 +494,8 @@ tools: owner: iuc revisions: - bcc5f03f1900 - - ba3720d7e68b - d6a479fd4281 + - ba3720d7e68b - 74217fbfba4d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -508,8 +509,8 @@ tools: owner: iuc revisions: - 56162e446004 - - 2fb4ee002432 - c2b82a94493e + - 2fb4ee002432 - 478f36effca1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -551,11 +552,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 05ab8d5e04a2 - - 65e7dea767ea - - 33406f5a445c - c5fbddcac63a - 5192f657f305 + - 33406f5a445c + - 05ab8d5e04a2 + - 65e7dea767ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -568,9 +569,9 @@ tools: owner: iuc revisions: - 1fdb25a8384d - - a35cba31d904 - - e406ac71165d - 6f0fb35b799c + - e406ac71165d + - a35cba31d904 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -582,10 +583,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - 37a1129c89d2 - c2c039e421af - - 7c7fbf13aadd + - 37a1129c89d2 - 964b7efe2639 + - 7c7fbf13aadd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -597,10 +598,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: + - 24e94d84adc9 - 047c22569787 - 1d689e4e1caf - eafea3083352 - - 24e94d84adc9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -612,10 +613,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 1812dbc5bb7b - 9871104ea630 - 04bb8bb7c198 - 3a4ac03d1266 + - 1812dbc5bb7b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -627,15 +628,15 @@ tools: - name: trinity owner: iuc revisions: - - 9fa24d5aac68 - - 48636f857c4b - - 8f1c3df4dd49 - db1f362cca3e + - cee61b3fcf78 - d84caa5a98ad - d2bc35f3d1c5 - - c9cfec002f71 - - cee61b3fcf78 - 32b86cd8eb50 + - 8f1c3df4dd49 + - c9cfec002f71 + - 48636f857c4b + - 9fa24d5aac68 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -647,10 +648,10 @@ tools: - name: trinotate owner: iuc revisions: + - 6fd16fad465d - 4383070d29ed - 9e61bc67866f - 2b093007fab9 - - 6fd16fad465d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/staging.usegalaxy.org.au/rseqc.yml b/staging.usegalaxy.org.au/rseqc.yml index ba833d62f..b2c45c52e 100644 --- a/staging.usegalaxy.org.au/rseqc.yml +++ b/staging.usegalaxy.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: - - 473382134e56 - 1a052c827e88 - 080fd5739bb4 + - 473382134e56 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/sambam.yml b/staging.usegalaxy.org.au/sambam.yml index 573ba0972..7968d95ee 100644 --- a/staging.usegalaxy.org.au/sambam.yml +++ b/staging.usegalaxy.org.au/sambam.yml @@ -15,9 +15,9 @@ tools: - name: bamtools_filter owner: devteam revisions: - - 1dfd95ee241e - 108db6635177 - cb20f99fd45b + - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -35,8 +35,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - ef11139d4545 - 9c1c0b947e46 + - ef11139d4545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -55,8 +55,8 @@ tools: owner: iuc revisions: - 19ece8afbaab - - 5f8e69cc4c6e - e7fd6754d093 + - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -68,8 +68,8 @@ tools: - name: sam2interval owner: devteam revisions: - - 75557c0908a9 - 8c737b8ddc45 + - 75557c0908a9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_bitwise_flag_filter @@ -81,8 +81,8 @@ tools: - name: sam_pileup owner: devteam revisions: - - 890d97772e2a - a3b4ad6858ff + - 890d97772e2a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam @@ -108,16 +108,16 @@ tools: owner: devteam revisions: - 649a225999a5 - - 56c31114ad4a - dc6ff68ea5e8 + - 56c31114ad4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: + - 9149ad20699a - 12749212f61b - 46c6639921f1 - - 9149ad20699a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -143,9 +143,9 @@ tools: - name: samtools_fastx owner: iuc revisions: - - a8d69aee190e - - b3d99709fe1a - 720217c23995 + - b3d99709fe1a + - a8d69aee190e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -157,10 +157,10 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - cc61ade70eb8 - fe34990e5ce7 - - db17d5321bad - 22970df7a40e + - db17d5321bad + - cc61ade70eb8 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -172,9 +172,9 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - 7def34e6cf4d - 7a6034296ae9 - 88b8c2916784 + - 7def34e6cf4d - 811fc2d75ad4 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -196,8 +196,8 @@ tools: owner: devteam revisions: - 583abf29fc8e - - fa7ad9b89f4a - 329deb17a9f7 + - fa7ad9b89f4a - 9da0311ab1dd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -210,8 +210,8 @@ tools: - name: samtools_phase owner: devteam revisions: - - b5c3b1856370 - 1e5880498f52 + - b5c3b1856370 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -223,9 +223,9 @@ tools: - name: samtools_reheader owner: devteam revisions: - - bb8cfc6f6e0c - - 30388d878f81 - db000c6007a0 + - 30388d878f81 + - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -256,9 +256,9 @@ tools: - name: samtools_sort owner: devteam revisions: - - 6c2c1836728b - cab3f8d35989 - e613c1ad4c4c + - 6c2c1836728b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -270,10 +270,10 @@ tools: - name: samtools_split owner: devteam revisions: - - b7f7826ef1cd - 5d9ae78f34d3 - bcedabb53ddf - 135c85f4cfaf + - b7f7826ef1cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -285,10 +285,10 @@ tools: - name: samtools_stats owner: devteam revisions: - - 5a08c09b9311 - 145f6d74ff5e - - 3a0efe14891f - 1cc79f49b8d5 + - 3a0efe14891f + - 5a08c09b9311 - 24c5d43cb545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -301,13 +301,13 @@ tools: - name: samtools_view owner: iuc revisions: - - b01db2684fa5 + - bf328cec6a42 - 5826298f6a73 - - b72793637686 - 350bbc5c2ffd - - c370440f901e - 0dbf49c414ae - - bf328cec6a42 + - b01db2684fa5 + - c370440f901e + - b72793637686 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view diff --git a/staging.usegalaxy.org.au/send_data.yml b/staging.usegalaxy.org.au/send_data.yml index fcda9cec8..5ee98c737 100644 --- a/staging.usegalaxy.org.au/send_data.yml +++ b/staging.usegalaxy.org.au/send_data.yml @@ -2,10 +2,10 @@ tools: - name: ena_upload owner: iuc revisions: - - 6f6537780379 - - a62c4a11a67d - - 59bb6d34fca6 - - d147d6455873 - 4aab5ae907b6 + - d147d6455873 + - 59bb6d34fca6 + - a62c4a11a67d + - 6f6537780379 tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/single_cell.yml b/staging.usegalaxy.org.au/single_cell.yml index 968f750a9..2d50fea62 100644 --- a/staging.usegalaxy.org.au/single_cell.yml +++ b/staging.usegalaxy.org.au/single_cell.yml @@ -2,11 +2,11 @@ tools: - name: anndata_import owner: iuc revisions: - - 55e35e9203cf - - 00712416fdaa - - fb9e030ffae4 - 32e547223c9e + - 00712416fdaa - cfc3f5a57dc6 + - 55e35e9203cf + - fb9e030ffae4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -18,11 +18,11 @@ tools: - name: anndata_inspect owner: iuc revisions: - - b9fac48532eb - - 39e945f0b2c1 - - 038e32885fec - 688357ad5e61 + - b9fac48532eb - ee98d611afc6 + - 038e32885fec + - 39e945f0b2c1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -35,10 +35,10 @@ tools: owner: iuc revisions: - d4af736e7b83 - - b85871dd69f9 - - 3d748954434b - 9bd945a03d7b - 43cb7b5a6fe7 + - 3d748954434b + - b85871dd69f9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -50,10 +50,10 @@ tools: - name: dropletutils owner: iuc revisions: - - 8855361fcfc5 + - cdf4443d5625 - a9caad671439 - 2c1200fba922 - - cdf4443d5625 + - 8855361fcfc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -71,15 +71,15 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 7ffaa0968da3 - 282819d09a4f + - 7ffaa0968da3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 2ba99a52bd44 - 56371b5a2da9 + - 2ba99a52bd44 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset @@ -118,8 +118,8 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: - - 37a47c4fd84d - f3eb2291da05 + - 37a47c4fd84d - 2b0d3e2f402a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -146,9 +146,9 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - 44b935f2271b - - c92d0f9338c5 - 2af7c5086a96 + - c92d0f9338c5 + - 44b935f2271b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -174,9 +174,9 @@ tools: - name: scanpy_filter owner: iuc revisions: + - 3c86f71498bc - a97abb8cd15b - b409c2486353 - - 3c86f71498bc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -188,10 +188,10 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - c5d3684f7c4c - - 6c145a6868cc - 5e9171dc8244 + - c5d3684f7c4c - cc0deb593fc8 + - 6c145a6868cc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -203,9 +203,9 @@ tools: - name: scanpy_normalize owner: iuc revisions: + - ab55fe8030b6 - 3bcd5445cd7a - a407e7f8bdc1 - - ab55fe8030b6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -218,8 +218,8 @@ tools: owner: iuc revisions: - 6adf98e782f3 - - aa0c474463c2 - dbbe1ea8ecb1 + - aa0c474463c2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -231,9 +231,9 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - bf2017df9837 - - 215733a383f2 - f2f6c703da06 + - 215733a383f2 + - bf2017df9837 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -246,8 +246,8 @@ tools: owner: iuc revisions: - 8f333f90d8d6 - - fd808de478b1 - b834074a9aff + - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -260,8 +260,8 @@ tools: owner: iuc revisions: - b7ea9f09c02f - - 652923ce664f - 7a365ec81b52 + - 652923ce664f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -273,9 +273,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 81e5bdff4853 - - 2e41b35b5bdd - ef4c80837bc5 + - 2e41b35b5bdd + - 81e5bdff4853 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter @@ -287,9 +287,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 9e5c0bb18d08 - - c99ba278dfa9 - 46fc6751d746 + - c99ba278dfa9 + - 9e5c0bb18d08 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca diff --git a/staging.usegalaxy.org.au/statistics.yml b/staging.usegalaxy.org.au/statistics.yml index c3ce2412f..3461d4ae0 100644 --- a/staging.usegalaxy.org.au/statistics.yml +++ b/staging.usegalaxy.org.au/statistics.yml @@ -33,24 +33,24 @@ tools: owner: iuc revisions: - 746e8e4bf929 - - 562f3c677828 + - 4c07ddedc198 - 2f3c6f2dcf39 + - 562f3c677828 - 419027d822d6 - - 4c07ddedc198 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - e01e8a9a82f4 - 8564f6927b87 + - e01e8a9a82f4 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all @@ -63,16 +63,16 @@ tools: - name: dwt_var_perclass owner: devteam revisions: - - cb422b6f49d2 - 781e68074f84 + - cb422b6f49d2 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - 7a15159140d1 - - 6c29c7e347e8 - cb1c59d69557 + - 6c29c7e347e8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,41 +120,41 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 9c3e1d3235c8 - aef56d0e7a61 - - 9160cb4069c2 - - 840f29aad145 - 118e230e85ce + - 840f29aad145 - b1eda492f063 + - 9c3e1d3235c8 + - 7442b94d6a1e tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - d0352e8b4c10 - - 375bbd555f4a - - 5a125d1ac9b9 - adaf2457d6ec + - 375bbd555f4a + - 9fda0b82f419 - 07843f917990 + - d0352e8b4c10 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - cd02bf168d23 - - 2c58b83c9bad - d33d37f32e54 + - 2c58b83c9bad - 4cc980df6265 - - 4db563e8d453 + - 7ae443e6217d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: + - 4bbaf77573ef - ad7e0b4291ee + - bb9fc9d46ea4 - 7dd3fb35904f - - aeca97d9a214 - - 4bbaf77573ef - 8eed73e8e04d - 1dd433d2c92c tool_panel_section_label: Statistics diff --git a/staging.usegalaxy.org.au/text_manipulation.yml b/staging.usegalaxy.org.au/text_manipulation.yml index 9993b3f41..a3bda3bc9 100644 --- a/staging.usegalaxy.org.au/text_manipulation.yml +++ b/staging.usegalaxy.org.au/text_manipulation.yml @@ -9,6 +9,7 @@ tools: owner: devteam revisions: - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -20,21 +21,21 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - 6c6d26ff01ff - f18f67056946 + - 6c6d26ff01ff tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: + - 626658afe4cb + - 9cd341095afd + - be25c075ed54 + - 6595517c2dd8 - 13b6f0007d9e - 02026300aa45 - - 626658afe4cb - - 464b9305180e - 6e8d94597139 - - 6595517c2dd8 - - be25c075ed54 - - 9cd341095afd + - 464b9305180e tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -46,8 +47,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 6f54dc6b37da - 3a4694d4354f + - 6f54dc6b37da tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -71,11 +72,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 557ec8d7087d - - 4d5aae46f850 - 34d29339abab + - 557ec8d7087d - 37cde8134c6a - 9cc411a62277 + - 4d5aae46f850 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -99,28 +100,28 @@ tools: - name: merge_cols owner: devteam revisions: - - dd40b1e9eebe - ae7843d06f8f - f2aac0c5c60d + - dd40b1e9eebe tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 3a6b78c39dca - - cf34c344508d - - 1ea4e668bf73 - 83069b38aa85 - 2e8f945f7285 - - 623f3eb7aa48 - 33d61c89fb8d + - cf34c344508d + - 623f3eb7aa48 + - 3a6b78c39dca + - 1ea4e668bf73 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - 399da6b5ec21 - 503bcd6ebe4b + - 399da6b5ec21 - ae8c4b2488e7 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -133,28 +134,28 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - bce29ec10b78 - f768f6183386 - - b722161a845a + - bce29ec10b78 - 575cd6cd537c + - b722161a845a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: - - 3bf5661c0280 - 60ff16842fcd + - 3bf5661c0280 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: + - 74a8bef53a00 - ddf54b12c295 - a6f147a050a2 - - 9ff72e942410 - - d698c222f354 - 0a8c6b61f0f4 - f46f0e4f75c4 - - 74a8bef53a00 + - 9ff72e942410 + - d698c222f354 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/variant_calling.yml