diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index f3f4bed40..25f9c5a5a 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -8180,3 +8180,55 @@ Install 1708 09/12/24 01:40:47 scanpy_run_umap False Installed ebi-gxa bd4a244fa Install 1708 09/12/24 01:41:38 scanpy_run_umap False Installed ebi-gxa fe562424a0a6 fe562424a0a6 HCA Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1708/install_log.txt Install 1708 09/12/24 01:42:29 scanpy_scale_data False Installed ebi-gxa 5605f8452eb3 5605f8452eb3 HCA Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1708/install_log.txt Install 1708 09/12/24 01:43:22 scanpy_scale_data False Installed ebi-gxa f86b2c3bc459 f86b2c3bc459 HCA Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1708/install_log.txt +Update 223 11/12/24 01:21:18 dada2_assigntaxonomyaddspecies False Installed iuc 3a89c3f99f3d 3a89c3f99f3d Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 01:21:56 dada2_removebimeradenovo False Installed iuc 1770d188f72d 1770d188f72d Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 02:27:21 data_manager_bowtie2_index_builder False Errored devteam 39865c64a4e1 39865c64a4e1 Production Installation 0/0 None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 03:31:50 data_manager_bwa_mem_index_builder False Errored devteam 0a87b85d9911 0a87b85d9911 Production Installation 0/0 None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 04:36:34 data_manager_fetch_genome_dbkeys_all_fasta False Errored devteam 4a82d1157b14 4a82d1157b14 Production Installation 0/0 None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 05:41:07 data_manager_sam_fasta_index_builder False Errored devteam defd3e9ddd2d defd3e9ddd2d Production Installation 0/0 None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 05:44:52 data_manager_star_index_builder False Installed iuc 71c994a11f71 71c994a11f71 0/0 None toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 06:06:35 flye False Installed bgruening cd11366d92cf cd11366d92cf 9/9 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 06:37:30 hicexplorer_chicaggregatestatistic False Installed bgruening c3ffb2c1e314 c3ffb2c1e314 2/2 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 06:41:22 hicexplorer_chicdifferentialtest False Installed bgruening 45828071edc3 45828071edc3 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 06:46:51 hicexplorer_chicexportdata False Installed bgruening 1a31e75e979e 1a31e75e979e 3/3 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 06:50:36 hicexplorer_chicplotviewpoint False Installed bgruening 920526260066 920526260066 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 06:54:54 hicexplorer_chicqualitycontrol False Installed bgruening f6a169b5e43b f6a169b5e43b 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 06:58:36 hicexplorer_chicsignificantinteractions False Installed bgruening ff1af7bac1cb ff1af7bac1cb 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 07:02:51 hicexplorer_chicviewpoint False Installed bgruening 37125838e360 37125838e360 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 07:09:12 hicexplorer_chicviewpointbackgroundmodel False Installed bgruening 6f8debcf2ac9 6f8debcf2ac9 2/2 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 07:13:39 hicexplorer_hicadjustmatrix False Installed bgruening e8760fc0e29b e8760fc0e29b 2/2 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 07:18:37 hicexplorer_hicaggregatecontacts False Installed bgruening 30677e95bc89 30677e95bc89 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 07:23:03 hicexplorer_hicaverageregions False Installed bgruening 3240e8a7c54f 3240e8a7c54f 2/2 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 07:29:55 hicexplorer_hicbuildmatrix False Installed bgruening d9967770de96 d9967770de96 2/2 HiCExplorer toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 07:34:41 hicexplorer_hiccomparematrices False Installed bgruening 5dd1aae12f03 5dd1aae12f03 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 07:41:02 hicexplorer_hiccompartmentspolarization False Installed bgruening 87eb9c58cd19 87eb9c58cd19 4/4 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 07:49:24 hicexplorer_hicconvertformat False Installed bgruening 574f295b5ba4 574f295b5ba4 7/7 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 07:58:26 hicexplorer_hiccorrectmatrix False Installed bgruening 937b7b9832d0 937b7b9832d0 5/5 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 08:04:10 hicexplorer_hiccorrelate False Installed bgruening 0f5786ffa10d 0f5786ffa10d 2/2 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 08:12:22 hicexplorer_hicdetectloops False Installed bgruening 4375e25de06a 4375e25de06a 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 08:17:28 hicexplorer_hicdifferentialtad False Installed bgruening 4977f65da0ff 4977f65da0ff 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 08:20:57 hicexplorer_hicfindrestrictionsites False Installed bgruening f0b1bd38745a f0b1bd38745a 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 08:33:54 hicexplorer_hicfindtads False Installed bgruening 478aacfbaa37 478aacfbaa37 2/2 HiCExplorer toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 08:44:55 hicexplorer_hichyperoptdetectloops False Installed bgruening 3e5c86c2f80d 3e5c86c2f80d 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 08:49:06 hicexplorer_hicinfo False Installed bgruening 7fbd6feba1ca 7fbd6feba1ca 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 08:52:45 hicexplorer_hicinterintratad False Installed bgruening 908fa330b93b 908fa330b93b 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 08:56:41 hicexplorer_hicmergedomains False Installed bgruening febfddb0b3e8 febfddb0b3e8 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 09:00:29 hicexplorer_hicmergeloops False Installed bgruening 1d9799f4b854 1d9799f4b854 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 09:05:33 hicexplorer_hicmergematrixbins False Installed bgruening 9d93c8fbe0a6 9d93c8fbe0a6 1/1 HiCExplorer toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 09:11:04 hicexplorer_hicnormalize False Installed bgruening 5e83c077e31d 5e83c077e31d 3/3 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 09:29:37 hicexplorer_hicpca False Installed bgruening f86ca478c6af f86ca478c6af 5/5 HiCExplorer toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 09:38:10 hicexplorer_hicplotaverageregions False Installed bgruening 3f1b286a5c34 3f1b286a5c34 4/4 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 09:52:42 hicexplorer_hicplotdistvscounts False Installed bgruening 89cfe7de541b 89cfe7de541b 3/3 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 10:04:44 hicexplorer_hicplotmatrix False Installed bgruening 025a128652dc 025a128652dc 3/3 HiCExplorer toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 10:09:17 hicexplorer_hicplotsvl False Installed bgruening 1602cc5b673c 1602cc5b673c 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 10:15:08 hicexplorer_hicplotviewpoint False Installed bgruening a10fce08c2dc a10fce08c2dc 2/2 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 10:18:58 hicexplorer_hicquickqc False Installed bgruening b13e7a200525 b13e7a200525 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 10:25:27 hicexplorer_hicsummatrices False Installed bgruening d74cf4a61d65 d74cf4a61d65 2/2 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 10:36:00 hicexplorer_hictransform False Installed bgruening df64cc4dfb4d df64cc4dfb4d 2/2 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 10:39:36 hicexplorer_hicvalidatelocations False Installed bgruening d890828ab02a d890828ab02a 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 10:48:25 infernal False Tests failed bgruening 3711f654044e 3711f654044e Staging Testing 7/12 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 10:54:14 krakentools_alpha_diversity False Tests failed iuc 78b69342c280 78b69342c280 Staging Testing 3/5 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 11:08:11 quast False Tests failed iuc a3b35edea53a a3b35edea53a Staging Testing 11/13 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 11:08:58 rgrnastar False Installed iuc 53255f6eecfc 53255f6eecfc RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 11:09:45 rna_starsolo False Installed iuc 381a32c51141 381a32c51141 Mapping toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt +Update 223 11/12/24 11:10:23 volcanoplot False Installed iuc ab01e379d29e ab01e379d29e Graph/Display Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_223/install_log.txt diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index 4a179745e..4b2fcc8d2 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,87 +2,87 @@ tools: - name: abricate owner: iuc revisions: + - 4efdca267d51 - 3f3e247c053d - - 78c75f134c16 - 6e9aea89e388 - - 4efdca267d51 + - 78c75f134c16 - c2ef298da409 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 owner: iuc revisions: - - 3f438bf5475d - c45c9dd066e2 + - 3f438bf5475d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_gaeval owner: iuc revisions: - - 8dc7512c9dc9 - 1dd7adc21b6d + - 8dc7512c9dc9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_locuspocus owner: iuc revisions: - - c4ac24510b55 - 1fdc517743e6 + - c4ac24510b55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_parseval owner: iuc revisions: - - 1b52f0c8ad7f - d6c074a93c51 + - 1b52f0c8ad7f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - 3e1f6f6d557e - - a79ee60b6926 - - 4f2967b27e67 - - cd2480f35935 - - 44018dd6b447 - - fe3ca740a485 - 133f36c29579 + - cd2480f35935 - f29602ae449e - - 1aae04680c4b + - 4f2967b27e67 + - 44018dd6b447 - b5d8e5475247 + - 1aae04680c4b + - 3e1f6f6d557e + - fe3ca740a485 + - a79ee60b6926 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 - - dc027fa56d55 - f1e653756174 + - dc027fa56d55 - 7be22100e5e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 09855551d713 - - bd0e53f3a891 - - 28433faa6e42 - ca6d970d931c + - 28433faa6e42 + - bd0e53f3a891 + - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - d77802fe76f7 - - 92eee5f31117 - da5f1924bb2e + - 92eee5f31117 + - d77802fe76f7 - 728dacaf08a9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -103,8 +103,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 1b9a9409831d - 8bd92f2404dd + - 1b9a9409831d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -116,17 +116,17 @@ tools: - name: cpat owner: bgruening revisions: - - 7ccc6234b54e - - 8e9e228c54c4 - 1ac12c0cc7a0 + - 8e9e228c54c4 + - 7ccc6234b54e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - 9d1fbff733cf - - d9c3016f7283 - 63662ae295d6 + - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -156,61 +156,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: + - 3bbe70fef6df + - 9f2455341fac + - 9c15ca7e764e - 756376aeb1ae - 14f588312c56 - - 3bbe70fef6df - 582fd74dc2a1 - b6b5cd37f2a2 - - 9c15ca7e764e - - 9f2455341fac tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 989f7c061f35 - 8e1ace8f77c6 + - 30fb23d4c31c - 0ffe5be70caf - a230ea445788 + - 989f7c061f35 - 73428a792541 - - 30fb23d4c31c - 1691af4a0d17 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 5a5ae61da69c - - 57c6718cbfcc - 0418d28136de - - 563a19373357 - 494f0bb4a993 + - 57c6718cbfcc + - 5a5ae61da69c - e94187d661df + - 563a19373357 - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - f77d7b685bb3 - - 1bc5a03faf2e - - f31125bb85ea - - 2bba2ff070d9 - 4b96ced19f75 - - 7abc5f6dd595 - d6c7106b7b2e + - 2bba2ff070d9 + - 1bc5a03faf2e + - 7abc5f6dd595 + - f77d7b685bb3 + - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - fed64e676186 - - b3cf4684e9c7 - - 54961e026fe4 + - d3af38b9c7e1 - d77fdcca400e - 52af33194019 - - d3af38b9c7e1 + - fed64e676186 + - b3cf4684e9c7 - 520e30695ec3 + - 54961e026fe4 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -222,8 +222,8 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 2aea122fbd25 - 07d7991bf205 + - 2aea122fbd25 - 79261884facd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -236,9 +236,9 @@ tools: - name: goseq owner: iuc revisions: - - 43798b4caee0 - - 8b3e3657034e - 602de62d995b + - 8b3e3657034e + - 43798b4caee0 - ef2ad746b589 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -270,9 +270,9 @@ tools: - name: interproscan owner: bgruening revisions: + - 74810db257cc - 98cafcbd2578 - c55643c3d813 - - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -297,19 +297,19 @@ tools: - name: maker owner: iuc revisions: - - 370c210d9541 - - 3c1a01127868 - d46d803ca6cc + - 3c1a01127868 + - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: + - e95d52d295d7 + - 033755194fe9 - c8ac28e8ac44 - 624606f7c996 - - 033755194fe9 - b815ec682418 - - e95d52d295d7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -351,11 +351,11 @@ tools: - name: prokka owner: crs4 revisions: - - a17498c603ec + - 8a22554cdde2 + - bf68eb663bc3 - eaee459f3d69 - d643e3b03500 - - bf68eb663bc3 - - 8a22554cdde2 + - a17498c603ec tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -367,15 +367,15 @@ tools: - name: repeat_masker owner: bgruening revisions: - - ba6d2c32f797 - 3f987772e283 + - ba6d2c32f797 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler owner: csbl revisions: - - 41bfbaf3c959 - 8661b2607b7e + - 41bfbaf3c959 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -399,22 +399,22 @@ tools: - name: snpeff owner: iuc revisions: + - c7275bd8b4d6 + - 5b80f544c67f + - 68693743661e - cfcf33df7fc0 - - 5a29ab10dba6 - 8f92c2b26e6d + - 5c7b70713fb5 + - 5a29ab10dba6 - 268d162b9c49 - 6322be79bd8e - - 5c7b70713fb5 - - 5b80f544c67f - - 68693743661e - - c7275bd8b4d6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 5fab4f81391d - 09d6806c609e + - 5fab4f81391d - 2b3e65a4252f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -427,8 +427,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - eb35257d2e29 - 10b84b577117 + - eb35257d2e29 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -440,18 +440,18 @@ tools: - name: tbprofiler owner: iuc revisions: + - 37213cf56392 - d03af1c7002c - - ac8250086ac3 - - 037a11682176 + - 45083d070fb8 - ba6f87115e13 - - 8cb134b8c1a5 - - 37213cf56392 - - 4839e590cb26 - - e1a9d6fd258d - 51dd22484644 - - 45083d070fb8 - - 200c378d85f3 + - e1a9d6fd258d + - 037a11682176 - 809dfc93d593 + - 8cb134b8c1a5 + - 200c378d85f3 + - ac8250086ac3 + - 4839e590cb26 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index 67307ae8a..a58955c36 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,28 +2,28 @@ tools: - name: abyss owner: iuc revisions: - - 7547fcab5d19 + - a929ce596a34 + - 841084c5fc46 - fa5259cc561b - - 553bfe8bd0b5 + - 7547fcab5d19 + - d6d5ccc2c581 + - 890b794c997d - 0e93176640ac - - 841084c5fc46 - 0124fce4654a - 8f1b150a2487 - - 890b794c997d - - a929ce596a34 - db9b10824c61 - - d6d5ccc2c581 + - 553bfe8bd0b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 21e491ad532a - - 067592b6b312 - - b9e31c5c01c7 + - 94fe43e75ddc - ddddce450736 + - 067592b6b312 - b2860df42e16 - - 94fe43e75ddc + - 21e491ad532a + - b9e31c5c01c7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -36,11 +36,11 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - faee8629b460 - 3371c5bdc17a - - 22286dab5aa1 - - 5258e18bbe23 + - faee8629b460 - a7f16f24e9a1 + - 5258e18bbe23 + - 22286dab5aa1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -53,32 +53,32 @@ tools: - name: busco owner: iuc revisions: - - 5ecdeca79a0d - - 2babe6d5c561 - - bb935709506a + - e5c372c91e46 - ea8146ee148f - - 1440ae06552f - - 46ae58b1d792 + - 41030a6c03b7 + - 2dd755c1c6ff + - bb935709506a + - 602fb8e63aa7 - cf13a1e03e5b - - 4048d82f0c88 - - e824f5d958d0 - 94170eee0ad8 - - 2dd755c1c6ff + - e824f5d958d0 + - e4bd1e99bacf + - 5ecdeca79a0d + - 46ae58b1d792 + - 4048d82f0c88 - 0d243f458b53 - f18f0b887c31 - - e4bd1e99bacf - - 41030a6c03b7 - - e5c372c91e46 + - 2babe6d5c561 + - 1440ae06552f - 1e62c28ba91d - - 602fb8e63aa7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - c5b7390290b1 - - 86f150c8019d - 5732f959936a + - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -90,44 +90,45 @@ tools: - name: flye owner: bgruening revisions: - - e27815e82dd4 - cb8dfd28c16f - - 3e4f8642c77e - - 3ee0ef312022 - 291923e6f276 - 1ce9b1d72ec3 - 276f5d8712d5 + - 3ee0ef312022 + - 3e4f8642c77e - 8d4f03b5fe9d + - cd11366d92cf - 1f0769f0b56b + - e27815e82dd4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - b2f674562a18 - - 460fad600dce - 01210c4e9144 - 3169a38c2656 + - 460fad600dce + - b2f674562a18 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 8b330a577046 - - 7348b69e5109 - ba88bc5a6446 + - 7348b69e5109 - 06bcf65179fb + - 8b330a577046 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 3ef480892a9f - - f4a3eff8ab85 - - 3fba9c77550a - - 6ec1b853c8fd - 690c2caa367e - 5127a713de83 + - 6ec1b853c8fd + - f4a3eff8ab85 + - 3fba9c77550a + - 3ef480892a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -139,24 +140,24 @@ tools: - name: hifiasm owner: bgruening revisions: - - 5f625c63b8bc - - 5bec28269d95 - - 284a1cb82b61 - - df25d4fb79b7 - 366a11d316a7 + - 9ef6920c3089 - 5161f204ba63 + - 60024a528cbd - 71740308d412 + - 5f625c63b8bc + - 045c7c3d8e59 + - 41cea2aa2dce - da9d8bf98802 - 2061fb3b81b4 - - 6505bd37670d - f3c89da3af16 - - 9ef6920c3089 - - 41cea2aa2dce + - 5bec28269d95 - ec9e21e9c71b + - df25d4fb79b7 - 3f7be05a1597 - 0ee0c3089254 - - 60024a528cbd - - 045c7c3d8e59 + - 284a1cb82b61 + - 6505bd37670d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -174,43 +175,43 @@ tools: - name: megahit owner: iuc revisions: - - de387b2b2803 + - a96f3ad4e0d8 - 14ddfc8ffb93 + - de387b2b2803 - 7518ee87b53d - - a96f3ad4e0d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - f8113c25bc6b - - 39edec572bae + - d7edbc9c3a07 - eb7b00ec347d - 9d79beb19ac3 - - d7edbc9c3a07 - 09c589057ee8 + - 39edec572bae + - f8113c25bc6b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: + - 51c2360aa807 - eadfd71dde37 - 29dabd8db6f2 - - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - f369ef5f210b - - 606b09cc9860 - - 99ecfdafc64f - - f338e9942b27 - 3ca2d2a9068c - fd128c111ab0 + - f338e9942b27 + - e731ea24e48d + - 606b09cc9860 + - f369ef5f210b - eb7a370f6588 + - 99ecfdafc64f - 2ecf5a570907 - - e731ea24e48d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -222,11 +223,11 @@ tools: - name: miniasm owner: iuc revisions: - - 8dee0218ac7d - - 8b6d0d85252b - - b799a615995d - - 73a3846701e1 - a7b889b90140 + - 73a3846701e1 + - b799a615995d + - 8b6d0d85252b + - 8dee0218ac7d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -244,8 +245,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 64a1c751d99b - 15200570e926 + - 64a1c751d99b - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -258,46 +259,46 @@ tools: - name: pretext_map owner: iuc revisions: - - dfb8a4497339 - - bbe19ef04a74 - - d256a51a656b - 2b16ba799da9 - - c6cec5ab35c1 - 8fef980d48b5 + - bbe19ef04a74 + - c6cec5ab35c1 + - d256a51a656b - 02831bf9e95f + - dfb8a4497339 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: - - 342a1d1fed7b - ebb0dcdb621a - - 875d0f36d66f - - 3061c8b029e5 - 6fcbee531de6 + - 875d0f36d66f - 59db8ea8c845 - - 675488238c96 - - 7594365c546b + - 3061c8b029e5 + - 342a1d1fed7b - 72472698a2df + - 7594365c546b + - 675488238c96 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - 39bed8de8017 - a199cd7ac344 - - d865b62f501c + - 39bed8de8017 - cd06929b224b - 78c533842eeb - aa39b19ca11e + - d865b62f501c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -315,19 +316,19 @@ tools: - name: raven owner: iuc revisions: + - 3edba9afc9bc + - 2b2a352488fa + - 5c55448d0f33 - f11b994b7eb2 - 33b7d8481a76 - - 5c55448d0f33 - - 3edba9afc9bc - f8564b2d7f63 - - 2b2a352488fa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast owner: iuc revisions: - - f73ab5187eed - 8e66f695d859 + - f73ab5187eed tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades @@ -335,11 +336,11 @@ tools: revisions: - ef69617ecb42 - 5fc94b3a4704 - - e122f9101584 - - 53c2bc8c2ae3 - - 378e55aeeb25 - 28189050e437 - 1d06c8b38e77 + - e122f9101584 + - 378e55aeeb25 + - 53c2bc8c2ae3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -351,21 +352,21 @@ tools: - name: shovill owner: iuc revisions: - - f698c7604b3b - ee17a294d3a3 + - 196a599ec43d + - f698c7604b3b - ad80238462c1 - - 865119fcb694 - 83ead2be47b2 - d9f6a00b6db7 - - 196a599ec43d + - 865119fcb694 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 5e0825476fb7 - 015283de3004 - 24e471d13fe9 + - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades @@ -373,169 +374,169 @@ tools: revisions: - 7490b213baa9 - c33a476f4001 - - 051fd2db8a27 - - 904bf932cf78 + - 604782a8a53a - 1fc82fe7ebef + - 051fd2db8a27 - 1bb12736175c - - 604782a8a53a + - 904bf932cf78 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: + - ad8b536d1caa + - fee85957cebe - 808b3a0a6716 - - d6e617c4e338 - 9678993ca5bd - - 34305b013402 - - fee85957cebe - - ad8b536d1caa + - d6e617c4e338 - 655fa188c3cc + - 34305b013402 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - e5a3b75a271f - - 037f9927c4ff - - b8002c3f7141 - - 21da31ed41a1 - - 6b5a5842531e - 8d4b90bf9caf + - 6b5a5842531e + - 037f9927c4ff - 7e27faaad80e + - 21da31ed41a1 + - b8002c3f7141 + - e5a3b75a271f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: + - 86f66ab58e14 - 328aa71f0f3c - - 2a10645aeadd + - f1532cb33c75 - 7922870efcca - 5b26685e5d3b + - 2a10645aeadd - 9de69775f512 - - 86f66ab58e14 - - f1532cb33c75 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 6aad515a5270 - - 340bc17f49cf + - 1708851f8804 - 8cc856b935ee + - 340bc17f49cf - 85fb02c43042 - - 1708851f8804 + - 6aad515a5270 - e41dcb0e913b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - b3490b036c5a - - d5fb354f745d - 6357b127161e - - d159735a6a9f - - b65a43f70b99 - de1260f8a300 + - d5fb354f745d - 249f6a28c751 + - b3490b036c5a + - b65a43f70b99 + - d159735a6a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - d2d1df21dfb9 - - 33368fec3b70 - - b7829778729f - - a90db5dbaaf3 - - 7897763d14ec - dd7ad84f3943 + - 7897763d14ec - d5887ace0dd4 - 9006e5836729 + - a90db5dbaaf3 + - b7829778729f + - 33368fec3b70 + - d2d1df21dfb9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 6f4c8ad6ea01 + - 8f631679571f - 0368ac680e70 - - 505a9833ab5d - - ced385aa976d - 189e837009c9 - - 8f631679571f + - ced385aa976d + - 505a9833ab5d + - 6f4c8ad6ea01 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 9ded6109434a - - e59bee4565b3 - - 19bdfd1e6fe3 - - 356afed970b4 - - d40ed4eb0c0e - a7ed21de23fe + - d40ed4eb0c0e + - 356afed970b4 + - 19bdfd1e6fe3 + - e59bee4565b3 + - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - ebd801e712bc - 4688ae3b49b5 + - b23249f81bc4 + - 6dd935e4984b - 7673a6c920b2 + - ebd801e712bc - 80a17897564d - - 6dd935e4984b - - b23249f81bc4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - 59bd28f6265d - - 937ea677d437 - - b64696992ee9 - cb1e3db43020 - - b5e35a2ca4f3 + - b64696992ee9 + - 937ea677d437 + - 59bd28f6265d - ed312479d9eb + - b5e35a2ca4f3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 6015aa0303f2 - - 05bd7504fdb2 - b9b0246a2be3 - cb4768eeca3b - - 2628f6790eda + - 05bd7504fdb2 + - 6015aa0303f2 - 383bb5ad32e2 + - 2628f6790eda tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: + - 6e26c9afd301 + - e92675014ac9 + - 9e3e80cc4ad4 - 3e44ef016b45 + - e022dff952df - 8f9f06995f98 - 0a3a602cd1e3 - - 6e26c9afd301 - - e022dff952df - - 9e3e80cc4ad4 - - e92675014ac9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 920677cd220f - - 5da9a0e2fb2d - 08256557922f + - 5da9a0e2fb2d + - 920677cd220f - 8d09f8be269e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - d81360ea69d8 - - 4a53b89fa703 - - 82398ba86ba7 - 37d88f41c810 + - 82398ba86ba7 + - 4a53b89fa703 - 0e2b4e3f9ca1 + - d81360ea69d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index 9dd4ec51c..877344ac3 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,10 +2,10 @@ tools: - name: integron_finder owner: iuc revisions: - - 1ae00120dd24 - 4768f7f8e93f - - bfd290fe1588 - 392f100eebcd + - bfd290fe1588 + - 1ae00120dd24 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -17,17 +17,17 @@ tools: - name: mlst owner: iuc revisions: + - 1f5641a52664 - 31812e7a1315 - 8e8dc9a1e3e5 - - 1f5641a52664 - ded48b36f3b7 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: + - 17fcac7ddf54 - 24a7a95867b0 - 5c8ff92e38a9 - - 17fcac7ddf54 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bb_tools.yml b/staging.gvl.org.au/bb_tools.yml index 52d5136ee..5c1b8fa6d 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,14 +2,14 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - d58c27d2c5a7 - - 7beb76ffbc0f + - 1c427e24fb79 - d1f62024a08b - - a9c9d768b751 - 204a131e47db - - 0840ba83860c - 159b04e36791 - - 1c427e24fb79 + - a9c9d768b751 + - 0840ba83860c + - d58c27d2c5a7 + - 7beb76ffbc0f tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index 38777d513..ace394327 100644 --- a/staging.gvl.org.au/bed.yml +++ b/staging.gvl.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - a8eabd2838f6 - - a1a923cd89e8 + - ce3c7f062223 + - 07e8b80f278c - dde39ba9c031 - - 87ee588b3d45 - - a68aa6c1204a - 589e7e57fd6d - - 0a5c785ac6db - - e19bebe96cd2 + - a8eabd2838f6 + - a68aa6c1204a - b28e0cfa7ba1 - - ce3c7f062223 + - 0a5c785ac6db - 64e2edfe7a2c - - 07e8b80f278c + - e19bebe96cd2 + - 87ee588b3d45 + - a1a923cd89e8 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/blast.yml b/staging.gvl.org.au/blast.yml index 838363517..2022e5d9c 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -8,10 +8,10 @@ tools: - name: diamond owner: bgruening revisions: - - 54f751e413f4 - - 62c9df8382c2 - e8ac2b53f262 + - 62c9df8382c2 - f921014aba5a + - 54f751e413f4 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,15 +23,15 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: + - 5edc472ec434 + - 6f386c5dc4fb - 0e3cf9594bb7 + - acf4e47b734c + - 2889433c7ae1 - d999e774072a + - cbf3f518b668 - e25d3acf6e68 - - 2889433c7ae1 - - 5edc472ec434 - - acf4e47b734c - a52d2d93e595 - - cbf3f518b668 - - 6f386c5dc4fb tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus @@ -43,8 +43,8 @@ tools: - name: taxonomy_krona_chart owner: crs4 revisions: - - e9005d1f3cfd - 1334cb4c6b68 + - e9005d1f3cfd tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index e73bb3709..9c1fee18d 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -8,12 +8,12 @@ tools: - name: ambertools_acpype owner: chemteam revisions: + - f4230f116196 - 6ca543ec1bf8 - 095ad4d096d1 + - 27ee142314a9 - c8cdde00b105 - da6bd1975a71 - - f4230f116196 - - 27ee142314a9 - 710301bc46fa tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -92,8 +92,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 7255688c77f3 - 8e214e52e461 + - 7255688c77f3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_conformers @@ -111,8 +111,8 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - 2a868592ebcb - 67ee76f0e497 + - 2a868592ebcb tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -131,73 +131,73 @@ tools: owner: chemteam revisions: - 79cfd9ead848 - - 0fac8e2afc13 - bfb65cb551d8 - 3b8a9d5ced85 + - 0fac8e2afc13 - 88076940fa94 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - 55918daa5651 + - d532b7e5f64b - 715cd0e87781 - f5d979cb4b54 - eb6564a60136 - - d532b7e5f64b + - 55918daa5651 - b46d4b4d995c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: + - 97872d87ba80 + - f26afd1b7104 - 5579659312e6 - d2f955aea23a - fdf2cc80adb5 - - f26afd1b7104 - - 97872d87ba80 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - d1d0efda35c0 - bc31d02be922 - 319a28774da9 + - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 4da9ee404eab - - 2c349b027a01 - - ed736e6eee39 - cac1886249a2 + - ed736e6eee39 + - 4da9ee404eab - 070e3ecc3fda + - 2c349b027a01 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - 807aa4c9293d - - 73008ef1f487 - - 2e219a2d9327 + - 525ca7c8065f - d1f803b5943c + - da8753545526 + - 807aa4c9293d - f197e34c33a9 + - 73008ef1f487 - c0c9a5024177 - - da8753545526 - - 525ca7c8065f + - 2e219a2d9327 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 1809414a9454 - - 7568ae18908a - - 27ea4e1a3f95 - - 2c8ed1b52bf7 - 61094e01eff9 - c4fbab8e03c5 + - 1809414a9454 + - 2c8ed1b52bf7 + - 27ea4e1a3f95 + - 7568ae18908a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -209,18 +209,18 @@ tools: - name: md_converter owner: chemteam revisions: + - ba83f0923369 + - 730ef07b90ae - d7ec25187599 - ccfbd956a2d3 - - 730ef07b90ae - 79e8ab8f1e81 - - ba83f0923369 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 9a3a1f698fc6 - 48d6a6eb438b + - 9a3a1f698fc6 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_dihedral @@ -268,10 +268,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - b59c91adeac1 + - 1400d1977e7b - e6011617c748 - 4242b4d68e9c - - 1400d1977e7b + - b59c91adeac1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -283,8 +283,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 7672039a0bb0 - 75ee9c410951 + - 7672039a0bb0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -296,8 +296,8 @@ tools: - name: qcxms_neutral_run owner: recetox revisions: - - 33b7a99b6de3 - 8f465c0c3b6c + - 33b7a99b6de3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_production_run @@ -339,10 +339,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - d4c67ced6abc - - 85fad59f8168 - - 9b48456a96fe - bf99565cec1f + - 9b48456a96fe + - 85fad59f8168 + - d4c67ced6abc tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index db5e6e4e8..5d4e0f673 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -2,10 +2,10 @@ tools: - name: diffbind owner: bgruening revisions: + - f907216064f6 - c97a786e8fb5 - 163688bb8f73 - fa56d93f7980 - - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -23,17 +23,17 @@ 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: - - 86e2413cf3f8 - - 640d3af5d833 - - f5d67c722d67 - 495a4173006f + - f5d67c722d67 + - 640d3af5d833 + - 86e2413cf3f8 - 424aefbd7777 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -46,16 +46,16 @@ tools: - name: rnachipintegrator owner: pjbriggs revisions: - - b695071de766 - 087d9872fb0d + - b695071de766 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer owner: devteam revisions: - - 4a14714649b4 - - 74c9214cc8e6 - 5c2cc3b58c7d + - 74c9214cc8e6 + - 4a14714649b4 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/staging.gvl.org.au/collection_operations.yml b/staging.gvl.org.au/collection_operations.yml index bd0b0a56b..f4a53d3ce 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -10,9 +10,9 @@ tools: owner: nml revisions: - 33151a38533a + - 830961c48e42 - 90981f86000f - 25136a2b0cfe - - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 0046692724f9 - 2dae863c8f42 - baabc30154cd - 6cbe2f30c2d7 + - 0046692724f9 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 38eec75fbe9b - 57f0914ddb7b + - 38eec75fbe9b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index c07d9d58a..86061f1e5 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -2,9 +2,9 @@ tools: - name: agat owner: bgruening revisions: - - abba05ead5d7 - e7449b2c14bf - d6ede73082da + - abba05ead5d7 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -16,39 +16,39 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 0b3c3ad92827 - - ab9350a8ab4d - - f3a19509108a - - 3b6f97e7094c - e3cbd2287f63 - - 4a6ee918c13a - - 6ef0b5664c69 - 5e1240a87bcb + - 6ef0b5664c69 + - 3b6f97e7094c - a3b86937ead6 - 367b1ed91207 + - ab9350a8ab4d + - 4a6ee918c13a + - f3a19509108a + - 0b3c3ad92827 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 1b5fc03380d4 - - 501c21cce614 + - 091bb5922a82 + - bd46669113b9 - d4d4e9febf5c - 54ccb7e1f49a - - bd46669113b9 - - 33c99804a32f + - e525f9ffb9ac + - 72ed72122deb + - 1b5fc03380d4 - e177a8ea0bf1 + - 33c99804a32f + - 501c21cce614 - 584008e574b2 - - 091bb5922a82 - - 72ed72122deb - - e525f9ffb9ac 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 @@ -68,16 +68,16 @@ tools: owner: devteam revisions: - 186b8d913e6c - - 77b41c89d856 - 8979c288aefb + - 77b41c89d856 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - 4b347702c4aa - - 43807a65369f - 614a63f14adf + - 43807a65369f tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fml_gff3togtf @@ -102,9 +102,9 @@ tools: - name: gffread owner: devteam revisions: - - 4dea02886337 - - 154d00cbbf2d - 3e436657dcd0 + - 154d00cbbf2d + - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -136,16 +136,16 @@ tools: - name: tabular_to_fasta owner: devteam revisions: - - 0b4e36026794 - 0a7799698fe5 + - 0b4e36026794 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq owner: devteam revisions: - - 2dcfbbf9071a - 68f57cc8fad0 - 78fb18899c99 + - 2dcfbbf9071a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter @@ -153,9 +153,9 @@ tools: revisions: - 19e45916daf9 - 63769c4217a7 - - 26c6706bfb07 - 92ac8e086317 - b9b385097f13 + - 26c6706bfb07 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf @@ -168,9 +168,9 @@ tools: - name: ucsc_twobittofa owner: iuc revisions: - - e9bbe2f71784 - - 8067dfa00ed2 - 3c6f9e8a4c17 + - 8067dfa00ed2 + - e9bbe2f71784 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index f28522915..3336b32b3 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,205 +2,205 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: + - 29451af70c52 - de72ba3ed6f2 - - e821645ef8fc + - a1ca9bccc7f2 - 5f6d123679f4 - - 268e91e540ee - - 29451af70c52 - c929a006727f - - a1ca9bccc7f2 + - 268e91e540ee + - e821645ef8fc tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 0e143b4c3987 - - 12af64f93288 - 5d11599b8a7d - bb1e4f63e0e6 - - 2d2cf5c1ea8a - - 7a7fd0f5f15d - 0e49b109abc2 + - 7a7fd0f5f15d + - 12af64f93288 + - 0e143b4c3987 + - 2d2cf5c1ea8a tool_panel_section_label: 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revisions: - - 004aea905d4d - - 69a8621ca2f0 - - 1fcb7adc39b8 - 78f405266706 + - 1fcb7adc39b8 + - 69a8621ca2f0 - 2d466b530754 - 01fb6a7654e6 + - 004aea905d4d - 192ef85c0b0b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 459cfa861f0b + - 2f9e4843f480 + - db940c262830 - 137c4beed34b - d9ce4897dbb2 + - 459cfa861f0b - d580d6acd1df - - 3c9f0c486cca - - 2f9e4843f480 - 9ecba5e225a6 - - db940c262830 + - 3c9f0c486cca tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - bd7db9e2f2cb - - 2c66e43f1c86 - - f264afa9fa6f - - bad3ca889618 - fd408d755394 - - 32e451def88c + - 2c66e43f1c86 - fbe773640707 + - 32e451def88c + - bad3ca889618 + - f264afa9fa6f + - bd7db9e2f2cb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 9368fbc49c8b - - 56bce3c82278 - - 7fda5607e777 - - 7e361d147872 - 231994413f89 + - 9368fbc49c8b - 4e12ea27f788 + - 7e361d147872 + - 7fda5607e777 + - 56bce3c82278 - 3b9d990a0a0e tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: + - c03c3384cd81 + - 94ca68515826 - e65d16fb2724 - - d9114ef1c8a5 - - b1779366c8e9 - ce4ce3316f74 - - 94ca68515826 - 4431f39ede55 - - c03c3384cd81 + - d9114ef1c8a5 + - b1779366c8e9 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 793665fff0f8 - 4ed32329e0ed - 23f7c5f1fdaf - f8fc4e5aff9d - 2da482e408b8 - b88ebb3672a1 - d57251071381 + - 793665fff0f8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: + - e4c7985d4585 + - 010e58e9d822 + - a4dfb122e52b - 25d830337d31 + - 512155688d98 - ba6efa77fb79 - - c60570fa602f - - 010e58e9d822 - a7849312d328 - - 512155688d98 - - e4c7985d4585 - - a4dfb122e52b + - c60570fa602f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: + - c899e0ccff8c - 38e3f226248b - - 443d9a9d6d11 - - 69264da0ce77 - 4d678170d29b - - c899e0ccff8c + - 69264da0ce77 - aa200e4f3939 + - 443d9a9d6d11 - 00d869ea03a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: + - 6662b1a8d326 + - 10301d137111 - aac8444d6681 + - a2d70c4fd406 - c361b12d207a - d806504e96d9 - - 10301d137111 - - a2d70c4fd406 - - 6662b1a8d326 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/dna_metabarcoding.yml b/staging.gvl.org.au/dna_metabarcoding.yml index 61f922109..6cb272111 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -16,8 +16,8 @@ tools: - name: obi_convert owner: iuc revisions: - - 4d705e3443a7 - e328ced6cf0a + - 4d705e3443a7 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep @@ -37,8 +37,8 @@ tools: - name: obi_ngsfilter owner: iuc revisions: - - 76e69de726b2 - 91a1ed0b486f + - 76e69de726b2 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort @@ -51,15 +51,15 @@ tools: - name: obi_stat owner: iuc revisions: - - 5f4544915893 - 39320fee9d70 + - 5f4544915893 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab owner: iuc revisions: - - 4cf47c504672 - 3299c7d5268f + - 4cf47c504672 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index c20dc3f9c..931e5eb7a 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -3,8 +3,8 @@ tools: owner: devteam revisions: - 832c20329690 + - 63dd26468588 - ce385837c160 - dba489bfcd62 - - 63dd26468588 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index 18bf4bfca..01b09e704 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -8,11 +8,11 @@ tools: - name: bwameth owner: iuc revisions: - - 62f5fab76dfb - - cf1322aeb137 - 6da3972210ee - - 29bdbc353f20 + - cf1322aeb137 + - 62f5fab76dfb - d82648ad25a3 + - 29bdbc353f20 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 2355b7e6e..5385c6efc 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -9,25 +9,25 @@ tools: owner: lparsons revisions: - 48f587c13075 - - 4e5056fefd88 - - 64172f1c1202 - - c4b82dce8335 - - c5e2e5902201 - e4691e1589d3 - - 44e2cc14f75b - - fe74900d6dc7 - - 49370cb85f0f - 5eb7e84243f2 - - 288f97432497 - - 660cffd8d92a - - c053d4cad713 - - 135b80fb1ac2 - - 8665bcc8b847 - - de6cebe3c043 - - 8c0175e03cee - - 093678460093 - b1c926deaa2d + - 8c0175e03cee - 5915ea1ec9b1 + - 8665bcc8b847 + - c4b82dce8335 + - 64172f1c1202 + - 44e2cc14f75b + - 093678460093 + - 135b80fb1ac2 + - de6cebe3c043 + - 4e5056fefd88 + - 288f97432497 + - c053d4cad713 + - 49370cb85f0f + - fe74900d6dc7 + - 660cffd8d92a + - c5e2e5902201 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -39,9 +39,9 @@ tools: - name: fasta_clipping_histogram owner: devteam revisions: + - f666895cbebd - 8889eb864cef - 9db07fd39f85 - - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -53,9 +53,9 @@ tools: - name: fasta_compute_length owner: devteam revisions: + - 5cbde03c1103 - de2db1bdfbf8 - 7d37cfda8e00 - - 5cbde03c1103 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length @@ -67,8 +67,8 @@ tools: - name: fasta_concatenate_by_species owner: devteam revisions: - - 25b8736c627a - 717aee069681 + - 25b8736c627a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_extract @@ -108,9 +108,9 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: + - f773e98b26cf - f81d4362b6c1 - ec0b5076173a - - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -122,10 +122,10 @@ tools: - name: fasta_stats owner: iuc revisions: - - 56022eb50bbd - - 0dbb995c7d35 - - 9c620a950d3a - cd0874854f51 + - 9c620a950d3a + - 0dbb995c7d35 + - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -137,14 +137,14 @@ tools: - name: fastp owner: iuc revisions: - - a626e8c0e1ba - dbfc505896e9 - - 1d8fe9bc4cb0 - - ecb9f4854617 - 65b93b623c77 - - dbf9c561ef29 + - 1d8fe9bc4cb0 + - a626e8c0e1ba - c59d48774d03 + - dbf9c561ef29 - d60c3f704da0 + - ecb9f4854617 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -156,8 +156,8 @@ tools: - name: fastq_combiner owner: devteam revisions: - - 9115b978ce10 - f1dc2a761c30 + - 9115b978ce10 - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -170,9 +170,9 @@ tools: - name: fastq_filter owner: devteam revisions: - - '144275714590' - 81a9090d6df3 - 10b75444feae + - '144275714590' tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -184,9 +184,9 @@ tools: - name: fastq_groomer owner: devteam revisions: + - e9f8633db0a2 - 8611b80a14d6 - 47e5dbc3e790 - - e9f8633db0a2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -198,9 +198,9 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 7861f3b10c68 - - 5b87038565bb - e30352e889fe + - 5b87038565bb + - 7861f3b10c68 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation @@ -213,8 +213,8 @@ tools: owner: devteam revisions: - 4e1d64e6385f - - 9dfda4e310ed - 9282652e7234 + - 9dfda4e310ed tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality @@ -240,9 +240,9 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: + - 3e396e702cea - b41c2c1bcfbf - 2ccb8dcabddc - - 3e396e702cea tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -254,9 +254,9 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: + - 09a2199cd356 - c885369b207b - 8d958759cf2a - - 09a2199cd356 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner @@ -268,10 +268,10 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - 35e38452bb3f + - 397dc333436b - e39cc71d3ed6 + - 35e38452bb3f - 249c8393f2d4 - - 397dc333436b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -284,8 +284,8 @@ 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 @@ -297,8 +297,8 @@ tools: - name: fastq_stats owner: devteam revisions: - - b1cea1b2fcd0 - f86c27295151 + - b1cea1b2fcd0 - f0e7deab6518 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -332,10 +332,10 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - d5e9e83cd3d8 - 09070cacefd8 - - 567d5b3c52b1 - 529bccd5e4a1 + - d5e9e83cd3d8 + - 567d5b3c52b1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter @@ -347,9 +347,9 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: + - 8abdedf55101 - 4bedca26c133 - 0b7ec11b3c7c - - 8abdedf55101 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -361,10 +361,10 @@ tools: - name: fastx_clipper owner: devteam revisions: - - 90858c306551 - cb1e251cac37 - - 736b8f6ee456 + - 90858c306551 - bdf1ce174e39 + - 736b8f6ee456 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -390,10 +390,10 @@ tools: - name: fastx_renamer owner: devteam revisions: + - 02f8a17a4ebd + - f984bb114520 - 3599f5451ee2 - b29d37ca9e41 - - f984bb114520 - - 02f8a17a4ebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -405,10 +405,10 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: - - 6027ef51ef91 - - 0c2907307ba4 - e246088b6e34 + - 6027ef51ef91 - 177f0621c266 + - 0c2907307ba4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -420,9 +420,9 @@ tools: - name: fastx_trimmer owner: devteam revisions: + - 61b4cedc8934 - 73194cdd4f57 - 377ac2829eac - - 61b4cedc8934 - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -447,10 +447,10 @@ tools: - name: pear owner: iuc revisions: - - 2f804526f5fd - - b4c6f054210a - 037f0acc7830 + - b4c6f054210a - f69501361cec + - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -462,39 +462,39 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 8e1a90917fa7 - 3b0a14722175 + - 8e1a90917fa7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort owner: iuc revisions: + - fdc21382376d - 61eb4cfc7313 - 29ef2c5ec205 - - fdc21382376d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: - - fe1ae2ebf63d - - 812705bcf39c - 795cd16de38f + - 812705bcf39c + - fe1ae2ebf63d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: + - 3da72230c066 - a019807f4e67 - 4b494533146a - - 3da72230c066 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - a019807f4e67 - 4b494533146a + - a019807f4e67 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: split_paired_reads @@ -506,16 +506,16 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - dfa082f84068 - 51b771646466 + - dfa082f84068 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - bf04bd405d5b - - 71f649c23021 - d3f58a0dc09d + - 71f649c23021 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -527,12 +527,12 @@ tools: - name: umi_tools_count owner: iuc revisions: - - 71ad4a56c40c - b557acca0b56 + - 24013bf85a6f + - 8250ea3a1501 - a535cf1e5da4 - e654095ab143 - - 8250ea3a1501 - - 24013bf85a6f + - 71ad4a56c40c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -551,14 +551,14 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - f3759eec3018 - - 828dba98cdb4 - - 015cf18f4a15 - - 27ac32a22ad2 - - 7accf7407811 - - 9fa7803d1c51 - 6a675c3aa610 - 7a7e33d28f62 + - 7accf7407811 + - 27ac32a22ad2 + - 9fa7803d1c51 + - 015cf18f4a15 + - f3759eec3018 + - 828dba98cdb4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract @@ -570,8 +570,8 @@ tools: - name: umi_tools_group owner: iuc revisions: - - 428735be9764 - d6255614afd7 + - 428735be9764 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_whitelist diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index 16d6bb3f3..3541dc4a2 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,30 +2,30 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 64e9a6afdd0c - - e41385662e5e - 7b4468117008 - ce9cd02d5b88 + - 64e9a6afdd0c + - e41385662e5e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - 8050e091e99b - c64d534a763c + - 8050e091e99b tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - - 9da02be9c6cc - - 2b0c9d9fc6ca + - 5ec9f6bceaee - e7b2202befea - - 3d0c7bdf12f5 + - 2c64fded1286 - ff9530579d1f + - 9da02be9c6cc + - 2b0c9d9fc6ca - f2e8552cf1d0 - - 5ec9f6bceaee - - 2c64fded1286 + - 3d0c7bdf12f5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -38,40 +38,40 @@ tools: - name: fastx_nucleotides_distribution owner: devteam revisions: + - b6b54ba71bd8 - ad116ae3f4d9 - 18a51655db17 - - b6b54ba71bd8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: + - cc0fd298cc17 - 59003d0543cd - 7306ec78632a - - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - 8880fb74ef56 - - a72af9de6bf5 - 1f296803dfa3 + - a72af9de6bf5 + - 8880fb74ef56 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: + - 9a913cdee30e + - 3d93dd18d9f8 + - 1c2db0054039 + - 5e33b465d8d5 - bf675f34b056 + - f7e2f1eb3a16 - abfd8a6544d7 - - 5e33b465d8d5 - - 3d93dd18d9f8 + - 75c93c70d094 - b2f1f75d49c4 - f7985e0479b9 - - f7e2f1eb3a16 - - 1c2db0054039 - - 9a913cdee30e - - 75c93c70d094 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore diff --git a/staging.gvl.org.au/fetch_alignmentssequences.yml b/staging.gvl.org.au/fetch_alignmentssequences.yml index c01999d90..0dfc5355c 100644 --- a/staging.gvl.org.au/fetch_alignmentssequences.yml +++ b/staging.gvl.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 9e776e7fab4f - 19f42b3ea391 + - 9e776e7fab4f tool_panel_section_label: Fetch Alignments/Sequences tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index ab23c208f..ae96506a7 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.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 @@ -15,8 +15,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: - - 83a19df00eab - 85ef5f5a0562 - 141612f8c3e3 + - 83a19df00eab tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index 3b4f18f40..f5f9ce53d 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -2,30 +2,30 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 142d95ab942e - 3630a6e624d4 + - 142d95ab942e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend owner: iuc revisions: - - be828b79bd4d - 4bd4870ecd33 + - be828b79bd4d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - - f2f3bc622a16 - 0c8f7322f8fc + - f2f3bc622a16 - 8f53b238a360 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden owner: iuc revisions: - - df57188562f0 - 1a4c5adcd587 + - df57188562f0 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets @@ -45,15 +45,15 @@ tools: - name: gemini_de_novo owner: iuc revisions: - - 9db3e299b1c8 - d5b01cc263be + - 9db3e299b1c8 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - d46017ddbf94 - 452104bdc655 + - d46017ddbf94 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -115,8 +115,8 @@ tools: - name: gemini_qc owner: iuc revisions: - - 86e46972e183 - 9e83673fa6d2 + - 86e46972e183 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_query @@ -130,8 +130,8 @@ tools: - name: gemini_recessive_and_dominant owner: iuc revisions: - - 86f3aac4418d - 05124dc72dba + - 86f3aac4418d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region @@ -158,14 +158,14 @@ tools: - name: gemini_stats owner: iuc revisions: - - ee894347fcd6 - 5c9efee9cb1e + - ee894347fcd6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - 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/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 301093442..8627a5283 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -2,15 +2,15 @@ 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 owner: iuc revisions: - - d46e36492bff - b946929d31c4 + - d46e36492bff tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index cc088c9e5..bc2719025 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -4,8 +4,8 @@ tools: revisions: - e9df53a75f3c - c1b437242fee - - 983bf725dfc2 - b39347891609 + - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,53 +17,53 @@ tools: - name: ncbi_acc_download owner: iuc revisions: + - e063168e0a81 - 28587613264f - 1c58de56d587 - - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: + - f5ea3ce9b9b0 + - 7068f48d0ef9 - 6591f049cf7e - - aad3885b3216 - - e407b9da183a - - f8054ea1c365 - - 69ebb7f46e45 - - 1ec814014652 - - 4df8de2d0e48 - 83c7d564b128 - - 5e6237d58b0c - - 6ea73833cf67 - - 7068f48d0ef9 - - 4317d3cb6cba - - e08a7ad4378b - - 9a776b080193 - 734abc7ac21d + - 4317d3cb6cba + - 516a54ddf218 - c441583adae5 - - f5ea3ce9b9b0 + - 9a776b080193 - 653e89d73fc4 - - 8848455c0270 - - 516a54ddf218 - ba931a59dd59 + - e08a7ad4378b + - 5e6237d58b0c - 1790dcf3c32d + - 6ea73833cf67 + - 1ec814014652 + - f8054ea1c365 + - 69ebb7f46e45 + - 8848455c0270 + - e407b9da183a + - 4df8de2d0e48 + - aad3885b3216 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: + - 9aaa46d45472 - 21a560af5913 - - 34758ab8aaa4 - 75b3b3d0adbf - - 9aaa46d45472 + - 34758ab8aaa4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - 468c71dac78a + - af5eccf83605 - 054483e27a35 - bfdc6a7ffd3a - - af5eccf83605 + - 468c71dac78a tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index eb3fca8c6..b1c81d785 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - ae9994cf526f - - fd59d783248a - df7356989ac1 - - a64dc31ab7f2 - - c4bde687c846 + - ae9994cf526f - 740057a5126d + - c4bde687c846 - 7f13dc906cb9 - - 290a11559985 - 4b519282a05b + - a64dc31ab7f2 + - fd59d783248a + - 290a11559985 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -34,9 +34,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 867ab348287d - f95284aa2946 - 7cf5b1d072b5 + - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -48,24 +48,24 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - '566197475670' - - 3b37b1b1c3a7 + - 51c6ccaace7e - 374e9062d874 - ca7cb0eaad62 - - 51c6ccaace7e - - 53460afd5115 - 48b42ee61bc5 + - 53460afd5115 + - 3b37b1b1c3a7 + - '566197475670' tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 3d059e9c2fba - - 1a72f938213e - - 391a4cc45fea - - 10515715c940 - da4c086cff5b + - 10515715c940 + - 391a4cc45fea - d3a9e32672ec + - 1a72f938213e + - 3d059e9c2fba tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -85,19 +85,19 @@ tools: - name: ggplot2_point owner: iuc revisions: - - d0fc8b746d57 - 1acf88921176 + - d0fc8b746d57 + - 5298e06f14f9 - 5fe1dc76176e - 299307abd804 - - 5298e06f14f9 - e3a675da7fd0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - - 17b666467c32 - 0e7290688b50 + - 17b666467c32 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -116,8 +116,8 @@ tools: - name: graphlan owner: iuc revisions: - - 6e8eb0c0d91f - 8f62f666dcb6 + - 6e8eb0c0d91f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -136,17 +136,17 @@ tools: - name: jbrowse owner: iuc revisions: + - ca2def38369c + - 4542035c1075 + - 836d1aa3e89a - fd5dbf0f732e - - 1cfc579079a6 - - 17359b808b01 - 6cd09d7b5f37 - - 667e17248bfe - 112eb40ba6cf + - 1cfc579079a6 - 2bb2e07a7a21 - - 836d1aa3e89a - - ca2def38369c - - 4542035c1075 + - 667e17248bfe - a6e57ff585c0 + - 17359b808b01 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -165,8 +165,8 @@ tools: owner: iuc revisions: - 03c13085aecc - - f1691de443a7 - fe154a7af404 + - f1691de443a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -179,18 +179,18 @@ tools: - name: plot_ragtag_paf owner: galaxy-australia revisions: + - c1bed78b9ed5 - 94e0834ae4ed - 501dcf66c0ce - - c1bed78b9ed5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: - - f234e2e59d76 - - 62e3a4e8c54c - - 85da91bbdbfb - 1c5dcef5ce0f + - 85da91bbdbfb + - 62e3a4e8c54c + - f234e2e59d76 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -209,9 +209,9 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 26f2fe7e53a1 - 44c66e8d21e6 - 7c9417381ad5 + - 26f2fe7e53a1 - 6c571966cfb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -224,23 +224,24 @@ tools: - name: pygenometracks owner: iuc revisions: - - 36b848d5f3ec - - 360df4999907 - - 4ac4e7083b7e - 326a3db8d9d1 - - 7dd841a32245 - 2824d77cd8f8 - a1abfa420d9d - 14e7c35f3d00 + - 360df4999907 + - 36b848d5f3ec + - 7dd841a32245 + - 4ac4e7083b7e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - ab01e379d29e - 83c573f2e73c - - 73b8cb5bddcd - - 2f557f6abbfb + - a363ba287b88 - 44608d0193ed + - 73b8cb5bddcd tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index 00aa36029..de845e9da 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -28,26 +28,26 @@ tools: - name: scanpy_compute_graph owner: ebi-gxa revisions: + - 22bd5861706d - 7779b9dcf040 - 6417cccad133 - - 22bd5861706d - bc9e8de21efb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells owner: ebi-gxa revisions: + - e9283529cba1 - bf1e0bdec1db - 55ccc0a121bc - 361608369dda - - e9283529cba1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes owner: ebi-gxa revisions: - - 23d838d1569d - 474a69c47184 + - 23d838d1569d - cc64914b0cf4 - da611a744112 tool_panel_section_label: HCA Single-cell @@ -55,17 +55,17 @@ tools: - name: scanpy_find_cluster owner: ebi-gxa revisions: - - fc4b3b46dc9d - ad6995afd2e6 - 2ccd9f9e2cd0 - 36735850e461 + - fc4b3b46dc9d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers owner: ebi-gxa revisions: - - d8f5224005bb - 49653e680ea4 + - d8f5224005bb - 81c34e67f262 - 0a8e527d1517 tool_panel_section_label: HCA Single-cell @@ -73,10 +73,10 @@ tools: - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 2861ca3bfe4d + - 64dd8bb151e1 - 4667fe07bd68 + - 2861ca3bfe4d - 79da59a0b180 - - 64dd8bb151e1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn @@ -89,39 +89,39 @@ tools: - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 352cdf3b2f75 - 3c47bc560688 + - 352cdf3b2f75 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - 6903bc865d63 - c354af93f567 + - 6903bc865d63 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - ff6decc0f432 - - 9a2f72d7dbd2 - 94697510d55f + - 9a2f72d7dbd2 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet owner: ebi-gxa revisions: - - 70cb0596ffef - 53ce0e336840 + - 70cb0596ffef tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalise_data owner: ebi-gxa revisions: - 28b1546857b0 - - 6b97ffba31da - - 8d9c22419c56 - 3027cb62adbd + - 8d9c22419c56 + - 6b97ffba31da tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator @@ -134,17 +134,17 @@ tools: - name: scanpy_plot_embed owner: ebi-gxa revisions: - - 7d5c97823f8b - - 35f6611fb8c3 - 56d22aa6cb3b - 1be0fc4d8654 + - 7d5c97823f8b + - 35f6611fb8c3 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet owner: ebi-gxa revisions: - - 4a74b45c1ce4 - 6f5509cf3176 + - 4a74b45c1ce4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory @@ -164,16 +164,16 @@ tools: - name: scanpy_regress_variable owner: ebi-gxa revisions: - - 0bab2ae44e7a - 36daab33aecf + - 0bab2ae44e7a - d18ed15697bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap owner: ebi-gxa revisions: - - 79cc06a557b0 - 6a6364b488db + - 79cc06a557b0 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt @@ -186,8 +186,8 @@ tools: - name: scanpy_run_fdg owner: ebi-gxa revisions: - - be019b069e31 - 65c3ec07502b + - be019b069e31 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_paga @@ -200,9 +200,9 @@ tools: - name: scanpy_run_pca owner: ebi-gxa revisions: - - 59028945c857 - 0cf90e01d9f8 - 4428dba93375 + - 59028945c857 - 3ee74b58c72d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -210,27 +210,27 @@ tools: owner: ebi-gxa revisions: - 3fb53f5e46ea - - abdb61e4afa3 - - 181d61d2f3cd - 8b0d6f6f44c8 + - 181d61d2f3cd + - abdb61e4afa3 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: - - 767a675b5254 - - 0f98603d0116 - bd4a244faeb8 - ea91cfd0444e + - 767a675b5254 - fe562424a0a6 + - 0f98603d0116 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - f86b2c3bc459 - - 5605f8452eb3 - e2d0dc8a50ca + - 5605f8452eb3 + - f86b2c3bc459 - 4cc9362782b4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 31eb96f5a..0884f9f31 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,56 +2,61 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 9edf8894a22d - 29f66c353bcb - - 0f611e7d7858 - - a4c13ddcc8ee - 921a2da49a0c + - d9967770de96 - ed2cca6b5de4 + - 9edf8894a22d + - a4c13ddcc8ee + - 0f611e7d7858 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 5746d61f0a91 - ec4b948dc6f0 - d404277cc87a - 755df866ad0c - - 11de0d28ab30 - 78fb5e286609 + - 11de0d28ab30 + - 478aacfbaa37 + - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 977dc15add20 + - 4d511437b1e5 - 11fa44ee0603 - - 03dd3c16ae4e - - 9e357a8b2ec3 - f72063d9426b - - 4d511437b1e5 + - 9e357a8b2ec3 + - 03dd3c16ae4e + - 9d93c8fbe0a6 + - 977dc15add20 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 1da5f169b491 - - 0ba4f56a3613 + - f86ca478c6af + - 41dbf4d162a2 + - 3b5b54ed6392 - 77919cc3618e + - 0ba4f56a3613 - c3e5e2cf12b7 - - 3b5b54ed6392 - - 41dbf4d162a2 + - 1da5f169b491 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - f741330d4a71 - - 9939786dd9c9 - - 7babd8a46fe0 - b63363075c2e + - 9939786dd9c9 - 12d51d7be66f + - 7babd8a46fe0 - 5308ca68ef3d + - 025a128652dc tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index e3fc944ff..791d75e8e 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,29 +2,29 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: + - 3df9f0a4bf34 + - 0c777d708acc - 81f0cbca04a7 - - 699a5e9146b3 - 7db4fc31dbee - - 3df9f0a4bf34 - 8bccb36e055a - - 0c777d708acc + - 699a5e9146b3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 0a53256b48c6 - - 2436a8807ad1 - - 5bc8cdc17fd0 - 5791a7f65275 + - 5bc8cdc17fd0 + - 2436a8807ad1 + - 0a53256b48c6 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - 6ad1d3cfdea1 - e576b73a2e2f - 9d47aabda459 + - 6ad1d3cfdea1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization @@ -46,8 +46,8 @@ tools: - name: bfconvert owner: imgteam revisions: - - fcadded98e61 - b07f4839ca77 + - fcadded98e61 - 10eed33aa9b2 - f3360fbeda64 - 85edbb7a436b @@ -64,8 +64,8 @@ tools: owner: imgteam revisions: - b58447a2eed2 - - 5bf8eb50b280 - 664232d2a3f7 + - 5bf8eb50b280 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler @@ -86,65 +86,65 @@ tools: - name: cp_common owner: bgruening revisions: - - 6070780813d9 - e7273daa5ae2 + - 6070780813d9 - 670975e92458 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - ef4aed1d34c4 - df3ad3ba5c6f - cdf8e3c57dae + - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 2484086dee41 - 5d28ac336861 - 6a7da2e5f696 + - 2484086dee41 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - bace5a93a97c - - 11f177b1a59e - f2ed92b011a9 + - 11f177b1a59e + - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - d0178bdcd00e - f24c370e5ea4 - f8fa0f6718a3 + - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - ad271f78a87a - - 31d195bedf6d - 3245681b2f6d + - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - b6eec6087271 - - 993faa34333b - 87d4d92d7487 + - 993faa34333b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: + - ff1a86a87364 - c09dcda1143f - 6100a22bf4f2 - - ff1a86a87364 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image @@ -158,8 +158,8 @@ tools: - name: cp_measure_granularity owner: bgruening revisions: - - 2564f461de62 - ac5bea85a391 + - 2564f461de62 - a1a961c46d4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -174,40 +174,40 @@ tools: - name: cp_measure_image_intensity owner: bgruening revisions: - - 8536b1ae0254 - b64af54c5c09 + - 8536b1ae0254 - 5499dc6f8ac1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - d3890df07463 - - 6f4715b8540a - e972e07c7845 + - 6f4715b8540a + - d3890df07463 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - 980aed9e8fd5 - e52c75a28c4b - 407925835dd9 + - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - d85f11570109 - - 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 - b76841ee5560 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -220,9 +220,9 @@ tools: - name: cp_relate_objects owner: bgruening