b/staging.usegalaxy.org.au/variant_calling.yml index cce3c0c98..55bea13e8 100644 --- a/staging.usegalaxy.org.au/variant_calling.yml +++ b/staging.usegalaxy.org.au/variant_calling.yml @@ -16,32 +16,32 @@ tools: - name: freebayes owner: devteam revisions: - - 156b60c1530f - a5937157062f - - 57def2d7c093 - - ef2c525bd8cd - 04fa42777df9 + - ef2c525bd8cd + - 57def2d7c093 + - 156b60c1530f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 09d6e4693887 - - 435b157bed6d - - e61c9ac190ad - 791f73caa0c8 + - e61c9ac190ad + - 435b157bed6d + - 09d6e4693887 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 4805fe3d8fda + - e1461b5c52a0 - 074d44697036 - 03627f24605f - - 65432c3abf6c - - 3b4b2121842f - - e1461b5c52a0 - dfadc322b065 + - 3b4b2121842f + - 65432c3abf6c + - 4805fe3d8fda tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter @@ -55,18 +55,18 @@ tools: - name: lofreq_indelqual owner: iuc revisions: + - 426d707dfc47 - c27549b9aa1f - f4473557ffc7 - 971e07ca4456 - - 426d707dfc47 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - aa35ee7f3ab2 - dbd9f2db9ed8 - cdaab621d454 + - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -84,11 +84,11 @@ tools: - name: snippy owner: iuc revisions: - - d220115f882b + - 5bbf9eada9c2 + - 9bccc8404a3c - c9a8ef2aa380 + - d220115f882b - fa016f1eea1a - - 9bccc8404a3c - - 5bbf9eada9c2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -132,16 +132,16 @@ tools: revisions: - ee4a90760848 - 40f0591deda0 - - e7aff4a85df5 - 3b1e7c170b10 - 32f14a2723ec + - e7aff4a85df5 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - adc0645b945c - 02d81b994ef5 + - adc0645b945c - 4934c0ac6197 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.usegalaxy.org.au/vcfbcf.yml b/staging.usegalaxy.org.au/vcfbcf.yml index 9ef4bba2e..a9b51d3b0 100644 --- a/staging.usegalaxy.org.au/vcfbcf.yml +++ b/staging.usegalaxy.org.au/vcfbcf.yml @@ -2,13 +2,13 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - ebe5fc018e72 - - e075b1be5abb + - 8a2e296c07ef - b7ea370b8f5d - - 265fe0f9ea64 - 3f62d4939d54 + - e075b1be5abb + - ebe5fc018e72 + - 265fe0f9ea64 - 6a88248893c4 - - 8a2e296c07ef tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -20,13 +20,13 @@ tools: - name: bcftools_call owner: iuc revisions: + - 21687e35f066 - 0fba2c15b40d + - b03984136ce4 - c37b684e7f4e - - 21687e35f066 - - 22637b1a55bf - 544cb432072b + - 22637b1a55bf - f0d44631365f - - b03984136ce4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -38,14 +38,14 @@ tools: - name: bcftools_cnv owner: iuc revisions: + - 8627b2b383b4 + - 3a7084316a6e + - bf1f4994f104 + - 6d35a3780bfd - 8ca3647c90fd - 01d6b7d6365e - - 6d35a3780bfd - 8408bffd5616 - - 8627b2b383b4 - 0238f68ad641 - - 3a7084316a6e - - bf1f4994f104 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -57,14 +57,14 @@ tools: - name: bcftools_concat owner: iuc revisions: - - d144af39073a - 6b6c992d3a14 - - f430a1ec7ee4 + - 9b5abbf50d23 - 81426b3cf18b - 08296952d12f - - 62ca6da715bf - 03e0645395d2 - - 9b5abbf50d23 + - f430a1ec7ee4 + - 62ca6da715bf + - d144af39073a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -77,12 +77,12 @@ tools: owner: iuc revisions: - 95c6f3f4c77f - - d37e313a41be + - d3081540d175 - 147de996e34f - e522022137f6 - 2363ef414c9b + - d37e313a41be - 1829900b5dcd - - d3081540d175 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -94,13 +94,13 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - 348cd212dbad + - b14ff40958cb - 09f37afb3621 - - cacc9970727a - 92c0aff8b53e - 1137ce8efc1e - 9b29129fb491 - - b14ff40958cb + - cacc9970727a + - 348cd212dbad tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -113,11 +113,11 @@ tools: owner: iuc revisions: - 1f2183a23823 + - ecc9192912b8 + - de68c11034f6 - 4935320a59a8 - 367ba501b6eb - - ecc9192912b8 - 55c0e906c14c - - de68c11034f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -129,12 +129,12 @@ tools: - name: bcftools_csq owner: iuc revisions: - - 7cbf3c66d4ad - - 64a8f7dae3ad - - f01b2c9506b9 - - 6c790a091c7c - - 039ea3f1dea9 - ae68ceb4cca3 + - 039ea3f1dea9 + - 6c790a091c7c + - f01b2c9506b9 + - 64a8f7dae3ad + - 7cbf3c66d4ad tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -146,12 +146,12 @@ tools: - name: bcftools_filter owner: iuc revisions: - - e7452697afd9 - - 963a3635b2e1 - - 6ea7170a016d - cdb7b4927742 + - e7452697afd9 - 656a916779fe + - 963a3635b2e1 - 33bd9301568c + - 6ea7170a016d - 277719af4dd7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -164,13 +164,13 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: + - 501bfb078342 - a1213a0b7b66 - - 3eac729e66c9 - a29a2f40b665 - - 501bfb078342 - - b7f0f59baa7e - - 5a321fab1fe4 - 26d97cdd5410 + - 5a321fab1fe4 + - 3eac729e66c9 + - b7f0f59baa7e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -182,14 +182,14 @@ tools: - name: bcftools_isec owner: iuc revisions: - - 5f27e814a119 - - 709dd8291b83 - - 768d04526638 - - 97d19c008d15 - d7d1663559e9 + - 5f27e814a119 + - 81e4014fa809 - c803c34361e0 - 63aabc920911 - - 81e4014fa809 + - 768d04526638 + - 97d19c008d15 + - 709dd8291b83 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -201,13 +201,13 @@ tools: - name: bcftools_merge owner: iuc revisions: - - af163c712539 - - b1eba148b35b + - b931e65638b8 - 2215287d5cc9 - 7ba36babba2d - - 86296490704e + - b1eba148b35b - 85ee7e6c4204 - - b931e65638b8 + - 86296490704e + - af163c712539 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -219,15 +219,15 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - 4e1d23e5c691 - - 37757ffb4c5f - - 03191140c66a - - 5660b21a0dbd - - f506df85c652 + - 31ea13dfe5e6 - cf06b44624c7 + - 03191140c66a - ce9396ddcb2b + - 5660b21a0dbd - 9c711df3258d - - 31ea13dfe5e6 + - 4e1d23e5c691 + - 37757ffb4c5f + - f506df85c652 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -239,12 +239,12 @@ tools: - name: bcftools_norm owner: iuc revisions: - - 021693fdadaa - - 19905c025d2a + - a404f786a94c - ebb2e12a6de1 + - 19905c025d2a - 6deb4d549bc9 + - 021693fdadaa - 48291658fdf6 - - a404f786a94c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -256,13 +256,13 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - c450406f722b - - f7879f1e77f9 - - be6b217710af - 97e8145d7e30 - 71c78e0eea52 - - 69d8b7567281 - 5ad5d4243987 + - c450406f722b + - f7879f1e77f9 + - 69d8b7567281 + - be6b217710af tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -274,13 +274,13 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: - - 0fe007201caf - 79f7a1acc2cd - - cc7f9a4e186b - - 52f9e4a660e3 - - 2514e684f8a3 - 89720ec3d58e + - 2514e684f8a3 + - 0fe007201caf + - 52f9e4a660e3 - d31a2e310a52 + - cc7f9a4e186b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -292,13 +292,13 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 1411bef27a75 - - 230e424bde67 - - 99f4a81a47be - 80e6e399ccd0 + - 99f4a81a47be + - 1411bef27a75 - 0a62420cb9cd - 75ddd081f608 - 026a989b7cee + - 230e424bde67 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -310,13 +310,13 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - 444e6a756c35 - - ba20340426fe - - c01be0ab9806 - - 5acfca5a76af - e493702b19eb + - 5acfca5a76af - bca7ce81688f + - ba20340426fe - 5808f77b2bb6 + - c01be0ab9806 + - 444e6a756c35 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -328,13 +328,13 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - 157ffcdd3fa7 - - 7fe09ad6a939 - - 12152af85697 - - d52b8947b269 - 4d236c696844 - f2482aa4862e - 68fec03a63b7 + - 7fe09ad6a939 + - d52b8947b269 + - 12152af85697 + - 157ffcdd3fa7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -346,13 +346,13 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: - - cbe39e530cbf - - 0e5d11004815 - 8f2fc0ab30fb - - 8dbce095986c - - 6f8e223f78f3 - 27e2611639a9 + - 8dbce095986c + - cbe39e530cbf + - 0e5d11004815 - 29ba253e2e05 + - 6f8e223f78f3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -364,13 +364,13 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - a8630d4fbaf8 + - 9708e3086f32 - af36eb5418fe - - 3ff5654b4e7d - e0a856def0b0 - - 9708e3086f32 - - 88bb477f45f7 + - 3ff5654b4e7d - a367a15c6de5 + - 88bb477f45f7 + - a8630d4fbaf8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian @@ -382,13 +382,13 @@ tools: - name: bcftools_plugin_missing2ref owner: iuc revisions: - - 96d0145c041a + - 4ed46189d6c6 - 2f4eef1f0d22 - - 6ce175385dd9 - 31c096c6b156 - - 4ed46189d6c6 - 5c9729d54721 - 03e30f06f15f + - 96d0145c041a + - 6ce175385dd9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -400,13 +400,13 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: - - 40daf124be88 + - 2c4941386820 + - 262bba5b90ef - a1aad8b559c6 + - 11af7fce71cf - 46eb13bc2c73 - - 262bba5b90ef - - 2c4941386820 + - 40daf124be88 - 09f5e45a8212 - - 11af7fce71cf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -418,14 +418,14 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: + - 743cd1472aeb + - 8cb121b6a1d2 - 6cbb9c47795c - - 0594ea1417c8 - 12038f59c0f4 - 4b796b58938b - - f272b8ba0983 - 882b2e649602 - - 743cd1472aeb - - 8cb121b6a1d2 + - f272b8ba0983 + - 0594ea1417c8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -437,13 +437,13 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: - - 238f78e38a8b - - dba06328556a - cced6715f926 - - eccb508bb678 - adee7e8b746f - 8c3ff4ef1190 - 18cf9de1cf73 + - eccb508bb678 + - dba06328556a + - 238f78e38a8b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples @@ -455,12 +455,12 @@ tools: - name: bcftools_query owner: iuc revisions: - - a850902cac64 - - 9f36041495a3 - e53501abf992 - c9935c9e8a24 - - f64e7ca2efd2 + - 9f36041495a3 - e0ad88dec40d + - f64e7ca2efd2 + - a850902cac64 - 3ce32adc55b2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -473,12 +473,12 @@ tools: - name: bcftools_reheader owner: iuc revisions: - - d43eb39b989e - - fd3539749127 - b7be725976b6 + - 8057cf55fa41 + - d43eb39b989e - 4db0695a6fc7 - 79489d5685dd - - 8057cf55fa41 + - fd3539749127 - d68c43202172 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -491,12 +491,12 @@ tools: - name: bcftools_roh owner: iuc revisions: - - 6a636d58dfc2 + - 5296d26b0373 - bdc67eeb0bc9 - - b0d39ef600a7 - - 78cd8b69da4c - 58091e1be01b - - 5296d26b0373 + - 78cd8b69da4c + - b0d39ef600a7 + - 6a636d58dfc2 - 1ccf0e7fb4f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -509,13 +509,13 @@ tools: - name: bcftools_stats owner: iuc revisions: - - e8af591435d1 - - b17394940c7a - - baa8823f8073 - - a2f8dc22d7c0 - b641062a2587 - - '388983871932' - 4d3ce9dc1525 + - baa8823f8073 + - b17394940c7a + - '388983871932' + - e8af591435d1 + - a2f8dc22d7c0 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -527,13 +527,13 @@ tools: - name: bcftools_view owner: iuc revisions: - - 59fa8742285e - - abc3ced31cd1 - - 38d75661c235 - - d1f8f55f564d + - 3ca3de4e5291 - 3a233c8eb814 + - d1f8f55f564d + - abc3ced31cd1 + - 59fa8742285e - e6b5cbbf449b - - 3ca3de4e5291 + - 38d75661c235 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -545,8 +545,8 @@ tools: - name: vcf2tsv owner: devteam revisions: - - 285060661b45 - e92b3c0f9224 + - 285060661b45 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfaddinfo @@ -559,8 +559,8 @@ tools: - name: vcfallelicprimitives owner: devteam revisions: - - 57a16b310fe8 - a8a4f94aa321 + - 57a16b310fe8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate @@ -580,36 +580,36 @@ tools: - name: vcfbedintersect owner: devteam revisions: - - 9edfe5145ba8 - aea8e90ad788 + - 9edfe5145ba8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbreakcreatemulti owner: devteam revisions: - - 9fd5d91eb91b - 690b1d846263 + - 9fd5d91eb91b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcheck owner: devteam revisions: - - 5e850c85ba32 - aa8e8c96ca06 + - 5e850c85ba32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine owner: devteam revisions: - - 1f0ba67cc85a - 53edb91ed051 + - 1f0ba67cc85a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcommonsamples owner: devteam revisions: - - f1852ecef841 - 254f285dbaaa + - f1852ecef841 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance @@ -622,16 +622,16 @@ tools: - name: vcffilter owner: devteam revisions: - - eae7c08ebb6f - - fa24bf0598f4 - 6b935ab36d7b + - fa24bf0598f4 + - eae7c08ebb6f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - 11f62f071125 - fc5a64fdd5b2 + - 11f62f071125 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten @@ -658,22 +658,22 @@ tools: - name: vcfhethom owner: devteam revisions: - - b07ef36cf7e6 - 8254e0fe7358 + - b07ef36cf7e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfleftalign owner: devteam revisions: - - 29f9b782727e - d2406f98a782 + - 29f9b782727e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfprimers owner: devteam revisions: - - 17096387c0e6 - d226a7327946 + - 17096387c0e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample @@ -686,8 +686,8 @@ tools: - name: vcfselectsamples owner: devteam revisions: - - 2ba3b87f904f - 958b6484a7f1 + - 2ba3b87f904f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfsort diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 7f95eac63..dec6c1837 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: + - 4efdca267d51 - 6e9aea89e388 + - c2ef298da409 - 78c75f134c16 - 3f3e247c053d - - c2ef298da409 - - 4efdca267d51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -36,15 +36,15 @@ tools: - name: annotatemyids owner: iuc revisions: - - 3e1f6f6d557e + - 44018dd6b447 + - 133f36c29579 - cd2480f35935 + - 3e1f6f6d557e - fe3ca740a485 - - b5d8e5475247 - - 1aae04680c4b - - 4f2967b27e67 - - 133f36c29579 - - 44018dd6b447 - f29602ae449e + - 4f2967b27e67 + - 1aae04680c4b + - b5d8e5475247 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -57,16 +57,16 @@ tools: - name: augustus_training owner: bgruening revisions: - - 6519ebe25019 - dc027fa56d55 + - 6519ebe25019 - 7be22100e5e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 09855551d713 - 28433faa6e42 + - 09855551d713 - ca6d970d931c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -80,8 +80,8 @@ tools: owner: iuc revisions: - fe48aa4ccd5e - - 7355bbf5e05f - 8fd427007e93 + - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -124,41 +124,41 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 9f2455341fac - 14f588312c56 + - 9f2455341fac - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: + - 73428a792541 - a230ea445788 - 30fb23d4c31c - - 73428a792541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: + - 494f0bb4a993 - 563a19373357 - 30f08d74024f - - 494f0bb4a993 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 7abc5f6dd595 - - f31125bb85ea - 2bba2ff070d9 + - f31125bb85ea + - 7abc5f6dd595 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: + - b3cf4684e9c7 - d3af38b9c7e1 - 52af33194019 - - b3cf4684e9c7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -170,9 +170,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 2aea122fbd25 - 79261884facd - 07d7991bf205 + - 2aea122fbd25 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -184,10 +184,10 @@ tools: - name: goseq owner: iuc revisions: - - 602de62d995b - - 8b3e3657034e - ef2ad746b589 - 43798b4caee0 + - 8b3e3657034e + - 602de62d995b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -212,8 +212,8 @@ tools: - name: interproscan owner: bgruening revisions: - - c55643c3d813 - 98cafcbd2578 + - c55643c3d813 - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -232,23 +232,23 @@ tools: - name: maker_map_ids owner: iuc revisions: - - e906fa778440 - 326f9c294b09 + - e906fa778440 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: - - d46d803ca6cc - 3c1a01127868 - 370c210d9541 + - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - 624606f7c996 - 033755194fe9 + - 624606f7c996 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -272,10 +272,10 @@ tools: - name: prokka owner: crs4 revisions: - - bf68eb663bc3 - - d643e3b03500 - 8a22554cdde2 - a17498c603ec + - d643e3b03500 + - bf68eb663bc3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -294,8 +294,8 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snap_training @@ -308,20 +308,20 @@ tools: owner: iuc revisions: - 68693743661e - - 5b80f544c67f - - 5c7b70713fb5 - cfcf33df7fc0 - - 5a29ab10dba6 - 8f92c2b26e6d - 268d162b9c49 + - 5b80f544c67f + - 5a29ab10dba6 + - 5c7b70713fb5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: + - 09d6806c609e - 5fab4f81391d - 2b3e65a4252f - - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -345,15 +345,15 @@ tools: - name: tbprofiler owner: iuc revisions: - - 45083d070fb8 - - 37213cf56392 - 809dfc93d593 - - 2c68b0c38785 - - 037a11682176 - - e1a9d6fd258d - ba6f87115e13 - ac8250086ac3 + - e1a9d6fd258d + - 037a11682176 + - 45083d070fb8 - 200c378d85f3 + - 37213cf56392 + - 2c68b0c38785 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index f48b21580..2233b68fc 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,25 +2,25 @@ tools: - name: abyss owner: iuc revisions: - - 553bfe8bd0b5 - - 890b794c997d - - 7547fcab5d19 - 841084c5fc46 + - fa5259cc561b - a929ce596a34 - - 8f1b150a2487 + - 890b794c997d - 0e93176640ac - - fa5259cc561b + - 553bfe8bd0b5 + - 7547fcab5d19 + - 8f1b150a2487 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - b2860df42e16 - - 21e491ad532a - - 067592b6b312 - b9e31c5c01c7 - - ddddce450736 + - 067592b6b312 + - 21e491ad532a - 94fe43e75ddc + - ddddce450736 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -33,10 +33,10 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 22286dab5aa1 - - 5258e18bbe23 - a7f16f24e9a1 + - 22286dab5aa1 - 3371c5bdc17a + - 5258e18bbe23 - faee8629b460 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -49,28 +49,28 @@ tools: - name: busco owner: iuc revisions: - - 602fb8e63aa7 - - cf13a1e03e5b - - 4048d82f0c88 - - 1440ae06552f - - 41030a6c03b7 + - e4bd1e99bacf - 46ae58b1d792 - - 2dd755c1c6ff + - 1440ae06552f - 5ecdeca79a0d - - e824f5d958d0 + - 41030a6c03b7 - 94170eee0ad8 + - bb935709506a + - 2dd755c1c6ff - 0d243f458b53 + - e824f5d958d0 - 1e62c28ba91d - - bb935709506a - - e4bd1e99bacf + - cf13a1e03e5b + - 602fb8e63aa7 + - 4048d82f0c88 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - 86f150c8019d - c5b7390290b1 - 5732f959936a - - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -83,36 +83,36 @@ tools: owner: bgruening revisions: - cb8dfd28c16f + - e27815e82dd4 + - 276f5d8712d5 - 8d4f03b5fe9d - 1ce9b1d72ec3 - 3ee0ef312022 - - 276f5d8712d5 - - e27815e82dd4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: + - 01210c4e9144 - 3169a38c2656 - b2f674562a18 - - 01210c4e9144 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 06bcf65179fb - 611219887a48 + - 06bcf65179fb - 8b330a577046 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 5127a713de83 - 690c2caa367e - - 3ef480892a9f + - 5127a713de83 - 3fba9c77550a + - 3ef480892a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -124,18 +124,18 @@ tools: - name: hifiasm owner: bgruening revisions: - - 045c7c3d8e59 + - 2061fb3b81b4 + - 5f625c63b8bc - ec9e21e9c71b - f3c89da3af16 - - 2061fb3b81b4 - - 366a11d316a7 - - 9ef6920c3089 - - 3f7be05a1597 - - 6505bd37670d - - 71740308d412 - 5bec28269d95 + - 3f7be05a1597 + - 9ef6920c3089 - da9d8bf98802 - - 5f625c63b8bc + - 71740308d412 + - 6505bd37670d + - 366a11d316a7 + - 045c7c3d8e59 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -153,37 +153,37 @@ tools: - name: megahit owner: iuc revisions: - - 14ddfc8ffb93 - - de387b2b2803 - 7518ee87b53d + - de387b2b2803 + - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: + - 39edec572bae - f8113c25bc6b - 9d79beb19ac3 - - 39edec572bae tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - eadfd71dde37 - - 51c2360aa807 - 29dabd8db6f2 + - 51c2360aa807 + - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - fd128c111ab0 - - f338e9942b27 - - 3ca2d2a9068c - 606b09cc9860 + - f338e9942b27 - e731ea24e48d - - 2ecf5a570907 - eb7a370f6588 + - 3ca2d2a9068c + - 2ecf5a570907 + - fd128c111ab0 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -195,10 +195,10 @@ tools: - name: miniasm owner: iuc revisions: + - 73a3846701e1 - a7b889b90140 - - 8dee0218ac7d - 8b6d0d85252b - - 73a3846701e1 + - 8dee0218ac7d - 80d1250bd5fd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -211,9 +211,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 64a1c751d99b - 7c2f5268d01c - 15200570e926 + - 64a1c751d99b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -225,10 +225,10 @@ tools: - name: pretext_map owner: iuc revisions: - - bbe19ef04a74 - - 2b16ba799da9 - dfb8a4497339 + - bbe19ef04a74 - d256a51a656b + - 2b16ba799da9 - 02831bf9e95f - 8fef980d48b5 tool_panel_section_label: Assembly @@ -236,43 +236,43 @@ tools: - name: purge_dups owner: iuc revisions: - - 76d4cbefff85 - e9bd16ba5ebd - a315c25dc813 + - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 342a1d1fed7b - - 59db8ea8c845 + - 7594365c546b + - 3061c8b029e5 - 875d0f36d66f - 675488238c96 - - 3061c8b029e5 - ebb0dcdb621a - - 6fcbee531de6 - - 7594365c546b + - 59db8ea8c845 - 72472698a2df + - 342a1d1fed7b + - 6fcbee531de6 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - 39bed8de8017 - cd06929b224b + - 936f0b5e7fcc + - 39bed8de8017 - d865b62f501c - - a199cd7ac344 - aa39b19ca11e - - 936f0b5e7fcc + - a199cd7ac344 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - - f8564b2d7f63 - 2b2a352488fa - - 3edba9afc9bc - f11b994b7eb2 + - 3edba9afc9bc + - f8564b2d7f63 - 33b7d8481a76 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -280,19 +280,19 @@ tools: owner: iuc revisions: - 1d06c8b38e77 - - 53c2bc8c2ae3 - - ef69617ecb42 - 378e55aeeb25 + - ef69617ecb42 - e122f9101584 + - 53c2bc8c2ae3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - - f77f7a7f3b83 - ba7b0f11e470 - - 9a22227bb6d0 - ab5b7f6b7198 + - f77f7a7f3b83 + - 9a22227bb6d0 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -304,174 +304,174 @@ tools: - name: shovill owner: iuc revisions: - - f698c7604b3b - - d9f6a00b6db7 + - 196a599ec43d - 83ead2be47b2 - - 865119fcb694 + - d9f6a00b6db7 + - f698c7604b3b - ad80238462c1 - - 196a599ec43d + - 865119fcb694 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: + - 24e471d13fe9 - 5e0825476fb7 - 5a0ddb4dc3a4 - - 24e471d13fe9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 1fc82fe7ebef - - 1bb12736175c - - 7490b213baa9 - - 051fd2db8a27 - 904bf932cf78 + - 051fd2db8a27 + - 7490b213baa9 + - 1bb12736175c + - 1fc82fe7ebef tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - fee85957cebe - 34305b013402 - d6e617c4e338 - - 808b3a0a6716 - ad8b536d1caa + - fee85957cebe + - 808b3a0a6716 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 8d4b90bf9caf - 21da31ed41a1 + - e5a3b75a271f - b8002c3f7141 - 6b5a5842531e - - e5a3b75a271f + - 8d4b90bf9caf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: + - 328aa71f0f3c - 9de69775f512 + - 86f66ab58e14 - 2a10645aeadd - f1532cb33c75 - - 328aa71f0f3c - - 86f66ab58e14 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - e41dcb0e913b - - 340bc17f49cf + - 1708851f8804 - 6aad515a5270 + - e41dcb0e913b - 85fb02c43042 - - 1708851f8804 + - 340bc17f49cf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - b65a43f70b99 - d5fb354f745d - b3490b036c5a - - d159735a6a9f + - b65a43f70b99 - 249f6a28c751 + - d159735a6a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - dd7ad84f3943 - - 33368fec3b70 - 9006e5836729 + - 33368fec3b70 + - b7829778729f + - dd7ad84f3943 - 7897763d14ec - d2d1df21dfb9 - - b7829778729f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - 8f631679571f - - 6f4c8ad6ea01 - - 505a9833ab5d - ced385aa976d + - 6f4c8ad6ea01 - 189e837009c9 + - 505a9833ab5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 9ded6109434a - - d40ed4eb0c0e - - 356afed970b4 - e59bee4565b3 + - d40ed4eb0c0e - 19bdfd1e6fe3 + - 356afed970b4 + - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: + - 80a17897564d - b23249f81bc4 - - ebd801e712bc - 6dd935e4984b - - 80a17897564d + - ebd801e712bc - 4688ae3b49b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - 937ea677d437 - - b64696992ee9 - - 59bd28f6265d - cb1e3db43020 + - b64696992ee9 - b5e35a2ca4f3 + - 937ea677d437 + - 59bd28f6265d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 05bd7504fdb2 - 2628f6790eda - 6015aa0303f2 - - cb4768eeca3b - 383bb5ad32e2 + - cb4768eeca3b + - 05bd7504fdb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 6e26c9afd301 - - 9e3e80cc4ad4 + - d10bdad2fd17 - e92675014ac9 + - 9e3e80cc4ad4 - 0a3a602cd1e3 - - d10bdad2fd17 + - 6e26c9afd301 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 8d09f8be269e - 08256557922f - - 920677cd220f - 5da9a0e2fb2d + - 8d09f8be269e + - 920677cd220f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 4a53b89fa703 - 82398ba86ba7 - 37d88f41c810 + - 4a53b89fa703 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs owner: iuc revisions: - - 39495e107274 - 425e63adcc5d + - 39495e107274 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index ce0a780a8..502076a87 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,24 +2,24 @@ tools: - name: integron_finder owner: iuc revisions: - - 1ae00120dd24 - 4768f7f8e93f + - 1ae00120dd24 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - 8e8dc9a1e3e5 - ded48b36f3b7 - - 1f5641a52664 - 31812e7a1315 + - 8e8dc9a1e3e5 + - 1f5641a52664 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - 5c8ff92e38a9 - - 17fcac7ddf54 - 24a7a95867b0 + - 17fcac7ddf54 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index 51d75d307..fdf1bf986 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: - - dde39ba9c031 - - 0a5c785ac6db - - b28e0cfa7ba1 - - e19bebe96cd2 - 07e8b80f278c - - ce3c7f062223 + - e19bebe96cd2 - a1a923cd89e8 + - 0a5c785ac6db - 87ee588b3d45 - a68aa6c1204a - - a8eabd2838f6 + - ce3c7f062223 + - dde39ba9c031 - 589e7e57fd6d + - a8eabd2838f6 + - b28e0cfa7ba1 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/blast.yml b/usegalaxy.org.au/blast.yml index 5024751bc..af0041f80 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,21 +8,21 @@ tools: - name: diamond owner: bgruening revisions: - - 62c9df8382c2 + - f921014aba5a - 1e3323a44643 + - 62c9df8382c2 - 54f751e413f4 - - f921014aba5a tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: + - acf4e47b734c + - e25d3acf6e68 - 0e3cf9594bb7 - - 6f386c5dc4fb - 5edc472ec434 - - e25d3acf6e68 - - acf4e47b734c - 2889433c7ae1 + - 6f386c5dc4fb tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 8c125da3b..933e2888d 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -3,12 +3,12 @@ tools: owner: chemteam revisions: - 095ad4d096d1 - - 710301bc46fa + - c8cdde00b105 - da6bd1975a71 - - 6ca543ec1bf8 - 27ee142314a9 + - 710301bc46fa - f4230f116196 - - c8cdde00b105 + - 6ca543ec1bf8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -81,8 +81,8 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - 67ee76f0e497 - 2a868592ebcb + - 67ee76f0e497 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -100,84 +100,84 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - bfb65cb551d8 - - 3b8a9d5ced85 - - 88076940fa94 - 0fac8e2afc13 + - 3b8a9d5ced85 + - bfb65cb551d8 - 79cfd9ead848 + - 88076940fa94 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - b46d4b4d995c - - 55918daa5651 - eb6564a60136 - - f5d979cb4b54 - - 715cd0e87781 + - 55918daa5651 - d532b7e5f64b + - 715cd0e87781 + - f5d979cb4b54 + - b46d4b4d995c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - dae135dfd519 - - 5579659312e6 - d2f955aea23a - - f26afd1b7104 - fdf2cc80adb5 + - 5579659312e6 + - dae135dfd519 + - f26afd1b7104 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - bc31d02be922 - 319a28774da9 - d1d0efda35c0 + - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 2c349b027a01 - - 070e3ecc3fda - - ed736e6eee39 - cac1886249a2 + - ed736e6eee39 + - 070e3ecc3fda - 4da9ee404eab + - 2c349b027a01 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: + - da8753545526 - f197e34c33a9 - - d1f803b5943c - 807aa4c9293d - - 73008ef1f487 - - da8753545526 - - 2e219a2d9327 - 525ca7c8065f + - 2e219a2d9327 + - d1f803b5943c - c0c9a5024177 + - 73008ef1f487 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 2c8ed1b52bf7 - - 7568ae18908a - 61094e01eff9 - - 1809414a9454 - - 27ea4e1a3f95 - c4fbab8e03c5 + - 27ea4e1a3f95 + - 1809414a9454 + - 7568ae18908a + - 2c8ed1b52bf7 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: - - ba83f0923369 - 79e8ab8f1e81 - - 730ef07b90ae - d7ec25187599 - ccfbd956a2d3 + - 730ef07b90ae + - ba83f0923369 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -196,8 +196,8 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - b59c91adeac1 - e2c36f62e22f + - b59c91adeac1 - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -228,10 +228,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: + - 9b48456a96fe - 85fad59f8168 - d4c67ced6abc - bf99565cec1f - - 9b48456a96fe tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index c973b0a27..5ea5bb5af 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,9 +2,9 @@ tools: - name: diffbind owner: bgruening revisions: - - c97a786e8fb5 - - fa56d93f7980 - 163688bb8f73 + - fa56d93f7980 + - c97a786e8fb5 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -16,16 +16,16 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 11cf21ee4242 - 4124781932db + - 11cf21ee4242 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: + - 424aefbd7777 - 640d3af5d833 - f5d67c722d67 - - 424aefbd7777 - 495a4173006f tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index 77e2c182d..8a93d57bb 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -9,10 +9,10 @@ tools: - name: collapse_collections owner: nml revisions: - - 830961c48e42 - 90981f86000f - - 33151a38533a - 25136a2b0cfe + - 830961c48e42 + - 33151a38533a tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -25,8 +25,8 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 6cbe2f30c2d7 - 0046692724f9 + - 6cbe2f30c2d7 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index e0d7bf481..864ae0c19 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -8,14 +8,14 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - e3cbd2287f63 - - 0b3c3ad92827 - 5e1240a87bcb + - 6ef0b5664c69 + - e3cbd2287f63 + - 367b1ed91207 - a3b86937ead6 + - 0b3c3ad92827 - f3a19509108a - - 6ef0b5664c69 - 4a6ee918c13a - - 367b1ed91207 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert @@ -23,13 +23,13 @@ tools: revisions: - e177a8ea0bf1 - 584008e574b2 - - 501c21cce614 - - e525f9ffb9ac - - 72ed72122deb - 1b5fc03380d4 + - 72ed72122deb + - 33c99804a32f + - 501c21cce614 - bd46669113b9 - 54ccb7e1f49a - - 33c99804a32f + - e525f9ffb9ac tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -47,16 +47,16 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - e7ed3c310b74 - 7e801ab2b70e + - e7ed3c310b74 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: + - 8979c288aefb - 186b8d913e6c - 77b41c89d856 - - 8979c288aefb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular @@ -121,11 +121,11 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: - - b9b385097f13 - - 19e45916daf9 + - 92ac8e086317 - 26c6706bfb07 + - 19e45916daf9 - 63769c4217a7 - - 92ac8e086317 + - b9b385097f13 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index 747ea36e5..a32376eb7 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,179 +2,192 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 29451af70c52 - - e821645ef8fc - a1ca9bccc7f2 - 5f6d123679f4 - de72ba3ed6f2 + - 29451af70c52 + - c929a006727f - 268e91e540ee + - e821645ef8fc tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 7a7fd0f5f15d - bb1e4f63e0e6 - - 2d2cf5c1ea8a - 0e143b4c3987 - - 12af64f93288 + - 2d2cf5c1ea8a - 5d11599b8a7d 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4e12ea27f788 - - 9368fbc49c8b + - 56bce3c82278 + - 7fda5607e777 + - 3b9d990a0a0e tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - c03c3384cd81 - - b1779366c8e9 - - 94ca68515826 - d9114ef1c8a5 - - ce4ce3316f74 - e65d16fb2724 + - 4431f39ede55 + - ce4ce3316f74 + - b1779366c8e9 + - c03c3384cd81 + - 94ca68515826 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 2da482e408b8 - - f8fc4e5aff9d - 793665fff0f8 - - d57251071381 + - 2da482e408b8 - b88ebb3672a1 + - 4ed32329e0ed + - d57251071381 - 23f7c5f1fdaf + - f8fc4e5aff9d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: + - e4c7985d4585 + - a7849312d328 - c60570fa602f - ba6efa77fb79 - - 512155688d98 - - a7849312d328 - - a4dfb122e52b - 25d830337d31 - 010e58e9d822 + - a4dfb122e52b + - 512155688d98 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 4d678170d29b + - 00d869ea03a1 + - c899e0ccff8c + - 443d9a9d6d11 - aa200e4f3939 - 38e3f226248b - - c899e0ccff8c - - 00d869ea03a1 - 69264da0ce77 + - 4d678170d29b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile @@ -182,8 +195,9 @@ tools: revisions: - d806504e96d9 - a2d70c4fd406 - - aac8444d6681 - c361b12d207a + - aac8444d6681 - 10301d137111 + - 6662b1a8d326 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/dna_metabarcoding.yml b/usegalaxy.org.au/dna_metabarcoding.yml index 7c19d5aa0..b059690b3 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -30,8 +30,8 @@ tools: - name: obi_illumina_pairend owner: iuc revisions: - - 83fbdf93d51e - 94f412098ac8 + - 83fbdf93d51e tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter @@ -44,22 +44,22 @@ tools: - name: obi_sort owner: iuc revisions: - - 12b9e285ca1c - e614dcabd870 + - 12b9e285ca1c tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_stat owner: iuc revisions: - - 723a93febe89 - 39320fee9d70 + - 723a93febe89 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab owner: iuc revisions: - - 3299c7d5268f - 5f7003111e32 + - 3299c7d5268f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index fe227f636..f664232e7 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - ce385837c160 - - 63dd26468588 - 832c20329690 + - 63dd26468588 - dba489bfcd62 + - ce385837c160 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index f5fbde272..905d6f50b 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -2,10 +2,10 @@ tools: - name: bwameth owner: iuc revisions: - - 29bdbc353f20 - 6da3972210ee - - d82648ad25a3 + - 29bdbc353f20 - 62f5fab76dfb + - d82648ad25a3 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index f7f9439aa..3df8bce97 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,30 +8,30 @@ tools: - name: cutadapt owner: lparsons revisions: - - 8c0175e03cee - - c053d4cad713 - - 4e5056fefd88 - - de6cebe3c043 + - 44e2cc14f75b - c4b82dce8335 + - 48f587c13075 - 093678460093 - - 44e2cc14f75b + - 4e5056fefd88 - 49370cb85f0f - - 288f97432497 + - 8c0175e03cee + - 135b80fb1ac2 - 660cffd8d92a + - c053d4cad713 + - c5e2e5902201 + - de6cebe3c043 - 8665bcc8b847 - 5915ea1ec9b1 - - 48f587c13075 - - c5e2e5902201 - - 135b80fb1ac2 - e4691e1589d3 + - 288f97432497 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: - f666895cbebd - - 8889eb864cef - 9db07fd39f85 + - 8889eb864cef tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length @@ -56,41 +56,41 @@ tools: - name: fasta_formatter owner: devteam revisions: + - 859422bcb689 - 9457a20156db - 516b97a23d7e - - 859422bcb689 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - 2904d46167da - f546e7278f04 + - 2904d46167da tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: - - f81d4362b6c1 - f773e98b26cf - ec0b5076173a + - f81d4362b6c1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: - cd0874854f51 - - 9c620a950d3a - 0dbb995c7d35 + - 9c620a950d3a - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - 65b93b623c77 - - 1d8fe9bc4cb0 - dbf9c561ef29 + - 1d8fe9bc4cb0 + - 65b93b623c77 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -103,8 +103,8 @@ tools: - name: fastq_filter owner: devteam revisions: - - 10b75444feae - 81a9090d6df3 + - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -124,8 +124,8 @@ tools: - name: fastq_masker_by_quality owner: devteam revisions: - - 9dfda4e310ed - 9282652e7234 + - 9dfda4e310ed tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -145,31 +145,31 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: - - c885369b207b - 09a2199cd356 + - c885369b207b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - - 249c8393f2d4 - - 35e38452bb3f - e39cc71d3ed6 + - 35e38452bb3f + - 249c8393f2d4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: + - 045f0e1043f7 - 54053ea6c77e - 74db4cffab1f - - 045f0e1043f7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats owner: devteam revisions: - - f0e7deab6518 - b1cea1b2fcd0 + - f0e7deab6518 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer @@ -188,62 +188,62 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 529bccd5e4a1 + - d5e9e83cd3d8 - 09070cacefd8 + - 529bccd5e4a1 - 567d5b3c52b1 - - d5e9e83cd3d8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 8abdedf55101 - 0b7ec11b3c7c + - 8abdedf55101 - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - - cb1e251cac37 - - 736b8f6ee456 - - bdf1ce174e39 - 90858c306551 + - bdf1ce174e39 + - 736b8f6ee456 + - cb1e251cac37 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: + - 7ce1891db6f5 - 07497255281e - 421f0af4ee95 - - 7ce1891db6f5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - - b29d37ca9e41 + - f984bb114520 - 3599f5451ee2 + - b29d37ca9e41 - 02f8a17a4ebd - - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - e246088b6e34 + - 6027ef51ef91 - 0c2907307ba4 - 177f0621c266 - - 6027ef51ef91 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - - 377ac2829eac - - 547e8d00f11c - - 61b4cedc8934 - 73194cdd4f57 + - 61b4cedc8934 + - 547e8d00f11c + - 377ac2829eac tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -275,8 +275,8 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - 51b771646466 - dfa082f84068 + - 51b771646466 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -289,10 +289,10 @@ tools: - name: umi_tools_count owner: iuc revisions: - - b557acca0b56 + - e654095ab143 - a535cf1e5da4 - 24013bf85a6f - - e654095ab143 + - b557acca0b56 - 8250ea3a1501 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -305,10 +305,10 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - f3759eec3018 - 7accf7407811 - - 6a675c3aa610 - 27ac32a22ad2 + - f3759eec3018 + - 6a675c3aa610 - 828dba98cdb4 - 9fa7803d1c51 tool_panel_section_label: FASTA/FASTQ diff --git a/usegalaxy.org.au/fastq_quality_control.yml b/usegalaxy.org.au/fastq_quality_control.yml index df08934db..d690a327a 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -4,8 +4,8 @@ tools: revisions: - ce9cd02d5b88 - e41385662e5e - - 64e9a6afdd0c - 7b4468117008 + - 64e9a6afdd0c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,65 +18,65 @@ tools: - name: fastqc owner: devteam revisions: - - 5ec9f6bceaee - - ff9530579d1f - - 3d0c7bdf12f5 - e7b2202befea + - ff9530579d1f - 2b0c9d9fc6ca - f2e8552cf1d0 + - 3d0c7bdf12f5 - 9da02be9c6cc + - 5ec9f6bceaee tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - 89d299153577 - a252d8415583 + - 89d299153577 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - b6b54ba71bd8 - ad116ae3f4d9 + - b6b54ba71bd8 - 18a51655db17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - 7306ec78632a - - 59003d0543cd - cc0fd298cc17 + - 59003d0543cd + - 7306ec78632a tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - a72af9de6bf5 - 41b2ad601cf0 + - a72af9de6bf5 - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: + - abfd8a6544d7 - b2f1f75d49c4 - - 9a913cdee30e - bf675f34b056 - - abfd8a6544d7 - - 5e33b465d8d5 - 1c2db0054039 - 3d93dd18d9f8 - - c1a4b5f3b432 - 75c93c70d094 + - 9a913cdee30e + - 5e33b465d8d5 + - c1a4b5f3b432 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: + - 949f01671246 - cd7e644cae1d - 084bbd8ba7b8 - - 949f01671246 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index 7946b577d..5b44a1c25 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - dff7df6fcab5 - 3c623e81be77 + - dff7df6fcab5 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index 751f02789..abe075ecb 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -9,23 +9,23 @@ tools: - name: gemini_amend owner: iuc revisions: - - 4bd4870ecd33 - be828b79bd4d + - 4bd4870ecd33 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - - 8f53b238a360 - f2f3bc622a16 + - 8f53b238a360 - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden owner: iuc revisions: - - 1a4c5adcd587 - df57188562f0 + - 1a4c5adcd587 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets @@ -52,8 +52,8 @@ tools: - name: gemini_dump owner: iuc revisions: - - 96a2d270bf0f - 40f85b45e472 + - 96a2d270bf0f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -79,16 +79,16 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 2550239feed5 - 184aa4e686e2 + - 2550239feed5 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load owner: iuc revisions: + - 45296e47d565 - cf61daf064fe - b2c25142267e - - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -108,8 +108,8 @@ tools: - name: gemini_pathways owner: iuc revisions: - - 9199331c3421 - 6b09debcfc49 + - 9199331c3421 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -122,9 +122,9 @@ tools: - name: gemini_query owner: iuc revisions: - - 666f60a9331a - - 840fb4850be3 - da74170c55c7 + - 840fb4850be3 + - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -137,22 +137,22 @@ tools: - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh owner: iuc revisions: - - 345d41f3f574 - 93967598e18e + - 345d41f3f574 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic owner: iuc revisions: - - e4e2128460e3 - ef9991a4a9a7 + - e4e2128460e3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats @@ -165,7 +165,7 @@ tools: - name: gemini_windower owner: iuc revisions: - - 0c58ba91d018 - 8f04952b8882 + - 0c58ba91d018 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index f729cfa4c..229318dc9 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -16,8 +16,8 @@ tools: - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway @@ -30,7 +30,7 @@ tools: - name: mageck_test owner: iuc revisions: - - 688a8eccea71 - 9b4f4533c9ee + - 688a8eccea71 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index 984c594e7..a3feadffb 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,54 +2,54 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - 983bf725dfc2 - - b39347891609 - c1b437242fee + - b39347891609 + - 983bf725dfc2 - e9df53a75f3c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download owner: iuc revisions: - - 1c58de56d587 - e063168e0a81 - 28587613264f + - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 69ebb7f46e45 - - 6ea73833cf67 + - 653e89d73fc4 + - 83c7d564b128 - e08a7ad4378b - f5ea3ce9b9b0 - 4317d3cb6cba - - aad3885b3216 - - 5e6237d58b0c - - 83c7d564b128 - - 653e89d73fc4 + - 9a776b080193 + - 69ebb7f46e45 + - 4df8de2d0e48 - c441583adae5 - - 734abc7ac21d + - 6ea73833cf67 - 1790dcf3c32d + - aad3885b3216 + - 5e6237d58b0c - 7068f48d0ef9 - - 9a776b080193 - - 4df8de2d0e48 + - 734abc7ac21d tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 9aaa46d45472 + - 7863f1abcdda - 34758ab8aaa4 - 75b3b3d0adbf - - 7863f1abcdda + - 9aaa46d45472 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - bfdc6a7ffd3a - - 054483e27a35 - af5eccf83605 + - 054483e27a35 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/graphdisplay_data.yml b/usegalaxy.org.au/graphdisplay_data.yml index 71d903a38..db6b7c000 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - 290a11559985 - c4bde687c846 + - a64dc31ab7f2 - 4b519282a05b - - 740057a5126d - - df7356989ac1 + - 7f13dc906cb9 - ae9994cf526f + - 290a11559985 + - df7356989ac1 - fd59d783248a - - a64dc31ab7f2 - - 7f13dc906cb9 + - 740057a5126d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,39 +28,39 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 7cf5b1d072b5 - f95284aa2946 - 867ab348287d + - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap2 owner: iuc revisions: + - '566197475670' - ca7cb0eaad62 - - 53460afd5115 - 3b37b1b1c3a7 - - '566197475670' + - 53460afd5115 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - da4c086cff5b - - 3d059e9c2fba + - d3a9e32672ec - 391a4cc45fea + - da4c086cff5b - 10515715c940 - - d3a9e32672ec + - 3d059e9c2fba tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 299307abd804 - - d0fc8b746d57 - 1acf88921176 + - d0fc8b746d57 + - 3b12bf9b4b87 - 5fe1dc76176e - e3a675da7fd0 - - 3b12bf9b4b87 + - 299307abd804 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -93,16 +93,16 @@ tools: owner: iuc revisions: - a6e57ff585c0 + - fd5dbf0f732e - 6cd09d7b5f37 - - 4542035c1075 - - 17359b808b01 - - 112eb40ba6cf - - ca2def38369c - - 1cfc579079a6 - - 667e17248bfe - 2bb2e07a7a21 - - fd5dbf0f732e + - 667e17248bfe + - 1cfc579079a6 + - ca2def38369c + - 17359b808b01 - 836d1aa3e89a + - 112eb40ba6cf + - 4542035c1075 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -120,9 +120,9 @@ tools: - name: pathview owner: iuc revisions: + - f1691de443a7 - fe154a7af404 - 03c13085aecc - - f1691de443a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -134,8 +134,8 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 62e3a4e8c54c - 85da91bbdbfb + - 62e3a4e8c54c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -167,22 +167,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 14e7c35f3d00 - - 59fd173ac850 - - 7dd841a32245 - - 360df4999907 - - a1abfa420d9d - 2824d77cd8f8 - 4ac4e7083b7e + - a1abfa420d9d + - 360df4999907 + - 59fd173ac850 + - 14e7c35f3d00 - 326a3db8d9d1 + - 7dd841a32245 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - 73b8cb5bddcd - 83c573f2e73c - 44608d0193ed - - 73b8cb5bddcd tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/usegalaxy.org.au/hca_single_cell.yml b/usegalaxy.org.au/hca_single_cell.yml index 565534d9b..c2bb385d2 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 14b3f2a4523b - 1a642de6db01 + - 14b3f2a4523b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph @@ -173,8 +173,8 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - 767a675b5254 - 0f98603d0116 + - 767a675b5254 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index 1bb24263a..e5c8c5ef3 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -10,32 +10,32 @@ tools: - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 5746d61f0a91 - - 78fb5e286609 - d404277cc87a + - 78fb5e286609 + - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 9e357a8b2ec3 - 4d511437b1e5 - 03dd3c16ae4e + - 9e357a8b2ec3 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - 0ba4f56a3613 - - 3b5b54ed6392 - 41dbf4d162a2 + - 3b5b54ed6392 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - 9939786dd9c9 - - 7babd8a46fe0 - 5308ca68ef3d + - 7babd8a46fe0 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index be7f9acd3..52bee0844 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -33,9 +33,9 @@ tools: - name: bfconvert owner: imgteam revisions: + - b07f4839ca77 - f3360fbeda64 - 10eed33aa9b2 - - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -74,8 +74,8 @@ tools: - name: cp_convert_objects_to_image owner: bgruening revisions: - - df3ad3ba5c6f - cdf8e3c57dae + - df3ad3ba5c6f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image @@ -95,8 +95,8 @@ tools: - name: cp_export_to_spreadsheet owner: bgruening revisions: - - d0178bdcd00e - f8fa0f6718a3 + - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color @@ -137,15 +137,15 @@ tools: - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 20dbb1f7ec7b - 91e03287f285 + - 20dbb1f7ec7b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - 5499dc6f8ac1 - 8536b1ae0254 + - 5499dc6f8ac1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality @@ -158,8 +158,8 @@ tools: - name: cp_measure_object_intensity owner: bgruening revisions: - - 407925835dd9 - 980aed9e8fd5 + - 407925835dd9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape @@ -192,8 +192,8 @@ tools: - name: cp_save_images owner: bgruening revisions: - - 4ecf93628f97 - 33f4fa1413fb + - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index 3211f83de..886291b69 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,88 +2,88 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 1069f6db0a0e - - a38934e303b9 + - d6e72da3ec35 - f362150bef41 - - 78bbd17d0703 - e319b5b65879 - - 3e4f434a69c6 - - d6e72da3ec35 + - 78bbd17d0703 - e4ee04da1c19 + - 3e4f434a69c6 - 17f911830a8c + - a38934e303b9 + - 1069f6db0a0e tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: + - 1ef5b6e3e09d + - c88553ec696e + - 0135f1d487a0 - 8f8df367470d - 72ddd32392cd + - 7fe36019c073 - 9537184d421f - f91cfb73d369 - - 1ef5b6e3e09d - - 0135f1d487a0 - - c88553ec696e - 2b95d5c04908 - - 7fe36019c073 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - fafb3d685fa9 - d7e79eb3bcb3 - - 2cf4a1cafc16 - ad0dc9f4c9e2 + - 2cf4a1cafc16 + - fafb3d685fa9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 8c05afb547fa - - ee2beb764a7b - - 9eaadf03e0df - - bd2a7d1316b9 - 7f1cfa4c0e32 - - 69797fa273c3 - - 3d18f8c3c0f6 + - bd2a7d1316b9 + - 28a6f1908fcc - ee29337f905c + - 8c05afb547fa - 8d36959b000d - - 28a6f1908fcc - - 43aac8d29685 - - 94df24c6bc00 - 6a1515bb0687 + - 3d18f8c3c0f6 + - 69797fa273c3 + - ee2beb764a7b + - 9eaadf03e0df + - 94df24c6bc00 + - 43aac8d29685 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 9f978da6528a - - 8858fa037a15 - - e3bb03cf207a + - 5d6ed46cc101 + - c092052ed673 + - d37ede8589b2 - db536ad45f28 + - 5671e1d3d5ee + - 8858fa037a15 - bcaa0d571ce2 - - cb903c9dc33d - - 5d6ed46cc101 + - 9f978da6528a - 0893a1dbb807 - - d37ede8589b2 + - cb903c9dc33d + - e3bb03cf207a - 364f4ffec275 - - c092052ed673 - - 5671e1d3d5ee tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 49236b03e4fd - - f95f403841ad - - e1a015876aa9 - 584beffa972b - - c5c9f02b6167 + - f95f403841ad + - 230b05597996 + - 3b6a16d82c1b + - 045d6d00f606 - ed28dd32141c - - 38b91a3190cd + - 49236b03e4fd - 12d66d0d05ac - - 045d6d00f606 - - 3b6a16d82c1b - - 230b05597996 + - c5c9f02b6167 + - e1a015876aa9 + - 38b91a3190cd tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/join_subtract_and_group.yml b/usegalaxy.org.au/join_subtract_and_group.yml index 90ae6982b..62c4e4e67 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,18 +2,18 @@ tools: - name: datamash_reverse owner: iuc revisions: - - 17e3b698dd52 - - b8a457820315 - f198773344e4 - 0f1724dd59d2 + - 17e3b698dd52 + - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: + - 374cb875d38a - ac092723240d - ba0c40780ecf - 22c2a1ac7ae3 - - 374cb875d38a tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index 932a2de40..df736ca77 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,46 +2,47 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - f7ecdde4b201 - 772e0e89fc68 - - 20cd4269deb2 + - f7ecdde4b201 + - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - 61a6132df9e0 + - f22a9297440f - 8a794e6d3388 - - b9906ce4756c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - 0af678661e20 + - b6ef6d0cb6b7 + - 818f9b69d8a0 - e1317b5502fa - f1b9a42d6809 - e29894cdea47 - - b6ef6d0cb6b7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: + - c80db5d6fd8c + - 1588f9076e32 + - 947c2eacccb8 - a536d2736c2d - 05143043ca13 - - 947c2eacccb8 - - c80db5d6fd8c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - 1552b8cb4a94 - - 980bf31faa05 - - 948eca2af157 - 29e4122c90de + - 980bf31faa05 - 83228baae3c5 + - 9991c4ddde14 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble @@ -50,50 +51,50 @@ tools: - 841a6cc5fc58 - 1682df52c084 - a07ab242b0b5 + - f3dfa4bdf87e - 53616c8b0865 - 1a53edc4b438 - - 315f01a9d2c2 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 91c4e3331208 - - c648d0716fb0 - - 2fc89dcd41c8 - dc4b5fd604a6 - - 40f4447733b2 + - 2fc89dcd41c8 - 14f0ccc85505 + - 927586a18553 + - 91c4e3331208 + - 40f4447733b2 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - 25ab6b4e376e + - d37a7f17e35d - 301e07345c93 - - c6ae57f774c6 - e5a5ad882f1f - - 1ddf415cb349 - - d37a7f17e35d + - 36e8d6d5d01b + - c6ae57f774c6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: + - 4ed102b922cb - b7c3e9a3b954 - 6d23883e0b94 - - 4ed102b922cb - - fa9d6a4d95ad - - f9639b488779 - 02d2be90dedb + - f9639b488779 + - 0630258dcf35 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - a4f18bbb4eca - - 2d53571c2f00 - ec69cbe34b73 + - 61634a87efc7 + - 2d53571c2f00 - 14180f9c831e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index 5cbdc195b..538276de5 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,15 +2,15 @@ tools: - name: bowtie2 owner: devteam revisions: + - 03e9b2fbc005 + - 3ba8d4563129 - 937aa69e715f - - f6877ad76b00 - 749c918495f7 - - 03e9b2fbc005 - 017aba02828d + - 17062a0decb7 + - f6877ad76b00 - a6d65b0c67af - cd659e8cc5fa - - 17062a0decb7 - - 3ba8d4563129 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -28,11 +28,11 @@ tools: - name: bwa owner: devteam revisions: - - e188dc7a68e6 - - 3fe632431b68 - - 53646aaaafef - dfd8b7f78c37 + - 3fe632431b68 + - e188dc7a68e6 - 64f11cf59c6e + - 53646aaaafef tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -44,41 +44,41 @@ tools: - name: lastz owner: devteam revisions: + - 2ff111fac1d7 - 3e1ea2facca6 - 37b497aa133f - - 60afcc2c1d05 - e7f19d6a9af8 - - 2ff111fac1d7 + - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 11a0d50a54e6 + - c0c2d0941de8 + - be1d967337e4 - 3f4d6399997b - - 6b1e195506a3 - - f54f5baedfdd + - 8c6cd2650d1f + - 11a0d50a54e6 - 09b53c1d4ab1 - - 53c0b7a1a0c3 - 77b2770508f6 - b3eab4b67562 + - 6b1e195506a3 - 037c6e54df11 - - be1d967337e4 - - 8c6cd2650d1f - - c0c2d0941de8 + - 53c0b7a1a0c3 + - f54f5baedfdd tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 00fbfac99d39 + - b8f5f6e87f5c + - e403d27e8f24 - 178bdbdb6d24 + - 00fbfac99d39 - 13022c3d3076 - - e403d27e8f24 - - b8f5f6e87f5c - - ec9cbd6b9a49 - 1cd2511a396e - 9ee34ba73ebf + - ec9cbd6b9a49 - 79b885ce78d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index ea5c6b011..3ba0936ef 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -2,8 +2,8 @@ tools: - name: cat_bins owner: iuc revisions: - - 0094893f5001 - 18676df0cb3a + - 0094893f5001 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise @@ -23,44 +23,44 @@ tools: owner: iuc revisions: - 5b5a7af9fbb4 - - 76d3d2b10738 - 63f86089423e + - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 18a502a9d287 - - 1c35dadbe76f - 96336c6a2bb7 + - 1c35dadbe76f + - 18a502a9d287 - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: + - a9f4a217dcd6 - 34e55239e68b - - f732237754fc - addaf9d22850 - - a9f4a217dcd6 + - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 