revisions: + - 8083a87d2fdf - 3a3033222f61 - 48102a685037 - - 8083a87d2fdf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images @@ -256,9 +256,9 @@ tools: - name: image_info owner: imgteam revisions: + - f8b4eada923c - 7b6d9412c7f8 - 236ec78b2e53 - - f8b4eada923c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images @@ -270,7 +270,7 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 22e573b7dcb1 - 8ad39f493587 + - 22e573b7dcb1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index 1427db5a8..66d6e97cf 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - f362150bef41 - - 3e4f434a69c6 - - 1069f6db0a0e - - 3a72fede57ce - 40737febe339 + - 1069f6db0a0e + - 78bbd17d0703 - e4ee04da1c19 - - e319b5b65879 - - a38934e303b9 - d6e72da3ec35 - - 78bbd17d0703 + - 3a72fede57ce + - a38934e303b9 + - f362150bef41 + - e319b5b65879 + - 3e4f434a69c6 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - f91cfb73d369 - - c88553ec696e - 9537184d421f - - 7fe36019c073 - 2b95d5c04908 - - 72ddd32392cd + - 8f8df367470d - 0135f1d487a0 - 618297d23022 + - 72ddd32392cd + - 7fe36019c073 + - f91cfb73d369 - fcbeda41d0ac - - 8f8df367470d + - c88553ec696e tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - ad0dc9f4c9e2 + - d7e79eb3bcb3 - fafb3d685fa9 + - ad0dc9f4c9e2 - 2cf4a1cafc16 - - d7e79eb3bcb3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - ee29337f905c - - 43aac8d29685 - - 5dc33613c288 - - ee2beb764a7b - - 7f1cfa4c0e32 - 28a6f1908fcc - - 8c05afb547fa - - a1c2aecd7a0d + - ee2beb764a7b + - bd2a7d1316b9 + - 5dc33613c288 - 8d36959b000d + - 8c05afb547fa - 9eaadf03e0df - - 3d18f8c3c0f6 - - bd2a7d1316b9 + - 7f1cfa4c0e32 + - a1c2aecd7a0d - 6a1515bb0687 + - 3d18f8c3c0f6 + - ee29337f905c - 94df24c6bc00 + - 43aac8d29685 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: + - 9f978da6528a + - 86a20ae274fc + - 5d6ed46cc101 - 364f4ffec275 + - e3bb03cf207a + - d37ede8589b2 + - db536ad45f28 - 8858fa037a15 - - 5d6ed46cc101 - 5671e1d3d5ee - - cb903c9dc33d - - bcaa0d571ce2 - c092052ed673 - - d37ede8589b2 - - 9f978da6528a - - db536ad45f28 - - 86a20ae274fc - - e3bb03cf207a - a250929be21b + - cb903c9dc33d + - bcaa0d571ce2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 3b6a16d82c1b - - ed28dd32141c - e1a015876aa9 - - 12d66d0d05ac + - c5c9f02b6167 - f95f403841ad - 49236b03e4fd - - c5c9f02b6167 - 194e3ceee923 - 230b05597996 + - ed28dd32141c + - 3b6a16d82c1b - 584beffa972b - - 38b91a3190cd + - 12d66d0d05ac - abbc8041e8ec + - 38b91a3190cd tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/join_subtract_and_group.yml b/staging.gvl.org.au/join_subtract_and_group.yml index c40dd66b7..5a076da58 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: - - 17e3b698dd52 - - 0f1724dd59d2 - f198773344e4 + - 0f1724dd59d2 - b8a457820315 + - 17e3b698dd52 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - ac092723240d - - a513e3fbb4c5 - 374cb875d38a - - ba0c40780ecf + - a513e3fbb4c5 - 22c2a1ac7ae3 + - ac092723240d + - ba0c40780ecf tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/machine_learning.yml b/staging.gvl.org.au/machine_learning.yml index 7c20d8272..63e9c75c4 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -10,28 +10,28 @@ tools: - name: keras_model_config owner: bgruening revisions: + - 8a794e6d3388 - 4d81e3e2fb63 - f22a9297440f - - 8a794e6d3388 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - 818f9b69d8a0 + - 2af1346e68c9 - f1b9a42d6809 - b6ef6d0cb6b7 + - 818f9b69d8a0 - e1317b5502fa - - 2af1346e68c9 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 1588f9076e32 - - c80db5d6fd8c - 8334dc98c48e + - c80db5d6fd8c - 05143043ca13 + - 1588f9076e32 - 947c2eacccb8 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -40,8 +40,8 @@ tools: revisions: - 25b46af53232 - 83228baae3c5 - - 1552b8cb4a94 - 9991c4ddde14 + - 1552b8cb4a94 - 29e4122c90de tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -49,52 +49,52 @@ tools: owner: bgruening revisions: - 060ca94ac049 + - 53616c8b0865 - 841a6cc5fc58 - a07ab242b0b5 - - 53616c8b0865 - - f3dfa4bdf87e - 1a53edc4b438 + - f3dfa4bdf87e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: + - 927586a18553 + - 91c4e3331208 + - d4808d5b83da + - dc4b5fd604a6 - 40f4447733b2 - 2fc89dcd41c8 - - dc4b5fd604a6 - - d4808d5b83da - - 91c4e3331208 - - 927586a18553 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 301e07345c93 - - 25ab6b4e376e - - c6ae57f774c6 - 7626ea9c2e1b - e5a5ad882f1f - 36e8d6d5d01b + - 25ab6b4e376e + - c6ae57f774c6 + - 301e07345c93 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 0630258dcf35 - - 4ed102b922cb - - 02d2be90dedb - f9639b488779 - - 80852884053f + - 02d2be90dedb + - 0630258dcf35 - b7c3e9a3b954 + - 80852884053f + - 4ed102b922cb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - ec69cbe34b73 - - 61634a87efc7 - - 14180f9c831e - caeb57858702 + - 14180f9c831e + - 61634a87efc7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index bab5e04f2..8bd20c38f 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: + - a6d65b0c67af - 749c918495f7 - 937aa69e715f - 0d4acadabb04 + - cd659e8cc5fa + - 3ba8d4563129 - 03e9b2fbc005 - f6877ad76b00 - 17062a0decb7 - - cd659e8cc5fa - - d5ceb9f3c25b - - 3ba8d4563129 - - a6d65b0c67af - 017aba02828d + - d5ceb9f3c25b tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -31,11 +31,11 @@ tools: - name: bwa owner: devteam revisions: - - 53646aaaafef - - 3fe632431b68 + - 2477830927ec - dfd8b7f78c37 + - 53646aaaafef - 64f11cf59c6e - - 2477830927ec + - 3fe632431b68 - e188dc7a68e6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -58,35 +58,36 @@ tools: - name: minimap2 owner: iuc revisions: - - 5cc34c3f440d - - c0c2d0941de8 - - 09b53c1d4ab1 - - 6b1e195506a3 - - 037c6e54df11 - f54f5baedfdd - - 53c0b7a1a0c3 - - b3eab4b67562 - 77b2770508f6 - - 3f4d6399997b + - b3eab4b67562 + - 5cc34c3f440d + - 53c0b7a1a0c3 + - 6b1e195506a3 - 11a0d50a54e6 - 8c6cd2650d1f + - c0c2d0941de8 + - 09b53c1d4ab1 + - 3f4d6399997b + - 037c6e54df11 - be1d967337e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: + - b8f5f6e87f5c + - 1cd2511a396e + - 5ef7ec16b04f + - 178bdbdb6d24 + - 381a32c51141 + - ec9cbd6b9a49 - 42ce70172b72 - - 9ee34ba73ebf + - 45795f582ae9 - 79b885ce78d7 - - ec9cbd6b9a49 - 13022c3d3076 - - 45795f582ae9 - - 1cd2511a396e - 00fbfac99d39 - - b8f5f6e87f5c - - 178bdbdb6d24 - - 5ef7ec16b04f + - 9ee34ba73ebf - e403d27e8f24 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/metabolomics.yml b/staging.gvl.org.au/metabolomics.yml index 8f6f2ec58..7e3f55770 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -14,8 +14,8 @@ tools: - name: biotransformer owner: recetox revisions: - - 6cd2a9e6ac49 - 90dc951da294 + - 6cd2a9e6ac49 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_annotate @@ -63,8 +63,8 @@ tools: - name: isolib owner: recetox revisions: - - 6b0fef8a77c0 - 2b1118bce0b1 + - 6b0fef8a77c0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: lcmsmatching @@ -101,8 +101,8 @@ tools: - name: matchms_filtering owner: recetox revisions: - - 83c4b4359ac4 - a177ac3c752c + - 83c4b4359ac4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity @@ -115,8 +115,8 @@ tools: - name: matchms_formatter owner: recetox revisions: - - 1b09315a3f87 - a5a5b147da70 + - 1b09315a3f87 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export @@ -129,8 +129,8 @@ tools: - name: matchms_metadata_match owner: recetox revisions: - - 03bc9b7f40f6 - 330b0dfae8da + - 03bc9b7f40f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge @@ -142,8 +142,8 @@ tools: - name: matchms_networking owner: recetox revisions: - - 8147d93d372d - f04b378325e5 + - 8147d93d372d tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key @@ -249,82 +249,82 @@ tools: - name: ramclustr owner: recetox revisions: - - 9b716db0a786 - da7722f665f4 + - 9b716db0a786 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features owner: recetox revisions: + - 7b42ee54d757 + - c53a97599181 - 79ad928a0dae - ec196e27a61a - - c53a97599181 - - 7b42ee54d757 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - 149b9cc7499b + - 18ec7635bac6 - f3a18e020cdd - 59c393d35e0e - - 18ec7635bac6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - dfebc82ba1f0 - - 481d769e2f7a - - 50b9918aeff2 - 134be5abb208 + - 50b9918aeff2 + - 481d769e2f7a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - a82db010c53e - - 30bf4e35da3e - 51332c2520c7 - - 02c772a49998 - 9064aecc78a7 - 501a232f3cd5 + - 02c772a49998 + - 30bf4e35da3e tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - b3413f335327 - - e7305ba0dd38 - 89178a72388a + - e7305ba0dd38 - b341cfd4baf8 + - b3413f335327 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - b7c8a44b9cc1 + - cf061712a184 - 17a48d0a80f4 + - b7c8a44b9cc1 - dd7bbc2b99d1 - - cf061712a184 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - 99d118321d5f - - d7f5878a98c3 - 24278c6b6d1c - f92b1b64da93 + - d7f5878a98c3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - 7acd11ddc061 - - ea0758b41473 - d90187b0f247 - ffbabefbd2e2 + - 7acd11ddc061 + - ea0758b41473 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -336,8 +336,8 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 6b5dec818827 - 2c6fa447f6a0 + - 6b5dec818827 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature @@ -355,8 +355,8 @@ tools: - name: rmassbank owner: recetox revisions: - - 0b28816c1c2c - 5a6bb93ec656 + - 0b28816c1c2c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: spec2vec_similarity diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index 68c8d73e1..99c4bff41 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -9,8 +9,8 @@ tools: owner: iuc revisions: - 18676df0cb3a - - 0e63d03c8790 - 0094893f5001 + - 0e63d03c8790 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -95,19 +95,19 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 65db807336bc - 5b5a7af9fbb4 + - 76d3d2b10738 - 7c2100246a2f + - 3a89c3f99f3d - 63f86089423e - - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: + - 1c35dadbe76f - 96336c6a2bb7 - 00f5005840fa - - 1c35dadbe76f - 18a502a9d287 - 84fd33a60b35 tool_panel_section_label: Metagenomic Analysis @@ -115,116 +115,117 @@ tools: - name: dada2_filterandtrim owner: iuc revisions: + - e8fba04706d3 - a9f4a217dcd6 - f732237754fc - addaf9d22850 - - e8fba04706d3 - 34e55239e68b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 5fe3edf19b9c + - 8c202e741d68 - 04c15826a0b8 - 75403243703a - - 5fe3edf19b9c - 0776d824d896 - - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 43c99742158b + - e96bbb9e24ea - 8470de786d47 - 75c8945b0da2 - - e96bbb9e24ea - 1c9b3bcd4261 + - 43c99742158b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 1d75bd0595e2 - - 306a40d4bb8f + - 5c865a382933 - 35176674168c - 84743da21318 - - 5c865a382933 + - 306a40d4bb8f + - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 8daf4564ccda - - 555ccac8a4c5 - 32c9ea835770 - - ac72310b038a + - 555ccac8a4c5 - 78faebd0879c + - 8daf4564ccda + - ac72310b038a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - d60df8727f59 - 7b8cb2b02978 - - a58e4a43f49c - - f947b4bb5107 - cae017b76acb + - d60df8727f59 + - f947b4bb5107 + - a58e4a43f49c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 1bc3657cd694 - - 04144473e59e - 073608a50ac3 - - 7136e9ab70db - 7f3b59dee073 + - 04144473e59e + - 7136e9ab70db + - 1770d188f72d + - 1bc3657cd694 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: + - d943081510da - 0a1224c4b781 + - 19299bb1c6af - 9058d8943303 - a7817705348e - - 19299bb1c6af - - d943081510da tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - e005e659ae21 - c7e73acfa3eb + - e005e659ae21 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: - - 4d9445dff47b - - 5c7ba3d85a01 - c4db8c4de66f - - f8f56dd6449f - - 65d52c693b8e + - 5c7ba3d85a01 - b907a3c0434f - - dbf1798c0dcc - a68b985913ab + - 4d9445dff47b + - dbf1798c0dcc + - f8f56dd6449f + - 65d52c693b8e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 15dbb444df71 - 213df31ba341 + - 15dbb444df71 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: - 6c84982ee6f7 - - 6d364c65c946 - 654548ae1357 + - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -237,24 +238,24 @@ tools: owner: iuc revisions: - bd7a9c6efb10 - - 6aad8ca3918b - e66ab198ec15 + - 6aad8ca3918b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - c6676a890f50 - d77397f09da1 + - c6676a890f50 - b084117133af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - 9704f1a3b32d - cad93abecac9 - 7f208f1eb64f + - 9704f1a3b32d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -272,8 +273,8 @@ tools: - name: humann_barplot owner: iuc revisions: - - 523ae8314ef5 - 5fea25ee6275 + - 523ae8314ef5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_join_tables @@ -286,40 +287,40 @@ tools: - name: humann_reduce_table owner: iuc revisions: - - 60749924ad62 - 6552df6efe6b + - 60749924ad62 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_regroup_table owner: iuc revisions: - - 31c6d107e7a5 - - c409a495841f - e88b731dad59 - 8237a0f225db + - c409a495841f + - 31c6d107e7a5 - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 71ea608ddfa3 - - 714d5a28cc5c + - aabf8cfb8fef + - 172920f67a84 - 094ad9c068af + - 714d5a28cc5c - d24841f5c3d2 - - 172920f67a84 - - aabf8cfb8fef + - 71ea608ddfa3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - d7e9a3c41657 - 12fb63b5f63f - - 2bdd84912a2b + - a293a742194f + - d7e9a3c41657 - a4d7148ccee4 - 4137b492233e - - a293a742194f + - 2bdd84912a2b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -331,13 +332,13 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - 64bc7acc22a9 - - a92c06a3afa7 - 6fcb8ac37a3e - - cf87759761eb - e2c71b852aba + - cf87759761eb - 75bedfb2078b + - 64bc7acc22a9 - 97f7bb0851e7 + - a92c06a3afa7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -356,11 +357,11 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 2d35528d2141 + - 4033827c76b8 - 5e5a999ffaa9 - 080ea153677c - 4e5e73d03f0d - - 4033827c76b8 + - 2d35528d2141 - c82508e76ad1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -368,10 +369,10 @@ tools: owner: iuc revisions: - 95bf7479d53c - - 6b7622dda516 - - 2cd76b089570 - fc6c328c292f - c2803012bbb3 + - 6b7622dda516 + - 2cd76b089570 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -389,8 +390,8 @@ tools: - name: jellyfish owner: iuc revisions: - - 11658afb8c87 - dcd30574a456 + - 11658afb8c87 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution_single @@ -403,22 +404,22 @@ tools: - name: khmer_abundance_distribution owner: iuc revisions: - - 7624945cacd3 - e699e2747356 + - 7624945cacd3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_count_median owner: iuc revisions: - - 570505540a7b - b3d513c7093e + - 570505540a7b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_extract_partitions owner: iuc revisions: - - 1061711538c6 - adb3dd5a899f + - 1061711538c6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance @@ -431,8 +432,8 @@ tools: - name: khmer_filter_below_abundance_cutoff owner: iuc revisions: - - 19607c740d19 - 00f7064c564b + - 19607c740d19 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_normalize_by_median @@ -458,17 +459,17 @@ tools: - name: kraken2 owner: iuc revisions: - - 4a9da2b6c2e3 - cdee7158adf3 - 20e2f64aa1fe - 328c607150ff + - 4a9da2b6c2e3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax owner: devteam revisions: - - 50bd98b3ae5a - f03c7ba8d8bc + - 50bd98b3ae5a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -480,22 +481,22 @@ tools: - name: kraken_filter owner: devteam revisions: - - 5bee9adae474 - 67236d921e83 + - 5bee9adae474 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 1c677354ab18 - 6c09bed3444f + - 1c677354ab18 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_taxonomy_report owner: iuc revisions: - - bfae8da6082c - 27d65c78863c + - bfae8da6082c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -580,22 +581,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 327d9f4cc95f - - 27250f92a01a - - 2cff76cf35c6 + - e073891b2afc - 4fd3b5d8706b - 7f5d7b0e9884 - - e073891b2afc - - 3cc4a60615c0 + - 2cff76cf35c6 + - 327d9f4cc95f + - 27250f92a01a - 0270541aaf46 + - 3cc4a60615c0 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - 708abf08a626 - - eb50e7eca3dc - 76bc4efa1aeb + - eb50e7eca3dc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -661,33 +662,33 @@ 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: - - a92a632c4d9b - - 1a037928504c - - ec368db926f4 - - 6dee4abadccb - - fd69c607b43f - - 740fd2d16a28 - - 1a6cdf55390f - - 289b3807e80c - - b89b0765695d - ff8f55893e7d - - a16313517e55 - 2131d7dca455 + - 740fd2d16a28 - ef65b083bd0c + - a16313517e55 + - 1a037928504c + - b89b0765695d + - 289b3807e80c + - fd69c607b43f + - 1a6cdf55390f + - ec368db926f4 + - a92a632c4d9b + - 6dee4abadccb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning owner: galaxy-australia revisions: - - e3a64a1d2a6e - 2a8bc1d26d06 + - e3a64a1d2a6e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -711,22 +712,22 @@ tools: - name: picrust2_add_descriptions owner: iuc revisions: - - 2f47a294ef49 - 6034c3f3ecf0 + - 2f47a294ef49 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_hsp owner: iuc revisions: - - 3b133b8d578a - 6eafc1e01a8c + - 3b133b8d578a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 709adbfcf308 - 415cb5d91168 + - 709adbfcf308 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline @@ -739,8 +740,8 @@ tools: - name: picrust2_pipeline owner: iuc revisions: - - d6bb2e3febda - 540aedfc81c7 + - d6bb2e3febda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs @@ -753,8 +754,8 @@ tools: - name: picrust2_shuffle_predictions owner: iuc revisions: - - 677f3c8db525 - 881f2faa5fe7 + - 677f3c8db525 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -804,8 +805,8 @@ tools: - name: polypolish owner: iuc revisions: - - f355085dd2aa - 915637bd1d1a + - f355085dd2aa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: pynast @@ -830,13 +831,13 @@ tools: - name: staramr owner: nml revisions: - - 2fd4d4c9c5c2 - - 3b22de20bd4b - - 4d83eccf5f81 - - be818ae858e4 - 141afacabcfa + - 3b22de20bd4b - 4b9a8031ab74 - aeaa20b96ef2 + - 4d83eccf5f81 + - 2fd4d4c9c5c2 + - be818ae858e4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -866,8 +867,8 @@ tools: - name: vsearch owner: iuc revisions: - - 576963db5f1b - - b3c7199d8786 - 9495df9dd6ef + - b3c7199d8786 + - 576963db5f1b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index 334c2c5c3..0e15febb9 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - 12e856482d26 - bdb4a58a2025 + - 12e856482d26 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - 63b74bfc8052 - f4d7d5755f01 + - 63b74bfc8052 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index 7fc9bd788..8e5d757a3 100644 --- a/staging.gvl.org.au/multiple_alignments.yml +++ b/staging.gvl.