04c15826a0b8 - 0776d824d896 - - 75403243703a - 8c202e741d68 + - 75403243703a + - 04c15826a0b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 43c99742158b - - e96bbb9e24ea - 8470de786d47 + - 43c99742158b - 1c9b3bcd4261 + - e96bbb9e24ea tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs @@ -68,44 +68,44 @@ tools: revisions: - 306a40d4bb8f - 84743da21318 - - 5c865a382933 - 1d75bd0595e2 + - 5c865a382933 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 8daf4564ccda - 555ccac8a4c5 - 78faebd0879c - ac72310b038a + - 8daf4564ccda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - d60df8727f59 - - f947b4bb5107 - 7b8cb2b02978 + - f947b4bb5107 + - d60df8727f59 - a58e4a43f49c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 04144473e59e - 1bc3657cd694 - - 7136e9ab70db - 7f3b59dee073 + - 7136e9ab70db + - 04144473e59e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 19299bb1c6af - 0a1224c4b781 - - 9058d8943303 + - 19299bb1c6af - d943081510da + - 9058d8943303 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -118,8 +118,8 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - 6501b5b33988 - c4db8c4de66f + - 6501b5b33988 - dbf1798c0dcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -133,8 +133,8 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 6d364c65c946 - 654548ae1357 + - 6d364c65c946 - 6c84982ee6f7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -148,24 +148,24 @@ tools: owner: iuc revisions: - e66ab198ec15 - - bd7a9c6efb10 - 6aad8ca3918b + - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: + - b084117133af - c6676a890f50 - d77397f09da1 - - b084117133af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - 9704f1a3b32d - - 7f208f1eb64f - cad93abecac9 + - 7f208f1eb64f + - 9704f1a3b32d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -177,57 +177,57 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - 31c6d107e7a5 - 79706f10d680 - c409a495841f + - 31c6d107e7a5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: + - 71ea608ddfa3 - d24841f5c3d2 - 172920f67a84 - 714d5a28cc5c - - 71ea608ddfa3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - 4137b492233e - - a293a742194f - - a4d7148ccee4 - d7e9a3c41657 + - a4d7148ccee4 - 12fb63b5f63f + - a293a742194f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: - - 6fcb8ac37a3e - cf87759761eb - - e2c71b852aba - - 75bedfb2078b - 64bc7acc22a9 - 97f7bb0851e7 + - 75bedfb2078b + - e2c71b852aba + - 6fcb8ac37a3e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - - 5e5a999ffaa9 - 4033827c76b8 - - 2d35528d2141 - 080ea153677c - c82508e76ad1 + - 5e5a999ffaa9 + - 2d35528d2141 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 95bf7479d53c - 2cd76b089570 - 6b7622dda516 + - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: jellyfish @@ -287,9 +287,9 @@ tools: - name: kraken2 owner: iuc revisions: + - 4a9da2b6c2e3 - 328c607150ff - e674066930b2 - - 4a9da2b6c2e3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -301,15 +301,15 @@ tools: - name: kraken_filter owner: devteam revisions: - - 3d6570bffdb1 - 5bee9adae474 + - 3d6570bffdb1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 1902d3de4a4f - 6c09bed3444f + - 1902d3de4a4f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -328,8 +328,8 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 88d274322340 - 2deaada69b14 + - 88d274322340 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: mash_sketch @@ -353,11 +353,11 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - e073891b2afc - 4fd3b5d8706b + - e073891b2afc + - 0270541aaf46 - 27250f92a01a - 2cff76cf35c6 - - 0270541aaf46 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 @@ -430,20 +430,20 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - ebb74774457e - fdbd63e92b01 + - ebb74774457e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - 1a6cdf55390f - - b89b0765695d - - a92a632c4d9b - - a16313517e55 - 6dee4abadccb + - a92a632c4d9b - ff8f55893e7d - 2131d7dca455 + - 1a6cdf55390f + - b89b0765695d + - a16313517e55 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -556,17 +556,17 @@ tools: - 3b22de20bd4b - 4d83eccf5f81 - 2fd4d4c9c5c2 + - 141afacabcfa - aeaa20b96ef2 - 4b9a8031ab74 - be818ae858e4 - - 141afacabcfa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - - 576963db5f1b - 9495df9dd6ef + - 576963db5f1b - b3c7199d8786 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index 133b1eb2d..6c42ae5ca 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 682f97c30..0b2942ade 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,36 +2,36 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 80f03df2e2ce - - cd07731e4434 - - bdfbaf0c10aa - a74dbfee5a86 - - 9baa871cb1d1 + - 6ae5a7b5a0a2 + - 80f03df2e2ce - 8b67dd48fec1 + - bdfbaf0c10aa + - 9eeb13a92d79 - 48c13389050d - - 6ae5a7b5a0a2 - - 94b8c6013083 - 9422c5a87ee2 - - 9eeb13a92d79 + - 9baa871cb1d1 + - 94b8c6013083 + - cd07731e4434 - 2263989660f5 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - f14193ec1f50 - - bc3831dd65c1 + - 2e093badc689 + - 5abf2c2249aa + - be78f13134e2 + - aaa0d6a8b808 - d7ce0ec78e51 - 4a60927aaca5 - - f0af8936ed41 - - '764845535798' + - f14193ec1f50 - c18157c68134 + - '764845535798' - d390fe1567dc - - 2e093badc689 - - be78f13134e2 + - f0af8936ed41 + - bc3831dd65c1 - 3ff17bad4006 - - 5abf2c2249aa - - aaa0d6a8b808 - fc2e49f91e52 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -44,8 +44,8 @@ tools: - name: chromeister owner: iuc revisions: - - b768cc4cca40 - e483be1014b6 + - b768cc4cca40 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -74,15 +74,15 @@ tools: - name: mummer_delta_filter owner: iuc revisions: - - b3acbb3a6af0 - fbca557a4847 + - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 60698466facd - c9685bc0407c + - 60698466facd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer @@ -95,8 +95,8 @@ tools: - name: mummer_mummerplot owner: iuc revisions: - - ebe3b0f84de9 - 4fc0cb2ac8ae + - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer @@ -109,7 +109,7 @@ tools: - name: mummer_show_coords owner: iuc revisions: - - 959c1f8dae95 - b4124df98b26 + - 959c1f8dae95 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index 64729fdba..f6458e0aa 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -2,35 +2,35 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: + - 0e9e7fcdd543 - fc8804320156 - - 72b5e9dda577 - - a7228a7ea146 - cb34f00cc10f + - 72b5e9dda577 - 79e9a869f40e - - 0e9e7fcdd543 + - a7228a7ea146 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - db25ec99c3ea - d6cddc06aeae - - 18505fe2bdb1 - fa11aa8103b2 + - 18505fe2bdb1 + - db25ec99c3ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: - - edf6d4003fad + - 43815fa60f3a - 19f3b583a9b3 - - eb746fa6f514 - ec699520444c - - 2bf63b38ee9b - - 43815fa60f3a + - eb746fa6f514 + - 222669c4afb6 - 0f5f4a208660 - cc36773a3681 - - 222669c4afb6 + - edf6d4003fad + - 2bf63b38ee9b tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -50,9 +50,9 @@ tools: owner: iuc revisions: - a3c4fe6f49ab + - edbb6c5028f5 - 645159bcee2d - 0f1c34698076 - - edbb6c5028f5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign @@ -65,15 +65,15 @@ tools: - name: nanopolish_methylation owner: bgruening revisions: - - be95355fef8d - a8d4be409446 + - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - d376944466bf - 449e9aeded2d + - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants @@ -87,8 +87,8 @@ tools: owner: iuc revisions: - 5f76b20953e5 - - 93d623d9979c - 543cbeef3949 + - 93d623d9979c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events @@ -107,8 +107,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - 5a82eb9e1b89 - 47936349f3e9 + - 5a82eb9e1b89 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -140,8 +140,8 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - 34553d0caa5e - ce8af9373061 + - 34553d0caa5e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -171,8 +171,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - ca22d8497db5 - 64a83664b814 + - ca22d8497db5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index 350ad7aa6..a0a5314c5 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -20,16 +20,16 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - adfd6bf710bd - - 3e73c97f025d - d74850cf4e42 + - 3e73c97f025d + - adfd6bf710bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 1586b111d2a3 - 83da94c0e4a6 + - 1586b111d2a3 - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -69,30 +69,30 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 48a42ca61006 - 5711fc06a63e + - 48a42ca61006 - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - 81a286e4c5a2 - fcb8bdd124f4 + - 81a286e4c5a2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco owner: iuc revisions: - - 2b4526fdf7fb - 15b97817550a + - 2b4526fdf7fb tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta @@ -111,17 +111,17 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 9a40272f56d0 - 6287d0ee459e + - 9a40272f56d0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - - b4b2b284230a - 172815da3d41 - 52b6a4d98009 - 27a6a256cd23 + - b4b2b284230a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -133,8 +133,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d210e1f185bd - d74c740bdb25 + - d210e1f185bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -193,18 +193,18 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - aec831b54a5b - - 0db22932bc39 - 9d09724f2bf1 + - 0db22932bc39 + - aec831b54a5b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - df30a2f1db55 - 6e24e79d3d69 - - ed7a967cb11b - 29c738066906 + - df30a2f1db55 + - ed7a967cb11b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sam_fasta_index_builder @@ -231,17 +231,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - d63c1442407f - - 64deddb6a8ec - c520a52b5174 + - 64deddb6a8ec + - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: + - 9946bc39c834 - 94a50db37d1a - 625fd9476402 - - 9946bc39c834 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -734,8 +734,8 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - 544f6d2329ac - d64562a4ebb3 + - 544f6d2329ac tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index 036c264d1..3844a784e 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -20,8 +20,8 @@ tools: - name: gubbins owner: iuc revisions: - - 637ec5d5368c - 96e6283e4745 + - 637ec5d5368c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -33,87 +33,87 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 3b8b5bde0bd9 + - f73435dc282b + - 26de3a7b1cb9 - f04a1264e2a2 + - 3b8b5bde0bd9 + - 81e66674859e + - 6a457678efcb + - '841557158611' + - d7c7ef3353fe - 8834daeb9892 + - c78f3d7dd1db - a6619171428e - - '841557158611' + - cce7b18495e4 - 3f59ebfbfe3d - - 5a7c56a5cc08 + - d033ffc1c161 - 107d3ba7024a - - f73435dc282b + - 5a7c56a5cc08 - b89cac5156ec - - 26de3a7b1cb9 - - d7c7ef3353fe - - cce7b18495e4 - - 81e66674859e - - c78f3d7dd1db - - d033ffc1c161 - - 6a457678efcb tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 6283babe736e - - 6223845127ea - - 7a2092844346 - - 3b96e92e8ec3 - - 4755f52427c4 - b0af57c1a968 - e75442c7f4da + - 4755f52427c4 + - 3b96e92e8ec3 + - a185b079b095 - 5b777002c2de - - 5fcd1ece3a6e - - 659517798cc4 - - aa8cc71438cf - - 02b8758214b0 - df47d4845b62 + - aa8cc71438cf + - 6283babe736e + - 659517798cc4 - 88c4aa435ded - - a185b079b095 + - 6223845127ea + - 7a2092844346 - 6a726db04d4b + - 5fcd1ece3a6e + - 02b8758214b0 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: + - b8476e82ac20 - f97743d52b87 - c1d53e95327f - d1c340a5664b - 9b892d7f82cc - - b8476e82ac20 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - daddf188c13f - 9e10ba792be2 - - 128ba8da994f - feb40665d7cd + - 128ba8da994f + - daddf188c13f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - abf6dbe8c9d7 - 5f8727ff21e7 - - 14ae456b8cc5 - - 7bb8726be37c - - b6abccb1f25b - - 2f1019071464 - - 81804a978fc0 - - a2099fb98cdb - - 9d61d3fa046c - - 3a43c3982401 - - 42a174224817 - ca0d8cf80567 + - a2099fb98cdb - 03ed9524dcd1 - - 36912871ccdc + - abf6dbe8c9d7 - 83a69484cb87 + - 14ae456b8cc5 + - 42a174224817 + - b6abccb1f25b + - 2f1019071464 - ca337cce3888 - - b7e297c2ede6 - - 2fa9d4f1b48f - 437e28791761 + - 2fa9d4f1b48f + - 36912871ccdc + - b7e297c2ede6 + - 9d61d3fa046c + - 7bb8726be37c + - 81804a978fc0 + - 3a43c3982401 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -125,21 +125,21 @@ tools: - name: raxml owner: iuc revisions: - - a4b71be30c3c - - 73a469f7dc96 - - ba29b5e2a4be - 29ff6a849eac + - 73a469f7dc96 - ea30d3089354 + - ba29b5e2a4be + - a4b71be30c3c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: + - dbe2b2204555 - 15ac71df11a0 - - 91887494eb97 + - f1ccc8a6eb05 - e88a7de55d6e + - 91887494eb97 - 809e42326fc2 - - f1ccc8a6eb05 - - dbe2b2204555 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/picard.yml b/usegalaxy.org.au/picard.yml index 3b4f28d82..d6a69563b 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -3,12 +3,12 @@ tools: owner: devteam revisions: - 1aac2a13842a - - f9242e01365a - 7d34178f2812 - fc288950c3b7 + - 881d7645d1bf - b502c227b5e6 - - f6ced08779c4 - a1f0b3f4b781 - - 881d7645d1bf + - f6ced08779c4 + - f9242e01365a tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomic_ai.yml b/usegalaxy.org.au/proteomic_ai.yml index 51d71a354..7f88ffe85 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,13 +2,13 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - eb085b3dbaf8 - - ca90d17ff51b - - c0e71cb2bd1b - - a58f7eb0df2c - d00e15139065 - - 5b85006245f3 + - c0e71cb2bd1b - 7fbec959cf2b - 3bd420ec162d + - eb085b3dbaf8 + - a58f7eb0df2c + - 5b85006245f3 + - ca90d17ff51b tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomics.yml b/usegalaxy.org.au/proteomics.yml index a61883291..216d6cc5f 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,30 +2,30 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - f28ad96b76dc - - b574b84afc4d + - 0a18ac48ac53 - 277dc652246e + - f28ad96b76dc - b18329a8ac14 - - 0a18ac48ac53 - ece627528a78 + - b574b84afc4d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - e215f71d7983 - - b41107d8fe89 - - e988563cc6e5 - 525f201b86c1 + - b41107d8fe89 - bf06d196e23d + - e988563cc6e5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: + - 8da3511c9467 - bb6397b94018 - 4fbffddde8cd - - 8da3511c9467 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering @@ -33,36 +33,36 @@ tools: revisions: - b8c79e70516d - a8157342d9a3 - - 528fb09022be - f23d67e28cc8 + - 528fb09022be tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: + - 59e85306eae5 - 80600735685d - 25b83cbd596a - - a95a82eb4d50 - - 59e85306eae5 - a69865da6f80 + - a95a82eb4d50 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 611d80c0e29d - ed9ed1e6cca2 - e0669b1854b1 - f1897eb07081 - 798da6bdff3d + - 611d80c0e29d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 74b61bf5bc4b - - a7fb9b395ddf - 5a35e3a8d013 + - a7fb9b395ddf + - 74b61bf5bc4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations @@ -76,10 +76,10 @@ tools: - name: cardinal_spectra_plots owner: galaxyp revisions: - - 043f9c91f686 + - c5aa9fca18c6 - d2483487e077 + - 043f9c91f686 - 1693b2126f30 - - c5aa9fca18c6 - 10566783d718 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -99,6 +99,7 @@ tools: owner: galaxyp revisions: - 9fa3dbf06f17 + - ae4dc0c041f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -110,8 +111,8 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - d263296cd73e - d0ea7589e95f + - d263296cd73e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify @@ -144,82 +145,82 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - e66f552a3c47 - - d286ff4600dd - 160538a890a6 + - d286ff4600dd + - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 60ee8c592b13 - 71411ac28268 + - 60ee8c592b13 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar owner: galaxyp revisions: - - 9cb7dcc07dae - 3fc2116ac6d9 + - 9cb7dcc07dae tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - 4d17fcdeb8ff - - e42225f8a659 + - 837224ad1694 - 97a7f34fcb6a - f522c08e900c - - 7f432d87c82c - 37d669de2828 - 8934bc76bb52 - - 837224ad1694 - - 2133b0be850a + - 7f432d87c82c + - e42225f8a659 - 1f39c833f65f + - 2133b0be850a + - 4d17fcdeb8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - - 0ed07016d668 - - a72ac2c7cc5b - '860429737408' + - 0ed07016d668 - 85b8866f06d7 + - a72ac2c7cc5b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 352b37c66d97 - - 990b4560ead7 - 1974224d63c2 + - 990b4560ead7 + - 352b37c66d97 - 4187b6df1a40 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - deaf035bbe9f - 4f359549383c - 99450519d727 + - deaf035bbe9f - a1daafbf5233 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: + - e79958768a2c + - c7745841de24 - c1343e3389ca - 40ca115438d2 - - c7745841de24 - - e79958768a2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - d2eac53666f0 - - b648e45fd3cf - da986f83631b + - b648e45fd3cf + - d2eac53666f0 - d46d64e7964d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -247,25 +248,25 @@ tools: - name: msstats owner: galaxyp revisions: - - 28434abe6c5c - 8212e342e482 - - b7034eff0db1 - 593839e1f2c3 + - b7034eff0db1 + - 28434abe6c5c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - a5e394b36d87 - bd1535813cfe + - a5e394b36d87 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid owner: galaxyp revisions: - - 4e77b8f12cd3 - - 8960fb791701 - 01dbaf6a57e0 + - 8960fb791701 + - 4e77b8f12cd3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -277,58 +278,58 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: + - c9eff69a7c62 - 9cdf15d3cfc8 - 518b1730cf2a - f7fef900f5b2 - - c9eff69a7c62 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - 5e948629bc73 - - dff6c756eee5 - ca88bd28f116 + - dff6c756eee5 + - 5e948629bc73 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 658494a2cb00 - 41859bbdc16e + - 658494a2cb00 - 890025d6e426 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 6634cad7d797 - 5ad0b5bf1deb - 9b7977080f6d + - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - 0bb5056cb775 - - 05d5e1ddc985 - d6878d27f051 + - 05d5e1ddc985 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: + - febd569ad26f - 5ad830edc021 - 52ba9695e752 - - febd569ad26f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - 92352a475eed - - 27cba4c5fc42 - 39e8fde08881 + - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector @@ -342,9 +343,9 @@ tools: - name: openms_idconflictresolver owner: galaxyp revisions: - - c28f13cab67a - 8a04ed1c1d1b - 3720e349ba2a + - c28f13cab67a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter @@ -360,48 +361,48 @@ tools: owner: galaxyp revisions: - 39caaa778d2e - - 8ddb7bab1138 - b5d0905419da + - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: + - 1c5f31b8d632 - 18f93351f8b6 - f817513840a9 - 8d4db262964c - - 1c5f31b8d632 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 5d9f175dff81 - 111c3a00136d + - 5d9f175dff81 - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 0e52c85f3b15 - be74a8cd7d66 + - 0e52c85f3b15 - 476b5e296979 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter owner: galaxyp revisions: - - 9866e1170611 - e133b5c8878f + - 9866e1170611 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - - a407b6790342 - - c18d8efa4474 - 2b2a7551a857 + - c18d8efa4474 + - a407b6790342 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver @@ -414,8 +415,8 @@ tools: - name: openms_mztabexporter owner: galaxyp revisions: - - bf32e0bcf554 - 8098330f6d91 + - bf32e0bcf554 - ee860980edc6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -429,15 +430,15 @@ tools: - name: openms_openswathassaygenerator owner: galaxyp revisions: - - 2a9ff56cb279 - 8c01da82292c + - 2a9ff56cb279 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - e8f64a7dc470 - 1bf940c18d93 + - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator @@ -450,15 +451,15 @@ tools: - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - d4396637b9f5 - 0bddef8d144e + - d4396637b9f5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 8b814eafce2c - 89254095cbf6 + - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher @@ -478,32 +479,32 @@ tools: - name: openms_openswathworkflow owner: galaxyp revisions: - - 2aebe58de46e - bc63b4d12779 + - 2aebe58de46e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - 5ae104d0da6e - - 3d8d4ada5405 - decc397c3b7e + - 3d8d4ada5405 + - 5ae104d0da6e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - e039cc5c7aed - dd173849c3d8 - - 5182338d5e7c - 539a3a4dcc9e + - 5182338d5e7c + - e039cc5c7aed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 8a45fd5a608a - 16026cdb1330 + - 8a45fd5a608a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter @@ -528,35 +529,35 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: - - c8b225c69a7f - - 7f6a1f27553e - fb52e95a370c + - 7f6a1f27553e + - c8b225c69a7f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - 073a2965e3b2 - a6282baa8c6f + - 073a2965e3b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptide_genomic_coordinate owner: galaxyp revisions: - - 5f49ffce52cb - cb0378d2d487 + - 5f49ffce52cb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: + - da885ca16cb2 - 7fdd9119cc4f - 1beff3ddce58 - - 3634c90301af + - 3ec27b4cee7c - 07ff622ec007 + - 3634c90301af - a72c48001f7c - - 3ec27b4cee7c - - da885ca16cb2 - 943a34df6047 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -611,10 +612,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 1a5690a5eedc - - 265c35540faa - 12692567c7f9 + - 1a5690a5eedc - a371252a2cf6 + - 265c35540faa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index c83449283..1b26d0b7e 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,65 +2,65 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: + - cd5f98911089 + - 42201b90e3f4 - 110a346daf36 - 2f1d464ebfd2 - - cd5f98911089 - e345aadf914f - 289b7d6b69a4 - - 42201b90e3f4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - 0345dbaaa79b + - 42d9087b4789 + - 8501601a118d - 0cd2df8af811 - c207119ba5f6 - fcce77c09289 - - 8501601a118d - - 42d9087b4789 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - 89eb29319bf4 - - 421c33b8bf17 + - ad5ab22ffe24 - 04db7fd6b238 + - 89eb29319bf4 - 33486216eec0 - 405a212b32ab - - ad5ab22ffe24 + - 421c33b8bf17 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: + - 7b72fde3d27e + - 1d839ead7ad3 - eb784fa07f80 - 7370bb65bad4 - - 1d839ead7ad3 - fa51dc5e8386 - f6e91108b7b1 - - 7b72fde3d27e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - - 1544278c272e - 8a55d29c8fcf + - d30e36c48c93 + - c9b77ced9a78 - a3e86cd9cac7 + - 1544278c272e - 3d70c2996730 - - c9b77ced9a78 - - d30e36c48c93 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - 7b881f5f5ad5 - - a5969aa9347e - - 564c33e5c3e3 - 887cf585cafc + - 564c33e5c3e3 + - a5969aa9347e - b242deb58952 - e2db212d64ad tool_panel_section_label: RAD-seq @@ -68,55 +68,55 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - 9a171f9a450b - bd5ff77e2036 - - 8cff84759bf6 + - 9a171f9a450b - b4bab607eb05 + - 8cff84759bf6 - e897c74a48bb tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - 4f65e343ecdf - - 5e10f396979e - 33f0793edf93 - - adc7a7610d4f - 6dafad990086 - 887e0991eb24 + - 5e10f396979e + - 4f65e343ecdf + - adc7a7610d4f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - c287418eb288 + - 17d39bf0a63a + - c5d7050e4ad7 - 97575d01f06b + - c287418eb288 - 43e3eeb2e0ec - - c5d7050e4ad7 - 4e280b27a831 - - 17d39bf0a63a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - 9586f08634c0 - - 0b8c84a7fdb5 - - 09b8edb56d80 - d9bf483266a1 - - a819ec3b362d + - 09b8edb56d80 + - 0b8c84a7fdb5 + - 9586f08634c0 - cd034465d4a4 + - a819ec3b362d tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - 69842dd5aa48 - - a9c34a289493 - - bf0e43ab0416 - - a4b4bd84f69e - 95351dd0fd3f + - a9c34a289493 - 2645575d1bf2 + - a4b4bd84f69e + - bf0e43ab0416 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -124,10 +124,10 @@ tools: revisions: - 912f904a6e1e - d033e1ccb386 + - d1fda11e602f + - bb0475c884ff - cfb504394ae1 - 8a35a3bc6752 - - bb0475c884ff - - d1fda11e602f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -163,9 +163,9 @@ tools: - name: stacks_populations owner: iuc revisions: - - 95286af4139b - - d1fad35bdb4a - d504d945a655 + - d1fad35bdb4a + - 95286af4139b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 56c311eb9..2887ac5c8 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -9,8 +9,8 @@ tools: - name: arriba_get_filters owner: iuc revisions: - - 32e542c2a773 - 125d20cb23d7 + - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -46,23 +46,23 @@ tools: - name: cuffcompare owner: devteam revisions: - - e66b9b5b8580 - f648e5180e40 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: - - e04dbae2abe0 - d080005cffe1 + - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - - 86285ddd4512 - 6a6717a5f421 - cf747d1bd79a + - 86285ddd4512 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -93,44 +93,45 @@ tools: - name: describe_samples owner: iuc revisions: - - e3b16fd7dd08 - - 0693ccd171c4 - 3b36efd62b3e + - 0693ccd171c4 + - e3b16fd7dd08 - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - cd9874cb9019 - - d027d1f4984e - - 24a09ca67621 - - 9a882d108833 + - 8fe98f7094de - 0696db066a5b + - 24a09ca67621 + - d027d1f4984e + - cd9874cb9019 - 6a3a025714d3 - - 8fe98f7094de + - 9a882d108833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - 2872c633f07e - - df929f257179 - - 62adf13b86ea - b47c006d90c5 + - 62adf13b86ea + - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - f2843df56434 - - 334ce9b1bac5 - - a8305cf0c951 - - 555659de7321 - - df0c8d0a5992 - - 9bdff28ae1b1 + - 0cb907a2a810 - 3d89af8a44f0 - 6e53e565fc6a + - 555659de7321 + - a8305cf0c951 + - 334ce9b1bac5 + - 9bdff28ae1b1 + - df0c8d0a5992 + - f2843df56434 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -149,16 +150,16 @@ tools: - name: featurecounts owner: iuc revisions: - - e6a2a912677a - - 38b6d12edc68 - a37612abf7f9 + - e6a2a912677a - ea04b737afa0 - - af814359d244 + - 38b6d12edc68 - 90d16db017d7 - - f3a5f075498f - a56fbe2d6ba7 - - 7db9d3ea71c9 - 6f66ae7c5f7a + - f3a5f075498f + - 7db9d3ea71c9 + - af814359d244 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_transcripts_via_tracking @@ -176,8 +177,8 @@ tools: - name: gffcompare owner: iuc revisions: - - 3c97c841a443 - 0f710191a66d + - 3c97c841a443 - f99dd58de04f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -190,20 +191,20 @@ tools: - name: hisat2 owner: iuc revisions: - - 26371a1df031 - - 3fb01a8c902d + - f4af63aaf57a - a86e80d3c09c - d4b55e2beb12 - - 6c19daec423d - - f4af63aaf57a - 6ab42baa56e9 + - 6c19daec423d + - 26371a1df031 + - 3fb01a8c902d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - - 67b0b160903a - 916cb26bd9d3 + - 67b0b160903a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -215,18 +216,18 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 1c75aa5de15e + - 5ae5c312d718 - ce5d418183c5 - 87c11c05d238 + - 1c75aa5de15e - 01247aaf0a10 - - 5ae5c312d718 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - 4f9c4e6566e5 - 40985510cd98 + - 4f9c4e6566e5 - 10c98fab6c5a - c971db6f0fe5 tool_panel_section_label: RNA-seq @@ -234,13 +235,13 @@ tools: - name: limma_voom owner: iuc revisions: - - d6f5fa4ee473 - - 97e06a4c7c75 - - 58c35179ebf0 - 32511f586472 - - 708348a17fa1 - - 0921444c832d - e827f9aae031 + - 0921444c832d + - 708348a17fa1 + - 58c35179ebf0 + - 97e06a4c7c75 + - d6f5fa4ee473 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -252,8 +253,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - a8d24f4b6d95 - dbbe92348c7a + - a8d24f4b6d95 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_quantifier @@ -289,18 +290,18 @@ tools: - name: rgrnastar owner: iuc revisions: + - 980d2a2e1180 - b9e04854e2bb - - 0a563fd2f22e - - 5ec75f5dae3c - - 4074fc1940e2 - - e132e7d02a3e + - 99b17b74a8cd - 7ed2edc1337f - - c772497b2c32 - - 3ea5a2a63fa2 - 4df95e2d7f61 - - 99b17b74a8cd + - e132e7d02a3e + - 5ec75f5dae3c + - 0a563fd2f22e + - c772497b2c32 + - 4074fc1940e2 - c7c55b694974 - - 980d2a2e1180 + - 3ea5a2a63fa2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -312,34 +313,34 @@ tools: - name: salmon owner: bgruening revisions: - - 49121db48873 - - 53e9709776a0 + - e3d32471da11 + - ebab418107f5 - 2c0ca397d302 - cc05793bb896 + - 49121db48873 - 15cd64d7c58b - - e3d32471da11 - - ebab418107f5 + - 53e9709776a0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - fab6ff46e019 - - 56242ff81c84 - 8c28affc7c48 - c0fd285eb553 + - 56242ff81c84 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - 914cfcba0ec8 - - 1ebd14235b92 + - 76d290331481 + - 258d696dbd7e - cef79931dda5 - dd4df992d93d - - 76d290331481 + - 1ebd14235b92 - ae618321f34a - - 258d696dbd7e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -363,26 +364,26 @@ tools: - name: transdecoder owner: iuc revisions: - - ffd1300599a1 - - d0d4cef4f967 - 0db979fead3a - c6334cb383ff + - ffd1300599a1 + - d0d4cef4f967 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: + - ba3720d7e68b - d6a479fd4281 - - 74217fbfba4d - bcc5f03f1900 - - ba3720d7e68b + - 74217fbfba4d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 56162e446004 - c2b82a94493e + - 56162e446004 - 478f36effca1 - 2fb4ee002432 tool_panel_section_label: RNA-seq @@ -390,26 +391,26 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: - - fab23c3b5258 - 3f4094b6a565 - 9ff3765e7172 + - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 34a018cbee9c + - 4687ecf0eb2d - be3f26533209 - 870ac06dff8e - - 4687ecf0eb2d + - 34a018cbee9c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: + - 05ab8d5e04a2 - 65e7dea767ea - 5192f657f305 - - 05ab8d5e04a2 - 33406f5a445c - c5fbddcac63a tool_panel_section_label: RNA-seq @@ -419,49 +420,49 @@ tools: revisions: - 1fdb25a8384d - e406ac71165d - - a35cba31d904 - 6f0fb35b799c + - a35cba31d904 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - - 7c7fbf13aadd - 37a1129c89d2 - - 964b7efe2639 - c2c039e421af + - 964b7efe2639 + - 7c7fbf13aadd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - - 1d689e4e1caf - 24e94d84adc9 - eafea3083352 + - 1d689e4e1caf - 047c22569787 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: - - 9871104ea630 - - 3a4ac03d1266 - 1812dbc5bb7b + - 9871104ea630 - 04bb8bb7c198 + - 3a4ac03d1266 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity owner: iuc revisions: - - d2bc35f3d1c5 - - db1f362cca3e - - cee61b3fcf78 - - c9cfec002f71 - - 48636f857c4b - d84caa5a98ad + - 48636f857c4b - 9fa24d5aac68 - - 32b86cd8eb50 + - d2bc35f3d1c5 + - cee61b3fcf78 - 8f1c3df4dd49 + - 32b86cd8eb50 + - db1f362cca3e + - c9cfec002f71 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/usegalaxy.org.au/rseqc.yml b/usegalaxy.org.au/rseqc.yml index b2c45c52e..ba833d62f 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: + - 473382134e56 - 1a052c827e88 - 080fd5739bb4 - - 473382134e56 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/sambam.yml b/usegalaxy.org.au/sambam.yml index c481b0a05..12147e60d 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,16 +2,16 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 88eedb4abea0 - 10184eaa85fc + - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - - 1dfd95ee241e - 108db6635177 - cb20f99fd45b + - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamutil_diff @@ -42,8 +42,8 @@ tools: owner: iuc revisions: - e7fd6754d093 - - 5f8e69cc4c6e - 19ece8afbaab + - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -94,60 +94,60 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 12749212f61b - - 9149ad20699a - 46c6639921f1 + - 9149ad20699a + - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - 06dc50b7b711 - - 33208952b99d - 92ec40abcdcf + - 33208952b99d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx owner: iuc revisions: - - a8d69aee190e - 720217c23995 + - a8d69aee190e - b3d99709fe1a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - 22970df7a40e + - fe34990e5ce7 - db17d5321bad + - 22970df7a40e - cc61ade70eb8 - - fe34990e5ce7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - 7def34e6cf4d - 88b8c2916784 - 811fc2d75ad4 + - 7def34e6cf4d - 7a6034296ae9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - b40e2d865d52 - - 36677f429310 - 740ce0a18f0d + - 36677f429310 + - b40e2d865d52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: + - 583abf29fc8e - 329deb17a9f7 - 8da515fbc1bf - 9da0311ab1dd - - 583abf29fc8e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -160,9 +160,9 @@ tools: - name: samtools_reheader owner: devteam revisions: + - bb8cfc6f6e0c - db000c6007a0 - 30388d878f81 - - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -174,8 +174,8 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - a4a10c7924d1 - 344fc91e1bfd + - a4a10c7924d1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -198,22 +198,22 @@ tools: - name: samtools_stats owner: devteam revisions: - - 145f6d74ff5e - - 24c5d43cb545 - 3a0efe14891f - 1cc79f49b8d5 + - 145f6d74ff5e - 5a08c09b9311 + - 24c5d43cb545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - bf328cec6a42 - - 350bbc5c2ffd - - b72793637686 - - 0dbf49c414ae - 5826298f6a73 + - 350bbc5c2ffd - c370440f901e - b01db2684fa5 + - 0dbf49c414ae + - b72793637686 + - bf328cec6a42 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/send_data.yml b/usegalaxy.org.au/send_data.yml index a8bb55925..f78b39f07 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -3,9 +3,9 @@ tools: owner: iuc revisions: - 6f6537780379 - - a62c4a11a67d - d147d6455873 - - 59bb6d34fca6 - 4aab5ae907b6 + - 59bb6d34fca6 + - a62c4a11a67d tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/single_cell.yml b/usegalaxy.org.au/single_cell.yml index 5b9697950..9b5bc4e3a 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -2,40 +2,40 @@ tools: - name: anndata_import owner: iuc revisions: - - cfc3f5a57dc6 - - fb9e030ffae4 - - 32e547223c9e - 55e35e9203cf - 00712416fdaa + - 32e547223c9e + - fb9e030ffae4 + - cfc3f5a57dc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: + - 39e945f0b2c1 - b9fac48532eb + - 688357ad5e61 - ee98d611afc6 - 038e32885fec - - 688357ad5e61 - - 39e945f0b2c1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: + - 3d748954434b - 9bd945a03d7b - - 43cb7b5a6fe7 - d4af736e7b83 + - 43cb7b5a6fe7 - b85871dd69f9 - - 3d748954434b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils owner: iuc revisions: - - cdf4443d5625 - 2c1200fba922 - - a9caad671439 + - cdf4443d5625 - 8855361fcfc5 + - a9caad671439 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -47,15 +47,15 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 7ffaa0968da3 - 282819d09a4f + - 7ffaa0968da3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 56371b5a2da9 - 2ba99a52bd44 + - 56371b5a2da9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset @@ -126,16 +126,16 @@ tools: owner: iuc revisions: - ab55fe8030b6 - - a407e7f8bdc1 - 3bcd5445cd7a + - a407e7f8bdc1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - aa0c474463c2 - - dbbe1ea8ecb1 - 6adf98e782f3 + - dbbe1ea8ecb1 + - aa0c474463c2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -150,24 +150,24 @@ tools: owner: iuc revisions: - b834074a9aff - - fd808de478b1 - 8f333f90d8d6 + - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter owner: iuc revisions: - - 7a365ec81b52 - 652923ce664f - b7ea9f09c02f + - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter owner: iuc revisions: + - 2e41b35b5bdd - ef4c80837bc5 - 81e5bdff4853 - - 2e41b35b5bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index ce6fbf342..d23e9e5d2 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,11 +32,11 @@ tools: - name: datamash_ops owner: iuc revisions: - - 2f3c6f2dcf39 - - 562f3c677828 - - 419027d822d6 - 746e8e4bf929 + - 2f3c6f2dcf39 - 4c07ddedc198 + - 419027d822d6 + - 562f3c677828 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass @@ -49,15 +49,15 @@ tools: - name: dwt_cor_avb_all owner: devteam revisions: - - 8564f6927b87 - e01e8a9a82f4 + - 8564f6927b87 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all owner: devteam revisions: - - 0b89b03ad760 - 506ae7b0d85d + - 0b89b03ad760 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass @@ -70,9 +70,9 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: - - 6c29c7e347e8 - cb1c59d69557 - 7a15159140d1 + - 6c29c7e347e8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: + - 7442b94d6a1e + - 840f29aad145 - b1eda492f063 + - 9c3e1d3235c8 - aef56d0e7a61 - 9160cb4069c2 - - 118e230e85ce - - 840f29aad145 - - 9c3e1d3235c8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 5a125d1ac9b9 - - adaf2457d6ec - - d0352e8b4c10 - 07843f917990 - 375bbd555f4a + - 5a125d1ac9b9 + - d0352e8b4c10 + - 9fda0b82f419 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - cd02bf168d23 - - d33d37f32e54 + - 4cc980df6265 - 2c58b83c9bad + - 7ae443e6217d - 4db563e8d453 - - 4cc980df6265 + - cd02bf168d23 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: + - ad7e0b4291ee - 7dd3fb35904f - 1dd433d2c92c - - aeca97d9a214 - - ad7e0b4291ee - - 8eed73e8e04d - 4bbaf77573ef + - aeca97d9a214 + - bb9fc9d46ea4 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index 7cdf2e2ad..6d435749d 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -8,6 +8,7 @@ tools: - name: add_value owner: devteam revisions: + - 023f0a3760b3 - 745871c0b055 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -20,20 +21,20 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - 6c6d26ff01ff - f18f67056946 + - 6c6d26ff01ff tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: - - 6e8d94597139 + - 9cd341095afd - 02026300aa45 - - be25c075ed54 - - 464b9305180e + - 6e8d94597139 - 6595517c2dd8 + - be25c075ed54 - 13b6f0007d9e - - 9cd341095afd + - 464b9305180e tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -71,9 +72,9 @@ tools: owner: iuc revisions: - 9cc411a62277 - - 34d29339abab - 557ec8d7087d - 37cde8134c6a + - 34d29339abab tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -104,20 +105,20 @@ tools: - name: query_tabular owner: iuc revisions: - - cf34c344508d - - 33d61c89fb8d - - 1ea4e668bf73 - 623f3eb7aa48 - 2e8f945f7285 - - 3a6b78c39dca + - 1ea4e668bf73 - 83069b38aa85 + - 3a6b78c39dca + - 33d61c89fb8d + - cf34c344508d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - 399da6b5ec21 - ae8c4b2488e7 + - 399da6b5ec21 - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -130,26 +131,26 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: + - b722161a845a - bce29ec10b78 - f768f6183386 - - b722161a845a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: - - 60ff16842fcd - 3bf5661c0280 + - 60ff16842fcd tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: + - f46f0e4f75c4 + - 74a8bef53a00 - ddf54b12c295 - - 9ff72e942410 - - a6f147a050a2 - d698c222f354 - - 74a8bef53a00 - - f46f0e4f75c4 + - a6f147a050a2 + - 9ff72e942410 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/variant_calling.yml b/usegalaxy.org.au/variant_calling.yml index 4b88c80cc..38d0c9bfb 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -3,8 +3,8 @@ tools: owner: iuc revisions: - 0d18a3ba2d1c - - 82fb5e3bb93e - 85c57cc9b558 + - 82fb5e3bb93e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cutesv @@ -16,39 +16,39 @@ tools: - name: freebayes owner: devteam revisions: - - 156b60c1530f - 57def2d7c093 - - 04fa42777df9 - a5937157062f - ef2c525bd8cd + - 04fa42777df9 + - 156b60c1530f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 435b157bed6d - - 791f73caa0c8 - - e61c9ac190ad - 09d6e4693887 + - e61c9ac190ad + - 791f73caa0c8 + - 435b157bed6d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 3b4b2121842f - - e1461b5c52a0 - - 03627f24605f - dfadc322b065 - 4805fe3d8fda - - 074d44697036 - 65432c3abf6c + - 074d44697036 + - e1461b5c52a0 + - 3b4b2121842f + - 03627f24605f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 9cb929f21cfa - 701d134358ad + - 9cb929f21cfa - 7dfca164d2e3 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -56,17 +56,17 @@ tools: owner: iuc revisions: - 426d707dfc47 - - 971e07ca4456 - - f4473557ffc7 - c27549b9aa1f + - f4473557ffc7 + - 971e07ca4456 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - dbd9f2db9ed8 - - cdaab621d454 - aa35ee7f3ab2 + - cdaab621d454 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -84,8 +84,8 @@ tools: - name: snippy owner: iuc revisions: - - 5bbf9eada9c2 - d220115f882b + - 5bbf9eada9c2 - fa016f1eea1a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -122,19 +122,19 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - 32f14a2723ec - - 40f0591deda0 - ee4a90760848 - - 3b1e7c170b10 - e7aff4a85df5 + - 40f0591deda0 + - 32f14a2723ec + - 3b1e7c170b10 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: + - 02d81b994ef5 - 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