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: + - cd07731e4434 + - 9eeb13a92d79 + - 8b67dd48fec1 - 9baa871cb1d1 + - 48c13389050d - 80f03df2e2ce - - 9422c5a87ee2 - 2263989660f5 - - 8b67dd48fec1 - - 098506c54016 - a74dbfee5a86 - - 9eeb13a92d79 - - bdfbaf0c10aa - 6ae5a7b5a0a2 - - 48c13389050d + - 9422c5a87ee2 - 94b8c6013083 - - cd07731e4434 + - bdfbaf0c10aa + - 098506c54016 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: + - 3ff17bad4006 - fc2e49f91e52 - - 2e093badc689 - - bc3831dd65c1 - c18157c68134 - - 3ff17bad4006 - - d390fe1567dc - - aaa0d6a8b808 - - c44f824c051a + - d7ce0ec78e51 - be78f13134e2 - - 4a60927aaca5 - 5abf2c2249aa - - d7ce0ec78e51 + - bc3831dd65c1 + - d390fe1567dc + - 2e093badc689 - f14193ec1f50 - - f0af8936ed41 + - c44f824c051a + - aaa0d6a8b808 + - 4a60927aaca5 - '764845535798' + - f0af8936ed41 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,15 +46,15 @@ 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 owner: devteam revisions: - - d6694932c5e0 - 5b097fde95dd + - d6694932c5e0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -67,38 +67,38 @@ tools: - name: mafft owner: rnateam revisions: - - f0d493f8f84f - c5908940967d - - a65296ffb4a0 - - bf28a8cff401 + - f0d493f8f84f - f1a5908ea2cb - - 15974dd17515 - 6f28e90db932 + - bf28a8cff401 + - 15974dd17515 - 8e649f27aa0d + - a65296ffb4a0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: + - fbca557a4847 - b3acbb3a6af0 - e8fdceffea4c - - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 60698466facd - c9685bc0407c - 5561a1193611 + - 60698466facd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - bcd65de9725b - - 48823c9635a4 - 57f042937ba7 + - 48823c9635a4 + - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot @@ -112,8 +112,8 @@ tools: - name: mummer_nucmer owner: iuc revisions: - - 7cd7a55a678d - 636b049e6141 + - 7cd7a55a678d - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -121,7 +121,7 @@ tools: owner: iuc revisions: - b4124df98b26 - - 959c1f8dae95 - cf3c9489c088 + - 959c1f8dae95 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index afb02ed16..08e447752 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,9 +8,9 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: + - 9aa9d92c3c51 - 7c47b3c9e493 - 28928576e1ea - - 9aa9d92c3c51 - 18a8d140ec6f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -23,9 +23,9 @@ tools: - name: dorado owner: galaxy-australia revisions: - - 6942f170cc43 - 63d8ecfcfab1 - fc5b6491cf78 + - 6942f170cc43 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: guppy_basecaller @@ -37,19 +37,19 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - cb34f00cc10f - a7228a7ea146 - - fc8804320156 - - 79e9a869f40e - 72b5e9dda577 - 0e9e7fcdd543 + - 79e9a869f40e + - cb34f00cc10f + - fc8804320156 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - fa11aa8103b2 - d6cddc06aeae + - fa11aa8103b2 - 18505fe2bdb1 - db25ec99c3ea tool_panel_section_label: Nanopore @@ -63,15 +63,15 @@ tools: - name: medaka_variant owner: iuc revisions: - - cc36773a3681 - - 19f3b583a9b3 - 43815fa60f3a - 222669c4afb6 - - ec699520444c - - edf6d4003fad - 0f5f4a208660 - eb746fa6f514 + - cc36773a3681 + - edf6d4003fad + - ec699520444c - 2bf63b38ee9b + - 19f3b583a9b3 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -90,60 +90,60 @@ tools: - name: nanoplot owner: iuc revisions: + - 0f1c34698076 + - edbb6c5028f5 - a3c4fe6f49ab - - a02b8b3f5a0c - 645159bcee2d - 7b379e98b9a9 - - edbb6c5028f5 - - 0f1c34698076 + - a02b8b3f5a0c - a38bdcec9e4c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - d219b6d8158a - 85a394edc247 + - d219b6d8158a - 3b6f94fc7e1d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - be95355fef8d - - a8d4be409446 - 90a922f32523 + - a8d4be409446 + - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - 449e9aeded2d - - d376944466bf - 4857d5bcce52 + - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - bec636361cfd - - a3afc5f0a96c - de5b3d8f5b90 + - a3afc5f0a96c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 5f76b20953e5 - 93d623d9979c + - 5f76b20953e5 - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 1d835c691480 - daf8518d243a + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -155,8 +155,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - 47936349f3e9 - d1805f9c4c82 + - 47936349f3e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -168,8 +168,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 0433aad600e9 - 336791b5665f + - 0433aad600e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -219,8 +219,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - c5c5a3e84989 - 64a83664b814 + - c5c5a3e84989 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index 50c6a706d..f6d90744b 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -21,8 +21,8 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: - - 4e85a3a5dbd1 - 71186bb66ca2 + - 4e85a3a5dbd1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_frameshifts @@ -65,19 +65,19 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - adfd6bf710bd - d74850cf4e42 - - 97b1b5ad1cda - - baceff842902 - 3e73c97f025d + - baceff842902 + - adfd6bf710bd + - 97b1b5ad1cda tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 9dd107db92c2 - 1586b111d2a3 - 83da94c0e4a6 + - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -89,19 +89,19 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: + - ed1518ce2237 + - edacc4bcd3cb + - 2f27f3b86827 - e4b4837f06f5 - 1e34d2e3d285 - e9ee4d074d5d - - edacc4bcd3cb - - ed1518ce2237 - - 2f27f3b86827 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -113,30 +113,30 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 472dabcb03bf - 74af283d8ebd + - 472dabcb03bf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_dada2 owner: iuc revisions: - 48a42ca61006 - - 5711fc06a63e - 38ccd4589990 + - 5711fc06a63e 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 @@ -162,8 +162,8 @@ 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 @@ -185,8 +185,8 @@ 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 @@ -198,23 +198,23 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 87febc68b45b - fea85c467896 - 19bbd19b74b3 + - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 0df47f8552f6 - 7776cb18fdf8 + - 0df47f8552f6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 15c2fc266540 - 4c7ebbad42cf + - 15c2fc266540 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -233,11 +233,11 @@ tools: owner: iuc revisions: - d8dc037e3c13 - - 4ba60cb14cb0 - - 2c61c30a57e7 - - 5fe20c915fa6 - 0cb27ea69dc1 + - 2c61c30a57e7 - 9c43baa60906 + - 5fe20c915fa6 + - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -251,17 +251,17 @@ tools: owner: iuc revisions: - 0db22932bc39 - - 9d09724f2bf1 - aec831b54a5b + - 9d09724f2bf1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - 6e24e79d3d69 - 29c738066906 - ed7a967cb11b - df30a2f1db55 + - 6e24e79d3d69 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -279,16 +279,16 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: + - 1865e693d8b2 - 3e4d45aca422 - ad90c2da4f38 - - 1865e693d8b2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - d107d20dc6bd - def511e8e005 + - d107d20dc6bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -300,16 +300,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - 64deddb6a8ec - - c520a52b5174 - d63c1442407f + - 71c994a11f71 + - c520a52b5174 + - 64deddb6a8ec tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 94a50db37d1a - 9946bc39c834 + - 94a50db37d1a - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -1060,23 +1061,23 @@ 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: rdock_rbcavity owner: bgruening revisions: - - 744a777e9f90 - 7e5c2e4bc227 + - 744a777e9f90 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -1088,11 +1089,11 @@ tools: - name: salsa owner: iuc revisions: - - ba7b0f11e470 - f77f7a7f3b83 + - ab5b7f6b7198 - 9a22227bb6d0 + - ba7b0f11e470 - 58a870ef434c - - ab5b7f6b7198 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_merge diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index 782923f20..3aa61cf80 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -26,8 +26,8 @@ tools: - name: gubbins owner: iuc revisions: - - 637ec5d5368c - 96e6283e4745 + - 637ec5d5368c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -39,66 +39,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 8834daeb9892 - - 3f59ebfbfe3d - - a6619171428e - - c78f3d7dd1db - - f04a1264e2a2 - 3b8b5bde0bd9 - - 6a457678efcb - - f73435dc282b - '841557158611' - - d033ffc1c161 - d7c7ef3353fe - 5a7c56a5cc08 + - f73435dc282b + - d033ffc1c161 + - 6a457678efcb - cce7b18495e4 - - 26de3a7b1cb9 - - b89cac5156ec - 81e66674859e + - c78f3d7dd1db + - 8834daeb9892 + - f04a1264e2a2 - 107d3ba7024a + - 3f59ebfbfe3d + - b89cac5156ec + - a6619171428e + - 26de3a7b1cb9 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 659517798cc4 - - a185b079b095 - - aa8cc71438cf - - b0af57c1a968 - - 88c4aa435ded + - 6223845127ea - 5fcd1ece3a6e - 4755f52427c4 - 5b777002c2de + - 3b96e92e8ec3 + - 659517798cc4 - 02b8758214b0 - - 6223845127ea + - 7a2092844346 + - aa8cc71438cf - df47d4845b62 - - e75442c7f4da - 6283babe736e - - 7a2092844346 + - 88c4aa435ded + - a185b079b095 - 6a726db04d4b - - 3b96e92e8ec3 + - b0af57c1a968 + - e75442c7f4da tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - b8476e82ac20 + - 24d024316465 - 111bd54f6bc4 - - f87ac61981f0 - - 70acec670c30 - d1c340a5664b - - 24d024316465 - - f97743d52b87 - 524d31add34a + - b8476e82ac20 + - f97743d52b87 + - 70acec670c30 + - f87ac61981f0 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: + - 4f6349228462 + - feb40665d7cd - 9e10ba792be2 - daddf188c13f - - feb40665d7cd - - 4f6349228462 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -110,26 +110,26 @@ tools: - name: pangolin owner: iuc revisions: + - 2f1019071464 + - a2099fb98cdb - ca337cce3888 - - ca0d8cf80567 - 2fa9d4f1b48f - - a2099fb98cdb - - 81804a978fc0 - - 9d61d3fa046c - - b7e297c2ede6 - - 2f1019071464 - - 7bb8726be37c - - 03ed9524dcd1 - - abf6dbe8c9d7 - - 437e28791761 - - b6abccb1f25b - - 3a43c3982401 - 83a69484cb87 - - 36912871ccdc - 42a174224817 + - 81804a978fc0 - 5f8727ff21e7 - 8ad84c5753ea - 14ae456b8cc5 + - 03ed9524dcd1 + - 437e28791761 + - ca0d8cf80567 + - abf6dbe8c9d7 + - 3a43c3982401 + - b6abccb1f25b + - 7bb8726be37c + - 9d61d3fa046c + - b7e297c2ede6 + - 36912871ccdc tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -148,23 +148,23 @@ tools: - name: raxml owner: iuc revisions: - - ea30d3089354 - - b1e68bbe4cef - ba29b5e2a4be - - 29ff6a849eac - - a4b71be30c3c - 73a469f7dc96 + - b1e68bbe4cef + - a4b71be30c3c + - 29ff6a849eac + - ea30d3089354 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - dbe2b2204555 - - 809e42326fc2 - - f1ccc8a6eb05 - - e88a7de55d6e - 91887494eb97 - 15ac71df11a0 + - f1ccc8a6eb05 - 9b2b122d0415 + - e88a7de55d6e + - 809e42326fc2 + - dbe2b2204555 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/picard.yml b/staging.gvl.org.au/picard.yml index 838833e9a..95bd62e86 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - 1aac2a13842a - f9242e01365a + - fc288950c3b7 + - 3f254c5ced1d + - 7d34178f2812 - a1f0b3f4b781 + - 881d7645d1bf + - 1aac2a13842a - f6ced08779c4 - - 7d34178f2812 - - fc288950c3b7 - b502c227b5e6 - - 881d7645d1bf - - 3f254c5ced1d tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomic_ai.yml b/staging.gvl.org.au/proteomic_ai.yml index c4bd122ea..671f25000 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -2,18 +2,18 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - 2f7702fd0a4c - - d00e15139065 - - e4a053d67e24 - - eb085b3dbaf8 - - 3f188450ca4f - - ca90d17ff51b - e7f1b552a695 - - a58f7eb0df2c + - e4a053d67e24 - c0e71cb2bd1b - - 3bd420ec162d - - 7fbec959cf2b + - ca90d17ff51b - 5b85006245f3 - 6ab1a261520a + - 7fbec959cf2b + - 3f188450ca4f + - d00e15139065 + - eb085b3dbaf8 + - 3bd420ec162d + - a58f7eb0df2c + - 2f7702fd0a4c tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomics.yml b/staging.gvl.org.au/proteomics.yml index a056eeb68..61de06810 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -4,92 +4,92 @@ tools: revisions: - f28ad96b76dc - b18329a8ac14 - - 4c177985028a - - 277dc652246e - 0a18ac48ac53 + - 277dc652246e - b574b84afc4d - ece627528a78 + - 4c177985028a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - b41107d8fe89 - - e988563cc6e5 - a9a28e46d54a - - e215f71d7983 - - 525f201b86c1 + - e988563cc6e5 + - b41107d8fe89 - bf06d196e23d + - 525f201b86c1 + - e215f71d7983 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 56da27be956a - - 8da3511c9467 - bb6397b94018 - 4fbffddde8cd + - 56da27be956a + - 8da3511c9467 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - a8157342d9a3 - - 890845926d4b + - b8c79e70516d - 528fb09022be - f23d67e28cc8 - - b8c79e70516d + - 890845926d4b + - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: + - 59e85306eae5 + - 25b83cbd596a - a69865da6f80 - - a95a82eb4d50 - ae304a72db7b - 80600735685d - - 59e85306eae5 - - 25b83cbd596a + - a95a82eb4d50 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 611d80c0e29d - - f1897eb07081 - - ed9ed1e6cca2 - - e0669b1854b1 - 798da6bdff3d + - e0669b1854b1 + - ed9ed1e6cca2 + - 611d80c0e29d - 83aac7741200 + - f1897eb07081 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: + - 5a35e3a8d013 - 74b61bf5bc4b - - a7fb9b395ddf - d426a9107a6c - - 5a35e3a8d013 + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - cc430977c8ff - 82f6c2f4332d - - 91f0f5922011 + - cc430977c8ff - df2187f9013b + - 91f0f5922011 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: + - 1693b2126f30 + - d2483487e077 + - ba92b59cd529 - 043f9c91f686 - 10566783d718 - - d2483487e077 - c5aa9fca18c6 - - 1693b2126f30 - - ba92b59cd529 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -107,10 +107,10 @@ tools: - name: diann owner: galaxyp revisions: - - ae4dc0c041f9 - ff8c9e0e8a7b - - bf0728e000cd - 9fa3dbf06f17 + - bf0728e000cd + - ae4dc0c041f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -129,9 +129,9 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 1c5cbf8f79ce - 0fa397f4f40b - 4081e4faa4ab + - 1c5cbf8f79ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -158,8 +158,8 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - d286ff4600dd - 160538a890a6 + - d286ff4600dd - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -173,23 +173,23 @@ 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: - - 837224ad1694 - f522c08e900c - - 7f432d87c82c - - 1f39c833f65f - 4d17fcdeb8ff + - 97a7f34fcb6a - 37d669de2828 + - 2133b0be850a + - 837224ad1694 - 9c52362ae7bb - e42225f8a659 - - 97a7f34fcb6a - - 2133b0be850a + - 1f39c833f65f + - 7f432d87c82c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -201,17 +201,17 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - 85b8866f06d7 - - 0ed07016d668 - e63db1aa82ee + - 85b8866f06d7 - a72ac2c7cc5b + - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 990b4560ead7 - 352b37c66d97 + - 990b4560ead7 - 1974224d63c2 - 767c1d761aaf tool_panel_section_label: Proteomics @@ -219,44 +219,44 @@ tools: - name: metaquantome_filter owner: galaxyp revisions: - - 4f359549383c - - 99450519d727 - 35cc7ca0bdc7 + - 99450519d727 - deaf035bbe9f + - 4f359549383c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - e79958768a2c + - c7745841de24 - c1343e3389ca - 06f6826d380c - - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - b9d453dca8d3 - - da986f83631b - - d46d64e7964d - d2eac53666f0 + - d46d64e7964d + - da986f83631b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 9bf325045235 - 8bd7734309f6 - - 944b43462104 + - 9bf325045235 - 1199751329b0 + - 944b43462104 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus owner: galaxyp revisions: - - e0104a9f20f0 - 8295d959ca28 + - e0104a9f20f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert @@ -269,33 +269,33 @@ tools: - name: msstats owner: galaxyp revisions: - - 8212e342e482 - 593839e1f2c3 - - 28434abe6c5c - de7593c29499 + - 8212e342e482 + - 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: - - f4be248c3d47 - - 4e77b8f12cd3 - 01dbaf6a57e0 + - 4e77b8f12cd3 - 8960fb791701 + - f4be248c3d47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 370141bc0da3 - 06cca574e337 + - 370141bc0da3 - 25529df60a81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -303,64 +303,64 @@ tools: owner: galaxyp revisions: - 6ccbf9a2072c - - 518b1730cf2a - - 9cdf15d3cfc8 - f7fef900f5b2 - c9eff69a7c62 + - 9cdf15d3cfc8 + - 518b1730cf2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - ca88bd28f116 - - 9876bda3ec53 - 5e948629bc73 + - 9876bda3ec53 + - ca88bd28f116 - dff6c756eee5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: + - 41859bbdc16e - 658494a2cb00 - - 890025d6e426 - 1595601708ec - - 41859bbdc16e + - 890025d6e426 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 5ad0b5bf1deb - 9b7977080f6d - - 6634cad7d797 - 2a93a25f0599 + - 5ad0b5bf1deb + - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - d6878d27f051 - - 0bb5056cb775 - fe4e4587d265 - 05d5e1ddc985 + - 0bb5056cb775 + - d6878d27f051 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 4af67edd5aef + - 52ba9695e752 - febd569ad26f + - 4af67edd5aef - 5ad830edc021 - - 52ba9695e752 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: + - 27cba4c5fc42 - b2fc8da99bcc - 39e8fde08881 - 92352a475eed - - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector @@ -368,53 +368,53 @@ tools: revisions: - 9e26f5c770f8 - d413dc49d650 - - 0efbc235f314 - d3546bb9fd8e + - 0efbc235f314 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: + - 8a04ed1c1d1b - 3720e349ba2a - - ca1740533b59 - c28f13cab67a - - 8a04ed1c1d1b + - ca1740533b59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - c427a8628cbe + - 382cde407f81 - ca799a7246e7 - - a5d785af0ad8 - c55dddc5844a - - 382cde407f81 + - a5d785af0ad8 + - c427a8628cbe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - 39caaa778d2e - b5d0905419da - 8ddb7bab1138 - adca857b4884 + - 39caaa778d2e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - f817513840a9 + - 18f93351f8b6 + - 8d4db262964c - 34e7afee141d - 1c5f31b8d632 - - 8d4db262964c - - 18f93351f8b6 + - f817513840a9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 986e03d3201e - 111c3a00136d + - 986e03d3201e - 5d9f175dff81 - c69f69d7867a tool_panel_section_label: Proteomics @@ -422,10 +422,10 @@ tools: - name: openms_idscoreswitcher owner: galaxyp revisions: + - be74a8cd7d66 - 0e52c85f3b15 - 476b5e296979 - 4204882495f2 - - be74a8cd7d66 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter @@ -438,99 +438,99 @@ tools: - name: openms_msgfplusadapter owner: galaxyp revisions: - - a407b6790342 - - c18d8efa4474 - f5ec766d80cf - 2b2a7551a857 + - c18d8efa4474 + - a407b6790342 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: + - 4e66c4e73909 - d0304fb829c0 - 021fdb80f204 - - 4e66c4e73909 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - - 2735db4dd8d9 + - bf32e0bcf554 - ee860980edc6 + - 2735db4dd8d9 - 8098330f6d91 - - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - - 08488066d588 - - a2a6e9551046 - 0ced5bc9f4dd + - a2a6e9551046 + - 08488066d588 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: + - 8c01da82292c - de7a553552a6 - 2a9ff56cb279 - - 8c01da82292c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: + - 1bf940c18d93 - e8f64a7dc470 - c1809c05ae8c - - 1bf940c18d93 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 496cf619e311 - - 9f505cd4428f - f861ec9fbe59 + - 9f505cd4428f + - 496cf619e311 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: - c99d5004b74f - - 0bddef8d144e - d4396637b9f5 + - 0bddef8d144e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: + - 8b814eafce2c - 89254095cbf6 - 4bb198c0bd3e - - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - f82b320ceb90 - f9ed7e074900 - 05ec9fb05ed1 + - f82b320ceb90 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - d31426ef20f6 - 18826fb8e5db + - d31426ef20f6 - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - - 2aebe58de46e - - 4a7b96835140 - bc63b4d12779 + - 4a7b96835140 + - 2aebe58de46e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires @@ -546,50 +546,50 @@ tools: owner: galaxyp revisions: - d6aca689dd48 + - e039cc5c7aed + - 5182338d5e7c - 539a3a4dcc9e - dd173849c3d8 - - 5182338d5e7c - - e039cc5c7aed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 16026cdb1330 - 8a45fd5a608a - d426affe977c + - 16026cdb1330 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - 9c70a651a53e - - dd71e020e2aa - 43b9ed22e8ce + - dd71e020e2aa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: - 9020199dba0a - - d063e2fe4ba4 - 1b03536aa3c9 + - d063e2fe4ba4 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - f036e8cf1a55 - - ad2ba3a95a02 - 78c080d36945 + - ad2ba3a95a02 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - 5c2a97a234d6 - 7f6a1f27553e - fb52e95a370c + - 5c2a97a234d6 - c8b225c69a7f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -616,14 +616,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: + - 7fdd9119cc4f + - a72c48001f7c + - 1beff3ddce58 - 3ec27b4cee7c - - 943a34df6047 - 07ff622ec007 - - 1beff3ddce58 - da885ca16cb2 + - 943a34df6047 - 3634c90301af - - 7fdd9119cc4f - - a72c48001f7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator diff --git a/staging.gvl.org.au/qiime_2.yml b/staging.gvl.org.au/qiime_2.yml index 52697721b..bf015d3f9 100644 --- a/staging.gvl.org.au/qiime_2.yml +++ b/staging.gvl.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 18c6b2b6740f - 10447a4b0cc3 + - 18c6b2b6740f tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index 14c3a2994..e08e98364 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -3,11 +3,11 @@ tools: owner: iuc revisions: - e345aadf914f + - 42201b90e3f4 - 2f1d464ebfd2 - - 110a346daf36 - 289b7d6b69a4 - cd5f98911089 - - 42201b90e3f4 + - 110a346daf36 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: + - c207119ba5f6 - 0cd2df8af811 - - 42d9087b4789 - fcce77c09289 - - c207119ba5f6 - - 8501601a118d - 0345dbaaa79b + - 8501601a118d + - 42d9087b4789 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: + - 33486216eec0 + - ad5ab22ffe24 - 89eb29319bf4 - 405a212b32ab - - 04db7fd6b238 - - ad5ab22ffe24 - - 33486216eec0 - 421c33b8bf17 + - 04db7fd6b238 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 + - 7b72fde3d27e - 1d839ead7ad3 - - 7370bb65bad4 - f6e91108b7b1 - eb784fa07f80 - - 7b72fde3d27e + - fa51dc5e8386 + - 7370bb65bad4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -71,11 +71,11 @@ tools: owner: iuc revisions: - 3d70c2996730 - - 1544278c272e - - 8a55d29c8fcf - d30e36c48c93 - - a3e86cd9cac7 - c9b77ced9a78 + - 8a55d29c8fcf + - 1544278c272e + - a3e86cd9cac7 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: - - e2db212d64ad - - 7b881f5f5ad5 - - a5969aa9347e - - 564c33e5c3e3 - b242deb58952 + - e2db212d64ad - 887cf585cafc + - 564c33e5c3e3 + - a5969aa9347e + - 7b881f5f5ad5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,10 +104,10 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - e897c74a48bb - - 9a171f9a450b - bd5ff77e2036 + - 9a171f9a450b - 8cff84759bf6 + - e897c74a48bb - b4bab607eb05 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 6dafad990086 - - 4f65e343ecdf - - 5e10f396979e - adc7a7610d4f - - 887e0991eb24 - 33f0793edf93 + - 887e0991eb24 + - 5e10f396979e + - 6dafad990086 + - 4f65e343ecdf tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -137,12 +137,12 @@ tools: - name: stacks2_shortreads owner: iuc revisions: + - c287418eb288 + - 4e280b27a831 - 97575d01f06b + - 17d39bf0a63a - c5d7050e4ad7 - 43e3eeb2e0ec - - 17d39bf0a63a - - 4e280b27a831 - - c287418eb288 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 + - 09b8edb56d80 + - cd034465d4a4 - 9586f08634c0 + - a819ec3b362d - d9bf483266a1 - - cd034465d4a4 - - 09b8edb56d80 + - 0b8c84a7fdb5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -171,11 +171,11 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: + - 2645575d1bf2 - 69842dd5aa48 - 95351dd0fd3f - - 2645575d1bf2 - - a4b4bd84f69e - bf0e43ab0416 + - a4b4bd84f69e - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - cfb504394ae1 - 8a35a3bc6752 - - d033e1ccb386 - - d1fda11e602f - bb0475c884ff - 912f904a6e1e + - d033e1ccb386 + - d1fda11e602f + - cfb504394ae1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,8 +235,8 @@ tools: - name: stacks_populations owner: iuc revisions: - - d504d945a655 - 95286af4139b + - d504d945a655 - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -267,8 +267,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 96de7538bf0c - 563af4497055 + - 96de7538bf0c tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 6123428ca..eac788e17 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,27 +2,27 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: + - 31f8063eedea - cf01dd6c6b1f - 7acb00fc980a - - 31f8063eedea - 2d4e3aff9dc7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: + - 32e542c2a773 + - 703a2cb3fb38 - 7a5a2d28c539 - 125d20cb23d7 - - 703a2cb3fb38 - - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - 45c2ec061cf9 - - 01ccd366690d - 3d61a698e5e1 + - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -34,8 +34,8 @@ tools: - name: blockclust owner: rnateam revisions: - - dbb6ee3179bc - aab6cf87b40a + - dbb6ee3179bc tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockclust @@ -91,9 +91,9 @@ tools: - name: cufflinks owner: devteam revisions: + - e04dbae2abe0 - d080005cffe1 - 6926716bbfb5 - - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -105,11 +105,11 @@ tools: - name: cuffmerge owner: devteam revisions: - - 22cf48ad7b16 - 86285ddd4512 - cf747d1bd79a - - 6a6717a5f421 + - 22cf48ad7b16 - 04adc9db1581 + - 6a6717a5f421 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -121,9 +121,9 @@ tools: - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - - 28b94cfbfdb9 - 9a854107dbb2 + - 28b94cfbfdb9 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -160,10 +160,10 @@ tools: - name: describe_samples owner: iuc revisions: - - 0693ccd171c4 - 3b36efd62b3e - - 8f0181aacb7a - e3b16fd7dd08 + - 8f0181aacb7a + - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -175,13 +175,13 @@ tools: - name: deseq2 owner: iuc revisions: - - 0696db066a5b - - cd9874cb9019 - 24a09ca67621 - - 9a882d108833 + - 0696db066a5b - d027d1f4984e - 6a3a025714d3 + - 9a882d108833 - 8fe98f7094de + - cd9874cb9019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -193,11 +193,11 @@ tools: - name: dexseq owner: iuc revisions: - - 2872c633f07e - - b47c006d90c5 - - 62adf13b86ea - 9a7c5b6d8f1e + - 2872c633f07e - df929f257179 + - 62adf13b86ea + - b47c006d90c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -209,18 +209,18 @@ tools: - name: edger owner: iuc revisions: - - 5bf899c13979 - 6e53e565fc6a - - f2843df56434 - a8305cf0c951 - - 070900306913 - - 3d89af8a44f0 - - ae2aad0a6d50 - - 334ce9b1bac5 - 555659de7321 - - df0c8d0a5992 - - 0cb907a2a810 + - f2843df56434 - 9bdff28ae1b1 + - 5bf899c13979 + - 0cb907a2a810 + - ae2aad0a6d50 + - 3d89af8a44f0 + - 070900306913 + - df0c8d0a5992 + - 334ce9b1bac5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -251,18 +251,18 @@ tools: - name: featurecounts owner: iuc revisions: - - f3a5f075498f - - a37612abf7f9 - - 7db9d3ea71c9 - - af814359d244 - - e6a2a912677a - - a56fbe2d6ba7 - - f9d49f5cb597 - - ea04b737afa0 - 1b851f87fbe0 - 38b6d12edc68 + - 7db9d3ea71c9 + - f3a5f075498f + - a37612abf7f9 - 90d16db017d7 + - ea04b737afa0 - 6f66ae7c5f7a + - a56fbe2d6ba7 + - f9d49f5cb597 + - af814359d244 + - e6a2a912677a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -292,9 +292,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 0f710191a66d - 3c97c841a443 - 3c5e024a18cf + - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -312,13 +312,13 @@ tools: - name: hisat2 owner: iuc revisions: - - 26371a1df031 - - d4b55e2beb12 - - a86e80d3c09c - 3fb01a8c902d - - f4af63aaf57a - 6c19daec423d + - d4b55e2beb12 + - a86e80d3c09c - 6ab42baa56e9 + - 26371a1df031 + - f4af63aaf57a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -336,9 +336,9 @@ tools: - name: htseq_count owner: lparsons revisions: - - 916cb26bd9d3 - - 4418229c501e - 67b0b160903a + - 4418229c501e + - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -356,11 +356,11 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 01247aaf0a10 - 87c11c05d238 - 1c75aa5de15e - - ce5d418183c5 - 5ae5c312d718 + - ce5d418183c5 + - 01247aaf0a10 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -372,10 +372,10 @@ tools: - name: kallisto_quant owner: iuc revisions: + - c971db6f0fe5 - 10c98fab6c5a - - 4f9c4e6566e5 - 40985510cd98 - - c971db6f0fe5 + - 4f9c4e6566e5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -387,14 +387,14 @@ tools: - name: limma_voom owner: iuc revisions: - - d6f5fa4ee473 + - 58c35179ebf0 - 32511f586472 - - e827f9aae031 + - 119b069fc845 - 0921444c832d - - 97e06a4c7c75 - - 58c35179ebf0 + - e827f9aae031 - 708348a17fa1 - - 119b069fc845 + - d6f5fa4ee473 + - 97e06a4c7c75 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -443,8 +443,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - 72927fc9e9ed - d696cf0a9622 + - 72927fc9e9ed tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -462,27 +462,27 @@ tools: - name: rgrnastar owner: iuc revisions: - - b9e04854e2bb - - 4df95e2d7f61 + - 53255f6eecfc + - b0f2be869d6d + - 99b17b74a8cd + - 4074fc1940e2 + - 7ed2edc1337f + - e132e7d02a3e + - 0a563fd2f22e - c772497b2c32 + - b9e04854e2bb + - 5ec75f5dae3c - 980d2a2e1180 - 79de45b5069b - - 0a563fd2f22e - - e132e7d02a3e - - 5ec75f5dae3c + - 4df95e2d7f61 - 3ea5a2a63fa2 - - 4014de1b6daf - - 7ed2edc1337f - - b0f2be869d6d - - 99b17b74a8cd - c7c55b694974 - - 4074fc1940e2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar owner: iuc revisions: - - 4014de1b6daf + - 53255f6eecfc tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem @@ -500,14 +500,14 @@ tools: - name: salmon owner: bgruening revisions: - - 2c0ca397d302 + - f4d5237a84f6 - 53e9709776a0 + - ebab418107f5 + - 49121db48873 - 15cd64d7c58b - - cc05793bb896 - e3d32471da11 - - f4d5237a84f6 - - 49121db48873 - - ebab418107f5 + - 2c0ca397d302 + - cc05793bb896 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -519,23 +519,23 @@ tools: - name: seurat owner: iuc revisions: - - 56242ff81c84 + - c0fd285eb553 - fab6ff46e019 + - 56242ff81c84 - 8c28affc7c48 - - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - dd4df992d93d - - 1ebd14235b92 - - cef79931dda5 - - 258d696dbd7e - ae618321f34a - - cbf488da3b2c - 914cfcba0ec8 - 76d290331481 + - cbf488da3b2c + - 1ebd14235b92 + - cef79931dda5 + - 258d696dbd7e + - dd4df992d93d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -572,9 +572,9 @@ tools: owner: iuc revisions: - 0db979fead3a - - c6334cb383ff - - ffd1300599a1 - d0d4cef4f967 + - ffd1300599a1 + - c6334cb383ff tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -586,10 +586,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - d6a479fd4281 - - ba3720d7e68b - bcc5f03f1900 - 74217fbfba4d + - ba3720d7e68b + - d6a479fd4281 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -601,8 +601,8 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 56162e446004 - 478f36effca1 + - 56162e446004 - c2b82a94493e - 2fb4ee002432 tool_panel_section_label: RNA-seq @@ -616,9 +616,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: - - fab23c3b5258 - 9ff3765e7172 - 3f4094b6a565 + - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -630,10 +630,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: + - 870ac06dff8e - be3f26533209 - 34a018cbee9c - 4687ecf0eb2d - - 870ac06dff8e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -645,11 +645,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 65e7dea767ea - - 5192f657f305 - 05ab8d5e04a2 - - 33406f5a445c - c5fbddcac63a + - 65e7dea767ea + - 33406f5a445c + - 5192f657f305 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -661,10 +661,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d + - a35cba31d904 - e406ac71165d - 6f0fb35b799c - - a35cba31d904 + - 1fdb25a8384d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -676,10 +676,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - c2c039e421af + - 964b7efe2639 - 37a1129c89d2 + - c2c039e421af - 7c7fbf13aadd - - 964b7efe2639 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -692,9 +692,9 @@ tools: owner: iuc revisions: - eafea3083352 - - 047c22569787 - - 1d689e4e1caf - 24e94d84adc9 + - 1d689e4e1caf + - 047c22569787 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -706,10 +706,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 04bb8bb7c198 - - 1812dbc5bb7b - 9871104ea630 + - 04bb8bb7c198 - 3a4ac03d1266 + - 1812dbc5bb7b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -733,15 +733,15 @@ tools: - name: trinity owner: iuc revisions: - - c9cfec002f71 - - 9fa24d5aac68 - - 48636f857c4b - - d84caa5a98ad + - d2bc35f3d1c5 - 8f1c3df4dd49 - cee61b3fcf78 - - d2bc35f3d1c5 - - db1f362cca3e + - 48636f857c4b + - d84caa5a98ad + - c9cfec002f71 - 32b86cd8eb50 + - db1f362cca3e + - 9fa24d5aac68 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -753,10 +753,10 @@ tools: - name: trinotate owner: iuc revisions: + - 6fd16fad465d - 2b093007fab9 - 4383070d29ed - 9e61bc67866f - - 6fd16fad465d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index 233430f7b..e03e93b4c 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: - - 27e16a30667a - 080fd5739bb4 - - 473382134e56 - 1a052c827e88 + - 473382134e56 + - 27e16a30667a tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/sambam.yml b/staging.gvl.org.au/sambam.yml index 6a80a4428..194ebb4b1 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -2,9 +2,9 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 10184eaa85fc - 3c661e57a88f - 88eedb4abea0 + - 10184eaa85fc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -16,10 +16,10 @@ tools: - name: bamtools_filter owner: devteam revisions: - - cb20f99fd45b - - 108db6635177 - 993b19f20c76 - 1dfd95ee241e + - 108db6635177 + - cb20f99fd45b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -37,15 +37,15 @@ tools: - name: bamtools_split_paired owner: iuc revisions: - - 75d5afa09972 - 5325e44297b9 + - 75d5afa09972 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_tag owner: iuc revisions: - - e9b9c489aacc - e30af4e78cd3 + - e9b9c489aacc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamutil_diff @@ -63,8 +63,8 @@ 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 @@ -82,8 +82,8 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - e7fd6754d093 - 30a201c9c310 + - e7fd6754d093 - 5f8e69cc4c6e - 19ece8afbaab tool_panel_section_label: SAM/BAM @@ -97,8 +97,8 @@ tools: - name: qualimap_multi_bamqc owner: iuc revisions: - - e38af83df163 - 17b35d23731f + - e38af83df163 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -123,15 +123,15 @@ 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 owner: devteam revisions: - - cf1ffd88f895 - 0e60e2dd20af + - cf1ffd88f895 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam @@ -163,10 +163,10 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 12749212f61b - - 46c6639921f1 - 6856f8a01905 - 9149ad20699a + - 46c6639921f1 + - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -178,9 +178,9 @@ tools: - name: samtools_calmd owner: devteam revisions: - - 92ec40abcdcf - - 06dc50b7b711 - 33208952b99d + - 06dc50b7b711 + - 92ec40abcdcf - 26b4f9f98aca tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -205,8 +205,8 @@ tools: - name: samtools_fastx owner: iuc revisions: - - 720217c23995 - b906586a6596 + - 720217c23995 - a8d69aee190e - b3d99709fe1a - 66e23b11feae @@ -228,11 +228,11 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - fe34990e5ce7 - 22970df7a40e - - db17d5321bad - - cc61ade70eb8 - fefd89ab563c + - fe34990e5ce7 + - cc61ade70eb8 + - db17d5321bad tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -244,11 +244,11 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - 811fc2d75ad4 - - 7def34e6cf4d - 7a6034296ae9 - - 88b8c2916784 - fa5d3e61e429 + - 7def34e6cf4d + - 811fc2d75ad4 + - 88b8c2916784 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -269,19 +269,19 @@ tools: revisions: - b40e2d865d52 - cae2794d2deb - - 740ce0a18f0d - 36677f429310 - 65a38e8c8e2a + - 740ce0a18f0d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - b61f5d6a7f25 - - 9da0311ab1dd + - 329deb17a9f7 - fa7ad9b89f4a + - 9da0311ab1dd - 583abf29fc8e - - 329deb17a9f7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -293,8 +293,8 @@ 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 @@ -306,10 +306,10 @@ tools: - name: samtools_reheader owner: devteam revisions: + - db000c6007a0 + - 85e38b31e8b3 - 30388d878f81 - bb8cfc6f6e0c - - 85e38b31e8b3 - - db000c6007a0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -327,9 +327,9 @@ tools: - name: samtools_slice_bam owner: devteam revisions: + - 344fc91e1bfd - b8beef827165 - a4a10c7924d1 - - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -341,10 +341,10 @@ tools: - name: samtools_sort owner: devteam revisions: - - 6c2c1836728b - e613c1ad4c4c - d54a4df48867 - cab3f8d35989 + - 6c2c1836728b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -356,12 +356,12 @@ tools: - name: samtools_split owner: devteam revisions: - - 135c85f4cfaf - 818030fa6bbf + - 5d9ae78f34d3 + - 135c85f4cfaf - bd850490c7f1 - bcedabb53ddf - b7f7826ef1cd - - 5d9ae78f34d3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -373,11 +373,11 @@ tools: - name: samtools_stats owner: devteam revisions: - - 145f6d74ff5e - - 3a0efe14891f + - 24c5d43cb545 - 5a08c09b9311 + - 3a0efe14891f - 1cc79f49b8d5 - - 24c5d43cb545 + - 145f6d74ff5e - 541082d03bef tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -390,16 +390,16 @@ tools: - name: samtools_view owner: iuc revisions: - - bf328cec6a42 - - 5826298f6a73 - - b01db2684fa5 - - 350bbc5c2ffd - b72793637686 - 6be888be75f9 - - 0dbf49c414ae - - 32dc5f781059 + - 350bbc5c2ffd - 2dce91e11ca7 + - b01db2684fa5 + - bf328cec6a42 + - 5826298f6a73 - c370440f901e + - 32dc5f781059 + - 0dbf49c414ae tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view diff --git a/staging.gvl.org.au/send_data.yml b/staging.gvl.org.au/send_data.yml index 82b8fdc71..1dac5e8a5 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -8,13 +8,13 @@ tools: - name: ena_upload owner: iuc revisions: - - a62c4a11a67d - - ea5e944f447d - - 6f6537780379 - - 4aab5ae907b6 - 5cb6146337d8 + - 59bb6d34fca6 + - ea5e944f447d - d147d6455873 - 480d9e9d156b - - 59bb6d34fca6 + - 6f6537780379 + - a62c4a11a67d + - 4aab5ae907b6 tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/single_cell.yml b/staging.gvl.org.au/single_cell.yml index 9da320c0b..17b031385 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -9,8 +9,8 @@ tools: owner: bgruening revisions: - f2000bc73102 - - ecb9ea6269ee - b0fe3e482cb7 + - ecb9ea6269ee - e4c01dcece8b - e32b215b7c04 tool_panel_section_label: Single-cell @@ -19,21 +19,21 @@ tools: owner: iuc revisions: - 707023fa62fe - - e1c3c2f2a834 - 7a6655aa6eb2 + - e1c3c2f2a834 - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 55e35e9203cf - - 6f143dfe902a - - 93dd15e13e6a - - cfc3f5a57dc6 - fb9e030ffae4 - 32e547223c9e + - cfc3f5a57dc6 + - 55e35e9203cf - 00712416fdaa + - 93dd15e13e6a + - 6f143dfe902a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -45,13 +45,13 @@ tools: - name: anndata_inspect owner: iuc revisions: - - 39e945f0b2c1 - ee98d611afc6 - - 038e32885fec - 688357ad5e61 - - 6f0d0c784f09 - - 14c576ea6148 + - 038e32885fec - b9fac48532eb + - 14c576ea6148 + - 6f0d0c784f09 + - 39e945f0b2c1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -63,13 +63,13 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - 9bd945a03d7b - - d4af736e7b83 + - ed4996a16f7f - 3d748954434b + - d4af736e7b83 + - 43cb7b5a6fe7 - c4209ea387d4 + - 9bd945a03d7b - b85871dd69f9 - - 43cb7b5a6fe7 - - ed4996a16f7f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -81,47 +81,47 @@ tools: - name: anndata_ops owner: ebi-gxa revisions: - - 890fb06a2893 - - a4774b7b2e85 - - fe75d2414dc0 - 7ebc22f77d86 + - fe75d2414dc0 - 2e8022f1923c + - 890fb06a2893 + - a4774b7b2e85 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 769d815e4b0d - 4fff5a293013 - - 02b1fe7aed76 - 0e70b2dfe4be + - 02b1fe7aed76 + - 769d815e4b0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - c29e7bb492bf - - 344c2af50552 - a90f8efe08b4 - aa4a6f0916b4 + - c29e7bb492bf + - 344c2af50552 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - 050cf43887d3 - - b13d3e4c48e1 - c32347702e12 - 5b7c81b35b89 + - 050cf43887d3 + - b13d3e4c48e1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: + - ae969fdb8442 - 02fc39c8610d - 239193b96d72 - 1d77986f9ddc - - ae969fdb8442 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -157,11 +157,11 @@ tools: - name: dropletutils owner: iuc revisions: - - 8855361fcfc5 - - a9caad671439 - - cdf4443d5625 - cfe1e6c28d95 + - cdf4443d5625 + - a9caad671439 - 2c1200fba922 + - 8855361fcfc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -197,89 +197,100 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 952abbc4b1de - fb7068d30ec9 + - c3ffb2c1e314 + - 952abbc4b1de - 01c37e54e86e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - f1c35f3f310d - 9d42a6133690 + - f1c35f3f310d - 57aeaf6b237d + - 45828071edc3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: - 163fd744e235 - - 23b8d6b8960c - cab616fe7e64 + - 23b8d6b8960c + - 1a31e75e979e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - f47ac4a0b337 - - b9ab56aecd18 + - '920526260066' - 013e53ccc7ac + - b9ab56aecd18 + - f47ac4a0b337 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - 9ea228a9afc8 - - a63e9713c39d + - f6a169b5e43b - b892fa1fcaec + - a63e9713c39d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - f8320df1866b + - ff1af7bac1cb - 45a386d18509 - 640e0e45518a + - f8320df1866b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: - 9d02f1819e81 - - c354255ff705 - f963c251ac77 + - c354255ff705 + - 6f8debcf2ac9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - f881c94fb3b3 - - c4ed35f4f77f - 40fee49bc6c3 + - c4ed35f4f77f + - 37125838e360 + - f881c94fb3b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: + - 2dccb6bb0add - 782bdcb775fb + - e8760fc0e29b - e06265d204f6 - - 2dccb6bb0add tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - f0216498a666 - 63c8377c58b3 + - 30677e95bc89 - b05f662f9f35 + - f0216498a666 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions owner: bgruening revisions: - c72fa6cb8817 - - fe3aa71590d5 + - 3240e8a7c54f - 8a11d70b6cd8 + - fe3aa71590d5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices @@ -287,22 +298,25 @@ tools: revisions: - e03780179ee5 - 4f9305d3bb34 + - 5dd1aae12f03 - 3ee5332bf57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: + - a315574104c6 - 3a6a5381db36 - 4401ed529d2c - - a315574104c6 + - 87eb9c58cd19 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - c0737631eea1 - 2ba6cee8e4db + - c0737631eea1 + - 574f295b5ba4 - a83732c79949 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -310,6 +324,7 @@ tools: owner: bgruening revisions: - 62b720dceb56 + - 937b7b9832d0 - 30d7390bc918 - ea19190ce5e0 tool_panel_section_label: Single-cell @@ -317,54 +332,61 @@ tools: - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - 2b4d6a8dab36 - cd40ca76865a + - 2b4d6a8dab36 - 2786a931cad2 + - 0f5786ffa10d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops owner: bgruening revisions: - - ffc33339cd3e - - bf9379529c3e - 0410b6aada45 + - bf9379529c3e + - ffc33339cd3e + - 4375e25de06a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: - - 77d8e0fd162a + - 4977f65da0ff - 07dd436ea686 - 5dfba24d7bdd + - 77d8e0fd162a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - 6c5097f6d41e - - f1b3902f8baf - 972dcccb5bbc + - f0b1bd38745a + - f1b3902f8baf + - 6c5097f6d41e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - bb8849fca57c - 409396ea5cf0 + - 3e5c86c2f80d + - bb8849fca57c - 7f7c6ead2d0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo owner: bgruening revisions: + - 7fbd6feba1ca - 51e40e9b6c3c - - e4f8fceab96a - b0f33533181d + - e4f8fceab96a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad owner: bgruening revisions: + - 908fa330b93b - c261b6b05ee3 - 55b013e59018 - 32173084d53f @@ -373,55 +395,62 @@ tools: - name: hicexplorer_hicmergedomains owner: bgruening revisions: - - b6b8c8672756 - - 4b194e675916 + - febfddb0b3e8 - b376ef118807 + - 4b194e675916 + - b6b8c8672756 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - - ed900cd4a0a9 - 910c6a1c3a27 + - ed900cd4a0a9 + - 1d9799f4b854 - 1511a8ebe906 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - - 6d042c96aceb - - 2aa5b6b65197 - f34ab9882252 + - 2aa5b6b65197 + - 5e83c077e31d + - 6d042c96aceb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: - dd9988943f53 - - ea5d67ec94ab + - 3f1b286a5c34 - 9b383d429659 + - ea5d67ec94ab tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - - 6326cd29c1c3 - 06ced663d24f + - 89cfe7de541b + - 6326cd29c1c3 - 11f39d7f6c64 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: + - 1602cc5b673c + - 337705015ee8 - b4e780e93c91 - beb5b5917d2f - - 337705015ee8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: - 8d203e74869b + - a10fce08c2dc - 58de3c7c8e89 - e285920f8585 tool_panel_section_label: Single-cell @@ -429,17 +458,19 @@ tools: - name: hicexplorer_hicquickqc owner: bgruening revisions: + - 5cbd7a902a8d - 21d859ad4502 - ea8fb5e899e8 - - 5cbd7a902a8d + - b13e7a200525 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - 1d6af10874d5 + - d74cf4a61d65 - f81750434d70 - 36dfa2825a59 + - 1d6af10874d5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -458,27 +489,29 @@ tools: owner: bgruening revisions: - f36828ebdc54 - - 1de2276f633f - 27fe5cd1729c + - 1de2276f633f + - df64cc4dfb4d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: + - 11a3385e03b5 - 1d201e8378b3 + - d890828ab02a - cef9fb4ece1c - - 11a3385e03b5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: - e98619de2776 - - db575b4c8b22 + - 4b0adaa31c95 - 59be31ac9dc3 - 7784821452ac - - 4b0adaa31c95 - eeab712b0b99 + - db575b4c8b22 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -524,11 +557,11 @@ tools: - name: raceid_clustering owner: iuc revisions: - - f911a64454fb - - 49776718ae90 - c4f39bf4a068 - - 7e014059a88d + - f911a64454fb - a4b734cd253b + - 7e014059a88d + - 49776718ae90 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -540,10 +573,10 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: - - 8b917923f7d4 - - 43c146e25a43 - d45f092caf24 + - 43c146e25a43 - 7608d5faee41 + - 8b917923f7d4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf @@ -555,8 +588,8 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: - - 37a47c4fd84d - 2b0d3e2f402a + - 37a47c4fd84d - c7ddb719554d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -569,9 +602,9 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: + - 6e90c8adf84f - df8e4e54d367 - 69018f285aa3 - - 6e90c8adf84f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -583,11 +616,11 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - e93b008c637a - - 2bfd55b87af3 - - c92d0f9338c5 - - 44b935f2271b - 72979cac22b2 + - 44b935f2271b + - c92d0f9338c5 + - 2bfd55b87af3 + - e93b008c637a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -611,17 +644,17 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - f9353ee6a0d4 + - b2df381a6004 - 6f83f8fd381f - - 6acb08931836 + - 4d8f983cd751 + - edec35114f72 - 8983e7a04ba7 - - 77b91b9bdf52 - cb43c5d3acd3 - - b2df381a6004 + - 77b91b9bdf52 - aaa5da8e73a9 - - 4d8f983cd751 - - edec35114f72 - 38db3fef7aad + - 6acb08931836 + - f9353ee6a0d4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -633,16 +666,16 @@ tools: - name: scanpy_filter owner: iuc revisions: - - 277313130da5 - - fc0321c000a3 - - 64388be6d510 - - b409c2486353 - - 8cb783c81905 - - a03ff8633507 + - 3c86f71498bc - d636ce5cde16 - - a97abb8cd15b + - a03ff8633507 + - b409c2486353 + - 64388be6d510 - 72a6bebab2a5 - - 3c86f71498bc + - fc0321c000a3 + - a97abb8cd15b + - 8cb783c81905 + - 277313130da5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -654,17 +687,17 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - 6c145a6868cc - - 3081ff5c84a3 - - c5d3684f7c4c - - 18262103fa61 - - 6bd82ed14acd - c0a80a16560f - f54f0f0598ad - - 5c3ebe2adc77 - cc0deb593fc8 - - d86cb2ce311b + - 6bd82ed14acd + - 6c145a6868cc - 5e9171dc8244 + - 5c3ebe2adc77 + - c5d3684f7c4c + - 18262103fa61 + - d86cb2ce311b + - 3081ff5c84a3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -676,17 +709,17 @@ tools: - name: scanpy_normalize owner: iuc revisions: - - 9f354c7c8c92 - - 7b9fafe32c86 - - c9cb76cf8d6c - 94c19fb1281c + - 3bcd5445cd7a - a407e7f8bdc1 - - 4bda4412b8c2 - - 56c0d4acef02 - - ab55fe8030b6 - 146ae5d70b47 - - 3bcd5445cd7a + - ab55fe8030b6 + - 56c0d4acef02 - d844935c906c + - 4bda4412b8c2 + - c9cb76cf8d6c + - 7b9fafe32c86 + - 9f354c7c8c92 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -698,18 +731,18 @@ tools: - name: scanpy_plot owner: iuc revisions: - - 7647e5cd1b8b - - dbbe1ea8ecb1 - - 0185bd174ea0 + - aa0c474463c2 - 95777145cb92 - 6adf98e782f3 - - 40812a65a78b - - 9b0cdb8cf6be - - 1072ce66b426 - f7446fd8d5e7 - - 6f5349dd5c49 - 62acdd96d4a0 - - aa0c474463c2 + - 0185bd174ea0 + - dbbe1ea8ecb1 + - 40812a65a78b + - 6f5349dd5c49 + - 1072ce66b426 + - 9b0cdb8cf6be + - 7647e5cd1b8b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -721,17 +754,17 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: + - 9fb627495ec2 - f2f6c703da06 + - c5541bfb8feb + - c65fce500915 + - d18e7a6e5cd4 - 458e8f43a775 - - 215733a383f2 - - 9fb627495ec2 - 73ab2ac53d06 - - a39040ae0a38 - - d18e7a6e5cd4 - bf2017df9837 - - c65fce500915 - - c5541bfb8feb + - a39040ae0a38 - fe8f16c594ec + - 215733a383f2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -757,8 +790,8 @@ tools: - name: scater_filter owner: iuc revisions: - - 652923ce664f - b7ea9f09c02f + - 652923ce664f - 7a365ec81b52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -778,8 +811,8 @@ tools: owner: iuc revisions: - 2e41b35b5bdd - - 81e5bdff4853 - ef4c80837bc5 + - 81e5bdff4853 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter @@ -797,9 +830,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 9e5c0bb18d08 - - 46fc6751d746 - c99ba278dfa9 + - 46fc6751d746 + - 9e5c0bb18d08 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca @@ -1028,8 +1061,8 @@ tools: - name: sinto_fragments owner: iuc revisions: - - 29e6bfb2cf49 - 6f66f523a9b7 + - 29e6bfb2cf49 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: slice_image @@ -1041,8 +1074,8 @@ tools: - name: snapatac2_clustering owner: iuc revisions: - - d3ea0ba3d066 - 8f8bef61fd0b + - d3ea0ba3d066 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_peaks_and_motif @@ -1055,15 +1088,15 @@ tools: - name: snapatac2_plotting owner: iuc revisions: - - 05bd4db20227 - fecf9664c885 + - 05bd4db20227 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing owner: iuc revisions: - - c5c94e01a1b5 - cec3e76eaf05 + - c5c94e01a1b5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: squidpy @@ -1075,8 +1108,8 @@ tools: - name: velocyto_cli owner: iuc revisions: - - 883c33ef3372 - 90e95e9ee190 + - 883c33ef3372 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: vitessce_spatial diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index 2df93e485..ed3d488f2 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,11 +32,11 @@ tools: - name: datamash_ops owner: iuc revisions: - - 562f3c677828 - 4c07ddedc198 - - 2f3c6f2dcf39 + - 562f3c677828 - 419027d822d6 - 746e8e4bf929 + - 2f3c6f2dcf39 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass @@ -49,8 +49,8 @@ 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 @@ -63,8 +63,8 @@ tools: - name: dwt_var_perclass owner: devteam revisions: - - 781e68074f84 - cb422b6f49d2 + - 781e68074f84 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 7442b94d6a1e - 4c4ec859c31a - - 840f29aad145 - - b1eda492f063 + - 7442b94d6a1e - aef56d0e7a61 + - 840f29aad145 - 9c3e1d3235c8 + - b1eda492f063 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - 30d21a6041f6 - - 375bbd555f4a - - 9fda0b82f419 - d0352e8b4c10 + - 375bbd555f4a - 07843f917990 + - 9fda0b82f419 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - cd02bf168d23 - 8b1b2b91f8d0 - - 4cc980df6265 + - cd02bf168d23 - 2c58b83c9bad + - 4cc980df6265 - 7ae443e6217d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - 7dd3fb35904f - - 4bbaf77573ef - - 1dd433d2c92c - ad7e0b4291ee - - e10e776f2109 - bb9fc9d46ea4 + - 4bbaf77573ef + - e10e776f2109 + - 1dd433d2c92c + - 7dd3fb35904f tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/staging.gvl.org.au/text_manipulation.yml b/staging.gvl.org.au/text_manipulation.yml index d9ce57e3b..68cb9cb84 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -34,15 +34,15 @@ tools: - name: column_maker owner: devteam revisions: + - 6595517c2dd8 + - be25c075ed54 + - 13b6f0007d9e + - 464b9305180e - aff5135563c6 - - 02026300aa45 - 9cd341095afd - - 464b9305180e + - 02026300aa45 - 6e8d94597139 - - 13b6f0007d9e - - 6595517c2dd8 - 626658afe4cb - - be25c075ed54 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -54,8 +54,8 @@ 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 @@ -81,9 +81,9 @@ tools: revisions: - 90f657745fea - 37cde8134c6a + - 557ec8d7087d - 34d29339abab - 9cc411a62277 - - 557ec8d7087d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -107,30 +107,30 @@ tools: - name: merge_cols owner: devteam revisions: - - ae7843d06f8f - - dd40b1e9eebe - f2aac0c5c60d + - dd40b1e9eebe + - ae7843d06f8f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - cf34c344508d + - 1ea4e668bf73 + - 83069b38aa85 - cf4397560712 - 33d61c89fb8d - - 83069b38aa85 - - 1ea4e668bf73 + - cf34c344508d - 3a6b78c39dca - - 623f3eb7aa48 - 2e8f945f7285 + - 623f3eb7aa48 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - ae8c4b2488e7 - - 503bcd6ebe4b - 399da6b5ec21 + - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -143,8 +143,8 @@ tools: owner: iuc revisions: - c4d18aa4ec4a - - f768f6183386 - bce29ec10b78 + - f768f6183386 - b722161a845a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -158,15 +158,15 @@ tools: - name: text_processing owner: bgruening revisions: + - 74a8bef53a00 - ddf54b12c295 - 86755160afbf - fbf99087e067 - - a6f147a050a2 - - 74a8bef53a00 - 0a8c6b61f0f4 - - d698c222f354 - 12615d397df7 + - a6f147a050a2 - f46f0e4f75c4 + - d698c222f354 - 9ff72e942410 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/variant_calling.yml b/staging.gvl.org.au/variant_calling.yml index c85f74c3c..71e49236e 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -14,8 +14,8 @@ tools: - name: breseq owner: iuc revisions: - - 0d18a3ba2d1c - 82fb5e3bb93e + - 0d18a3ba2d1c - 85c57cc9b558 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -28,42 +28,42 @@ tools: - name: cutesv owner: iuc revisions: - - c0f8fe52948e - 23d7e75d850e + - c0f8fe52948e - cb441f258c37 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: freebayes owner: devteam revisions: - - 156b60c1530f - - 04fa42777df9 - 57def2d7c093 - - ef2c525bd8cd + - 04fa42777df9 + - 156b60c1530f - 3e954e7125bf - a5937157062f + - ef2c525bd8cd tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: + - 791f73caa0c8 + - e61c9ac190ad - 435b157bed6d - 09d6e4693887 - - e61c9ac190ad - - 791f73caa0c8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 65432c3abf6c - dfadc322b065 - - 03627f24605f - - e1461b5c52a0 - - b11e8e9c23bf - 3b4b2121842f - - 4805fe3d8fda + - 03627f24605f - 074d44697036 + - 4805fe3d8fda + - 65432c3abf6c + - b11e8e9c23bf + - e1461b5c52a0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter @@ -77,18 +77,18 @@ tools: - name: lofreq_indelqual owner: iuc revisions: + - c27549b9aa1f - f4473557ffc7 - 426d707dfc47 - 971e07ca4456 - - c27549b9aa1f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - aa35ee7f3ab2 - - cdaab621d454 - dbd9f2db9ed8 + - cdaab621d454 + - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -101,18 +101,18 @@ tools: owner: iuc revisions: - ceff2f6a5368 - - 93c4b04a0769 - 43fffeed243f + - 93c4b04a0769 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: - - fa016f1eea1a - 5bbf9eada9c2 + - d220115f882b - c9a8ef2aa380 - 9bccc8404a3c - - d220115f882b + - fa016f1eea1a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -154,21 +154,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - ee4a90760848 - - 3b1e7c170b10 - - 32f14a2723ec - e7aff4a85df5 + - 3b1e7c170b10 - 40f0591deda0 + - 32f14a2723ec + - ee4a90760848 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: + - 4934c0ac6197 - 42818629ec4c - 9793bc5d741b - - adc0645b945c - - 4934c0ac6197 - 02d81b994ef5 + - adc0645b945c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_copynumber diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index 9560b002d..ca785381f 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -3,13 +3,13 @@ tools: owner: iuc revisions: - 8a2e296c07ef - - b7ea370b8f5d - 6a88248893c4 - - 95815a0bb307 - - 265fe0f9ea64 + - 2c372041ed8c - e075b1be5abb + - b7ea370b8f5d - ebe5fc018e72 - - 2c372041ed8c + - 265fe0f9ea64 + - 95815a0bb307 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -22,12 +22,12 @@ tools: owner: iuc revisions: - c37b684e7f4e - - 0fba2c15b40d - 21687e35f066 + - 22637b1a55bf - 544cb432072b - 1001172b5089 + - 0fba2c15b40d - b03984136ce4 - - 22637b1a55bf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -39,15 +39,15 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - 8ca3647c90fd - - 8408bffd5616 - - 8627b2b383b4 - - 143796b504eb - 3a7084316a6e - - ccb83bf54de0 + - 143796b504eb + - 8408bffd5616 - 01d6b7d6365e - - bf1f4994f104 + - ccb83bf54de0 + - 8ca3647c90fd - 0238f68ad641 + - bf1f4994f104 + - 8627b2b383b4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -59,14 +59,14 @@ tools: - name: bcftools_concat owner: iuc revisions: - - abd489215f73 - - 6b6c992d3a14 - - 03e0645395d2 + - f430a1ec7ee4 - 9b5abbf50d23 + - 03e0645395d2 - 81426b3cf18b - - 62ca6da715bf - - f430a1ec7ee4 - d144af39073a + - 6b6c992d3a14 + - 62ca6da715bf + - abd489215f73 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -78,14 +78,14 @@ tools: - name: bcftools_consensus owner: iuc revisions: - - d3081540d175 - 2363ef414c9b - - 8aa352093d73 - - e522022137f6 - - 1171446da5db - 95c6f3f4c77f + - d3081540d175 + - 8aa352093d73 - 1829900b5dcd - d37e313a41be + - 1171446da5db + - e522022137f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -97,13 +97,13 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - 1137ce8efc1e - - 9b29129fb491 - - 348cd212dbad - - b14ff40958cb - 92c0aff8b53e - - 09f37afb3621 + - 348cd212dbad - 012656fd329f + - 9b29129fb491 + - 09f37afb3621 + - b14ff40958cb + - 1137ce8efc1e - d58d2e8c7a57 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -116,13 +116,13 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - 1f2183a23823 - - 55c0e906c14c - 367ba501b6eb - - 7291189e98b4 - - de68c11034f6 - cfd81f17580b + - 55c0e906c14c + - de68c11034f6 - ecc9192912b8 + - 7291189e98b4 + - 1f2183a23823 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -134,13 +134,13 @@ tools: - name: bcftools_csq owner: iuc revisions: + - d237eaef451f - ae68ceb4cca3 - e6f4badbe6f3 - - 6c790a091c7c - - 039ea3f1dea9 - 64a8f7dae3ad + - 039ea3f1dea9 - 7cbf3c66d4ad - - d237eaef451f + - 6c790a091c7c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -152,14 +152,14 @@ tools: - name: bcftools_filter owner: iuc revisions: - - 277719af4dd7 - - cdb7b4927742 - - 33bd9301568c - 5d6653c989cb - 6ea7170a016d + - cdb7b4927742 + - 277719af4dd7 + - 33bd9301568c + - e7452697afd9 - 963a3635b2e1 - 46fcafba49ec - - e7452697afd9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -171,14 +171,14 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: + - 91c1e57d5c7f - 501bfb078342 - - a1213a0b7b66 - a29a2f40b665 - - 91c1e57d5c7f - 26d97cdd5410 - - b7f0f59baa7e - 5a321fab1fe4 - 7b4454382d39 + - a1213a0b7b66 + - b7f0f59baa7e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -190,15 +190,15 @@ tools: - name: bcftools_isec owner: iuc revisions: - - 5f27e814a119 - - 81e4014fa809 - - d7d1663559e9 - 768d04526638 + - d7d1663559e9 + - 15da1ddcfeff + - 5f27e814a119 - 39bca000353d - 97d19c008d15 - 709dd8291b83 - c803c34361e0 - - 15da1ddcfeff + - 81e4014fa809 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -210,14 +210,14 @@ tools: - name: bcftools_merge owner: iuc revisions: + - 86296490704e + - 2215287d5cc9 + - b931e65638b8 - 7ba36babba2d - - 5b006286a458 - b1eba148b35b - - 2215287d5cc9 - - 86296490704e - - 85ee7e6c4204 + - 5b006286a458 - b84fda8ebef0 - - b931e65638b8 + - 85ee7e6c4204 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -229,16 +229,16 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - f506df85c652 - - 4e1d23e5c691 - - 0a5dcc9a8ec2 - - cf06b44624c7 - 37757ffb4c5f + - cf06b44624c7 - 9c711df3258d - 56556e1267de - - ce9396ddcb2b - - 5660b21a0dbd - 31ea13dfe5e6 + - 0a5dcc9a8ec2 + - 5660b21a0dbd + - f506df85c652 + - ce9396ddcb2b + - 4e1d23e5c691 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -251,12 +251,12 @@ tools: owner: iuc revisions: - 19905c025d2a - - 6deb4d549bc9 - - 48291658fdf6 + - a404f786a94c - 021693fdadaa - - 1ca7418e46ee - 271965b55437 - - a404f786a94c + - 1ca7418e46ee + - 6deb4d549bc9 + - 48291658fdf6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -268,14 +268,14 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - 71c78e0eea52 + - 97e8145d7e30 + - 5ad5d4243987 + - f7879f1e77f9 - 3f6fadf8b8ff - dadbd61dc4cf - - 5ad5d4243987 - 69d8b7567281 - - f7879f1e77f9 + - 71c78e0eea52 - c450406f722b - - 97e8145d7e30 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -287,13 +287,13 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: - - 0fe007201caf - - d31a2e310a52 - cc7f9a4e186b + - d31a2e310a52 - 6cf13a657cf6 - - 79f7a1acc2cd - - 283911fe7e1a - 52f9e4a660e3 + - 283911fe7e1a + - 0fe007201caf + - 79f7a1acc2cd - 2514e684f8a3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -306,14 +306,14 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 026a989b7cee - 75ddd081f608 - - 1411bef27a75 - 6963a6841d22 - - 0a62420cb9cd - a12844ca467a + - 1411bef27a75 - 230e424bde67 - 80e6e399ccd0 + - 0a62420cb9cd + - 026a989b7cee tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -325,14 +325,14 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - e493702b19eb - - 5acfca5a76af - ba20340426fe - - 444e6a756c35 - - 450a265f92e8 - - b10d1510fa84 - 5808f77b2bb6 - bca7ce81688f + - b10d1510fa84 + - 450a265f92e8 + - 444e6a756c35 + - 5acfca5a76af + - e493702b19eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -344,14 +344,14 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - dd72ff87cfd0 - - c43399f161f4 + - f2482aa4862e + - 12152af85697 - 4d236c696844 - - 68fec03a63b7 - d52b8947b269 - - 12152af85697 - - f2482aa4862e + - dd72ff87cfd0 - 157ffcdd3fa7 + - c43399f161f4 + - 68fec03a63b7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -363,13 +363,13 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: - - 6f8e223f78f3 - 75becf493cd3 + - 29ba253e2e05 + - 8dbce095986c - cbe39e530cbf - - 8f2fc0ab30fb + - 6f8e223f78f3 - 0e5d11004815 - - 8dbce095986c - - 29ba253e2e05 + - 8f2fc0ab30fb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -381,14 +381,14 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - e0a856def0b0 - - a367a15c6de5 - 3ff5654b4e7d - - 88bb477f45f7 - - a8630d4fbaf8 - f544f71adb73 + - e0a856def0b0 - 8f5962c43868 + - 88bb477f45f7 - 9708e3086f32 + - a367a15c6de5 + - a8630d4fbaf8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian @@ -400,14 +400,14 @@ tools: - name: bcftools_plugin_missing2ref owner: iuc revisions: - - 34dc0bbc7e93 - - 96d0145c041a - - 6ce175385dd9 - 03e30f06f15f - - 8b260d252ff4 - 5c9729d54721 - 31c096c6b156 + - 96d0145c041a + - 6ce175385dd9 + - 8b260d252ff4 - 4ed46189d6c6 + - 34dc0bbc7e93 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -421,12 +421,12 @@ tools: revisions: - 11af7fce71cf - 40daf124be88 + - 09f5e45a8212 - 46eb13bc2c73 - - a730269af659 - - 2c4941386820 - 681bdf1e22ff - - 09f5e45a8212 - a1aad8b559c6 + - 2c4941386820 + - a730269af659 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -438,15 +438,15 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - f272b8ba0983 - 3897eaadfbff - b74b8cbfc1f1 - - 0594ea1417c8 - - 8cb121b6a1d2 - 743cd1472aeb - - 12038f59c0f4 - 6cbb9c47795c + - 8cb121b6a1d2 - 882b2e649602 + - f272b8ba0983 + - 0594ea1417c8 + - 12038f59c0f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -458,13 +458,13 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: + - cced6715f926 - a9826db86d9a - eccb508bb678 - adee7e8b746f + - 238f78e38a8b - 18cf9de1cf73 - - cced6715f926 - dba06328556a - - 238f78e38a8b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples @@ -476,14 +476,14 @@ tools: - name: bcftools_query owner: iuc revisions: + - f64e7ca2efd2 - e0ad88dec40d - e53501abf992 - - fdec14f69010 - 31a1b89eab9b + - c9935c9e8a24 - 9f36041495a3 + - fdec14f69010 - 3ce32adc55b2 - - f64e7ca2efd2 - - c9935c9e8a24 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -496,13 +496,13 @@ tools: owner: iuc revisions: - fd3539749127 - - d43eb39b989e + - 79489d5685dd + - 3b7b1fe7b937 - d68c43202172 - b7be725976b6 - - 4db0695a6fc7 - - 79489d5685dd + - d43eb39b989e - 2331ddcbd5aa - - 3b7b1fe7b937 + - 4db0695a6fc7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -514,12 +514,12 @@ tools: - name: bcftools_roh owner: iuc revisions: + - 1a989b4110da + - 78cd8b69da4c + - 58091e1be01b - 5296d26b0373 - 6a636d58dfc2 - - 58091e1be01b - - 1a989b4110da - b0d39ef600a7 - - 78cd8b69da4c - 1ccf0e7fb4f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -533,13 +533,13 @@ tools: owner: iuc revisions: - bf8325a07ce7 - - e8af591435d1 - - b641062a2587 + - 4d3ce9dc1525 + - b17394940c7a - baa8823f8073 - - 591cc8518033 - '388983871932' - - b17394940c7a - - 4d3ce9dc1525 + - 591cc8518033 + - b641062a2587 + - e8af591435d1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -551,14 +551,14 @@ tools: - name: bcftools_view owner: iuc revisions: - - 1a2ef636f48e - - 3ca3de4e5291 - - 38d75661c235 - - e6b5cbbf449b - - d1f8f55f564d - - 3a233c8eb814 - c2ab91a0d506 + - 3a233c8eb814 - 59fa8742285e + - 3ca3de4e5291 + - d1f8f55f564d + - 1a2ef636f48e + - e6b5cbbf449b + - 38d75661c235 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -570,15 +570,15 @@ tools: - name: vcf2tsv owner: devteam revisions: - - e92b3c0f9224 - 285060661b45 + - e92b3c0f9224 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfaddinfo owner: devteam revisions: - - 6ea73d6151ec - afc0ba768690 + - 6ea73d6151ec tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives @@ -591,8 +591,8 @@ tools: - name: vcfannotate owner: devteam revisions: - - 01e0321aca98 - 6faa2c4c71d2 + - 01e0321aca98 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes @@ -612,15 +612,15 @@ tools: - 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: - - aa8e8c96ca06 - 5e850c85ba32 + - aa8e8c96ca06 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -633,30 +633,30 @@ tools: - name: vcfcommonsamples owner: devteam revisions: - - 254f285dbaaa - f1852ecef841 + - 254f285dbaaa tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance owner: devteam revisions: - - 5822b40f3037 - 48e458c721b3 + - 5822b40f3037 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter owner: devteam revisions: - - 6b935ab36d7b - - eae7c08ebb6f - 4bdc111b2470 + - eae7c08ebb6f + - 6b935ab36d7b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - fc5a64fdd5b2 - 11f62f071125 + - fc5a64fdd5b2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten @@ -669,8 +669,8 @@ tools: - name: vcfgeno2haplo owner: devteam revisions: - - b890055e07bd - a3dea556218d + - b890055e07bd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes @@ -711,15 +711,15 @@ 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 owner: devteam revisions: - - ee60203e68d9 - 5b7120c66efc + - ee60203e68d9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate diff --git a/staging.gvl.org.au/viral_tools.yml b/staging.gvl.org.au/viral_tools.yml index 15250eab7..06370d956 100644 --- a/staging.gvl.org.au/viral_tools.yml +++ b/staging.gvl.org.au/viral_tools.yml @@ -2,7 +2,7 @@ tools: - name: quasitools owner: nml revisions: - - 9def47f3c1e4 - 18aad692772a + - 9def47f3c1e4 tool_panel_section_label: Viral Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 3fef97aef..34b395726 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,18 +2,18 @@ tools: - name: abricate owner: iuc revisions: - - c2ef298da409 - - 6e9aea89e388 - - 3f3e247c053d - 78c75f134c16 + - 3f3e247c053d - 4efdca267d51 + - c2ef298da409 + - 6e9aea89e388 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 owner: iuc revisions: - - c45c9dd066e2 - 3f438bf5475d + - c45c9dd066e2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_gaeval @@ -40,50 +40,50 @@ tools: - name: annotatemyids owner: iuc revisions: - - 44018dd6b447 - - a79ee60b6926 - cd2480f35935 - - b5d8e5475247 + - f29602ae449e + - 133f36c29579 + - a79ee60b6926 - 3e1f6f6d557e + - 44018dd6b447 + - 4f2967b27e67 - 1aae04680c4b - fe3ca740a485 - - 133f36c29579 - - f29602ae449e - - 4f2967b27e67 + - b5d8e5475247 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - bc88856eddab - e78e25d3b4bd + - bc88856eddab tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: - - 6519ebe25019 - 7be22100e5e1 - dc027fa56d55 - f1e653756174 + - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 09855551d713 - - ca6d970d931c - 28433faa6e42 + - 09855551d713 - bd0e53f3a891 + - ca6d970d931c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - da5f1924bb2e - - d77802fe76f7 - 728dacaf08a9 - 92eee5f31117 + - da5f1924bb2e + - d77802fe76f7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap @@ -116,16 +116,16 @@ tools: - name: cpat owner: bgruening revisions: - - 7ccc6234b54e - - 1ac12c0cc7a0 - 8e9e228c54c4 + - 1ac12c0cc7a0 + - 7ccc6234b54e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - - 9d1fbff733cf - 63662ae295d6 + - 9d1fbff733cf - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -156,49 +156,49 @@ tools: - name: funannotate_annotate owner: iuc revisions: + - 582fd74dc2a1 + - 756376aeb1ae - b6b5cd37f2a2 - 9f2455341fac - - 756376aeb1ae + - 3bbe70fef6df - 9c15ca7e764e - 14f588312c56 - - 3bbe70fef6df - - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - 8e1ace8f77c6 - - 30fb23d4c31c - - 989f7c061f35 - 0ffe5be70caf + - 73428a792541 + - 989f7c061f35 - 1691af4a0d17 + - 30fb23d4c31c - a230ea445788 - - 73428a792541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 494f0bb4a993 - - 0418d28136de - 563a19373357 - - 57c6718cbfcc - - e94187d661df - - 30f08d74024f - 5a5ae61da69c + - 0418d28136de + - 30f08d74024f + - e94187d661df + - 57c6718cbfcc + - 494f0bb4a993 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 4b96ced19f75 - - d6c7106b7b2e - - 1bc5a03faf2e - 2bba2ff070d9 - 7abc5f6dd595 - f77d7b685bb3 + - 1bc5a03faf2e - f31125bb85ea + - d6c7106b7b2e + - 4b96ced19f75 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort @@ -206,11 +206,11 @@ tools: revisions: - 520e30695ec3 - d3af38b9c7e1 + - fed64e676186 - d77fdcca400e - - b3cf4684e9c7 - 52af33194019 - - fed64e676186 - 54961e026fe4 + - b3cf4684e9c7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -222,9 +222,9 @@ tools: - name: gff_to_prot owner: iuc revisions: + - 2aea122fbd25 - 07d7991bf205 - 79261884facd - - 2aea122fbd25 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -305,11 +305,11 @@ tools: - name: mitos2 owner: iuc revisions: - - c8ac28e8ac44 + - e95d52d295d7 - b815ec682418 - - 624606f7c996 + - c8ac28e8ac44 - 033755194fe9 - - e95d52d295d7 + - 624606f7c996 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -359,8 +359,8 @@ tools: revisions: - a17498c603ec - 8a22554cdde2 - - bf68eb663bc3 - d643e3b03500 + - bf68eb663bc3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -372,8 +372,8 @@ tools: - name: repeat_masker owner: bgruening revisions: - - ba6d2c32f797 - 3f987772e283 + - ba6d2c32f797 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler @@ -404,30 +404,30 @@ tools: - name: snpeff owner: iuc revisions: - - 5a29ab10dba6 - - 5b80f544c67f - 6322be79bd8e - - c7275bd8b4d6 - - cfcf33df7fc0 - - 68693743661e + - 5a29ab10dba6 + - 8f92c2b26e6d - 5c7b70713fb5 - 268d162b9c49 - - 8f92c2b26e6d + - 68693743661e + - 5b80f544c67f + - cfcf33df7fc0 + - c7275bd8b4d6 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 - name: sortmerna owner: rnateam revisions: - - eb35257d2e29 - 10b84b577117 + - eb35257d2e29 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -439,25 +439,25 @@ tools: - name: tbprofiler owner: iuc revisions: - - 51dd22484644 - 45083d070fb8 + - ba6f87115e13 + - d03af1c7002c - 8cb134b8c1a5 + - 51dd22484644 + - 037a11682176 - ac8250086ac3 - - 4839e590cb26 - - 37213cf56392 + - 809dfc93d593 - 200c378d85f3 - - ba6f87115e13 - - 037a11682176 - - d03af1c7002c + - 4839e590cb26 - e1a9d6fd258d - - 809dfc93d593 + - 37213cf56392 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - f50807720df1 - 8fc50fe60127 + - f50807720df1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_hmm diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index f46772600..22d244b08 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,28 +2,28 @@ tools: - name: abyss owner: iuc revisions: - - db9b10824c61 - - 7547fcab5d19 + - fa5259cc561b - 0e93176640ac + - 7547fcab5d19 + - db9b10824c61 + - d6d5ccc2c581 - 8f1b150a2487 - - 0124fce4654a - 890b794c997d - - 841084c5fc46 - - d6d5ccc2c581 - - fa5259cc561b + - 0124fce4654a - a929ce596a34 + - 841084c5fc46 - 553bfe8bd0b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 21e491ad532a - - b9e31c5c01c7 + - 067592b6b312 - b2860df42e16 + - b9e31c5c01c7 - ddddce450736 - - 067592b6b312 - 94fe43e75ddc + - 21e491ad532a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -37,47 +37,47 @@ tools: owner: bgruening revisions: - 22286dab5aa1 + - 5258e18bbe23 + - faee8629b460 - 3371c5bdc17a - a7f16f24e9a1 - - faee8629b460 - - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - 53dd00a4ab68 - '392811378515' + - 53dd00a4ab68 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: + - 46ae58b1d792 + - 94170eee0ad8 - 5ecdeca79a0d - e5c372c91e46 - - 0d243f458b53 - - 2dd755c1c6ff - - cf13a1e03e5b - - 602fb8e63aa7 - - 4048d82f0c88 - - 94170eee0ad8 - - 46ae58b1d792 + - e824f5d958d0 - bb935709506a + - cf13a1e03e5b - 2babe6d5c561 - 41030a6c03b7 + - 602fb8e63aa7 + - e4bd1e99bacf + - 0d243f458b53 + - 4048d82f0c88 + - 2dd755c1c6ff - 1e62c28ba91d - 1440ae06552f - - e824f5d958d0 - - e4bd1e99bacf - ea8146ee148f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - 5732f959936a - c5b7390290b1 - 86f150c8019d - - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -89,44 +89,45 @@ tools: - name: flye owner: bgruening revisions: - - 276f5d8712d5 - - e27815e82dd4 - - 3e4f8642c77e + - cb8dfd28c16f - 1f0769f0b56b - 1ce9b1d72ec3 - - 3ee0ef312022 - - cb8dfd28c16f - - 8d4f03b5fe9d + - 3e4f8642c77e + - cd11366d92cf - 291923e6f276 + - e27815e82dd4 + - 8d4f03b5fe9d + - 276f5d8712d5 + - 3ee0ef312022 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: + - 3169a38c2656 + - 460fad600dce - b2f674562a18 - 01210c4e9144 - - 460fad600dce - - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 06bcf65179fb - 8b330a577046 - - ba88bc5a6446 - 7348b69e5109 + - 06bcf65179fb + - ba88bc5a6446 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - 3ef480892a9f + - 6ec1b853c8fd - 690c2caa367e - 5127a713de83 - - 3fba9c77550a - - 6ec1b853c8fd - f4a3eff8ab85 + - 3fba9c77550a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -138,24 +139,24 @@ tools: - name: hifiasm owner: bgruening revisions: - - 3f7be05a1597 + - 0ee0c3089254 + - 2061fb3b81b4 - 6505bd37670d - - ec9e21e9c71b - - f3c89da3af16 + - df25d4fb79b7 - 60024a528cbd - - 2061fb3b81b4 + - 284a1cb82b61 - 5f625c63b8bc + - ec9e21e9c71b + - 5161f204ba63 + - 3f7be05a1597 + - 5bec28269d95 + - 41cea2aa2dce + - f3c89da3af16 + - 366a11d316a7 - 045c7c3d8e59 - 71740308d412 - da9d8bf98802 - - df25d4fb79b7 - - 0ee0c3089254 - - 284a1cb82b61 - - 366a11d316a7 - 9ef6920c3089 - - 41cea2aa2dce - - 5161f204ba63 - - 5bec28269d95 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -179,21 +180,21 @@ tools: - name: megahit owner: iuc revisions: - - a96f3ad4e0d8 + - 14ddfc8ffb93 - de387b2b2803 + - a96f3ad4e0d8 - 7518ee87b53d - - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - eb7b00ec347d - 9d79beb19ac3 - - d7edbc9c3a07 + - eb7b00ec347d - 39edec572bae - 09c589057ee8 - f8113c25bc6b + - d7edbc9c3a07 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl @@ -207,15 +208,15 @@ tools: - name: metaspades owner: nml revisions: - - e731ea24e48d - - fd128c111ab0 - - f369ef5f210b - - 606b09cc9860 - - 2ecf5a570907 - 3ca2d2a9068c + - fd128c111ab0 - f338e9942b27 - - eb7a370f6588 + - e731ea24e48d + - 606b09cc9860 - 99ecfdafc64f + - eb7a370f6588 + - f369ef5f210b + - 2ecf5a570907 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -227,10 +228,10 @@ tools: - name: miniasm owner: iuc revisions: + - b799a615995d - 8dee0218ac7d - 73a3846701e1 - a7b889b90140 - - b799a615995d - 8b6d0d85252b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -249,9 +250,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 15200570e926 - 64a1c751d99b - 7c2f5268d01c + - 15200570e926 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -263,21 +264,21 @@ tools: - name: pretext_map owner: iuc revisions: - - 8fef980d48b5 - - dfb8a4497339 - - bbe19ef04a74 - 2b16ba799da9 + - dfb8a4497339 + - c6cec5ab35c1 + - 8fef980d48b5 - 02831bf9e95f - d256a51a656b - - c6cec5ab35c1 + - bbe19ef04a74 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: + - e9bd16ba5ebd - a315c25dc813 - 76d4cbefff85 - - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast @@ -285,24 +286,24 @@ tools: revisions: - 59db8ea8c845 - 6fcbee531de6 - - ebb0dcdb621a - - 875d0f36d66f - - 7594365c546b - - 342a1d1fed7b + - 3061c8b029e5 - 675488238c96 - 72472698a2df - - 3061c8b029e5 + - 7594365c546b + - 342a1d1fed7b + - ebb0dcdb621a + - 875d0f36d66f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - aa39b19ca11e - - cd06929b224b - - 39bed8de8017 - - d865b62f501c - a199cd7ac344 + - 39bed8de8017 - 78c533842eeb + - d865b62f501c + - cd06929b224b + - aa39b19ca11e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragtag @@ -314,30 +315,30 @@ tools: - name: raven owner: iuc revisions: - - 2b2a352488fa - - f11b994b7eb2 - - f8564b2d7f63 - - 5c55448d0f33 - 3edba9afc9bc + - 5c55448d0f33 + - f8564b2d7f63 + - f11b994b7eb2 + - 2b2a352488fa - 33b7d8481a76 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast owner: iuc revisions: - - 8e66f695d859 - f73ab5187eed + - 8e66f695d859 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - 28189050e437 - - 53c2bc8c2ae3 + - e122f9101584 - ef69617ecb42 - 1d06c8b38e77 - - e122f9101584 - 5fc94b3a4704 + - 53c2bc8c2ae3 - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -350,189 +351,189 @@ tools: - name: shovill owner: iuc revisions: + - f698c7604b3b - ad80238462c1 - - 83ead2be47b2 - - 865119fcb694 - - d9f6a00b6db7 - 196a599ec43d - - f698c7604b3b - ee17a294d3a3 + - 83ead2be47b2 + - d9f6a00b6db7 + - 865119fcb694 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 5e0825476fb7 - - 015283de3004 - 24e471d13fe9 + - 015283de3004 + - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 604782a8a53a + - 904bf932cf78 - 1fc82fe7ebef + - 604782a8a53a + - 051fd2db8a27 + - c33a476f4001 - 7490b213baa9 - - 904bf932cf78 - 1bb12736175c - - c33a476f4001 - - 051fd2db8a27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 655fa188c3cc - - ad8b536d1caa - d6e617c4e338 + - 655fa188c3cc - fee85957cebe - - 808b3a0a6716 + - ad8b536d1caa - 9678993ca5bd - 34305b013402 + - 808b3a0a6716 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - b8002c3f7141 - - e5a3b75a271f - 037f9927c4ff - - 21da31ed41a1 - 8d4b90bf9caf - - 6b5a5842531e - 7e27faaad80e + - 21da31ed41a1 + - b8002c3f7141 + - 6b5a5842531e + - e5a3b75a271f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 328aa71f0f3c - - 5b26685e5d3b - - 2a10645aeadd - - 86f66ab58e14 - 7922870efcca - - f1532cb33c75 - 9de69775f512 + - 2a10645aeadd + - f1532cb33c75 + - 5b26685e5d3b + - 86f66ab58e14 + - 328aa71f0f3c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 85fb02c43042 - - 6aad515a5270 - e41dcb0e913b - - 8cc856b935ee + - 6aad515a5270 - 1708851f8804 - 340bc17f49cf + - 85fb02c43042 + - 8cc856b935ee tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - 249f6a28c751 - - de1260f8a300 - - d5fb354f745d + - 6357b127161e - d159735a6a9f + - de1260f8a300 - b65a43f70b99 - b3490b036c5a - - 6357b127161e + - 249f6a28c751 + - d5fb354f745d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - dd7ad84f3943 - 33368fec3b70 - - d5887ace0dd4 - 9006e5836729 - a90db5dbaaf3 - b7829778729f - d2d1df21dfb9 + - d5887ace0dd4 + - dd7ad84f3943 - 7897763d14ec tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: + - 6f4c8ad6ea01 - 189e837009c9 + - 505a9833ab5d - ced385aa976d - - 6f4c8ad6ea01 - - 8f631679571f - 0368ac680e70 - - 505a9833ab5d + - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: + - 19bdfd1e6fe3 - 9ded6109434a - - a7ed21de23fe - d40ed4eb0c0e - 356afed970b4 - e59bee4565b3 - - 19bdfd1e6fe3 + - a7ed21de23fe tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: + - b23249f81bc4 - 4688ae3b49b5 - - ebd801e712bc - - 6dd935e4984b - 7673a6c920b2 + - 6dd935e4984b - 80a17897564d - - b23249f81bc4 + - ebd801e712bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - 937ea677d437 - 59bd28f6265d - - b5e35a2ca4f3 - - cb1e3db43020 - b64696992ee9 - ed312479d9eb + - b5e35a2ca4f3 + - cb1e3db43020 + - 937ea677d437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - cb4768eeca3b - - b9b0246a2be3 - - 383bb5ad32e2 - - 05bd7504fdb2 - 2628f6790eda + - 05bd7504fdb2 + - b9b0246a2be3 - 6015aa0303f2 + - cb4768eeca3b + - 383bb5ad32e2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 8f9f06995f98 + - e022dff952df - 3e44ef016b45 - - 6e26c9afd301 + - 8f9f06995f98 - 0a3a602cd1e3 - - 9e3e80cc4ad4 - e92675014ac9 - - e022dff952df + - 6e26c9afd301 + - 9e3e80cc4ad4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f + - 920677cd220f - 8d09f8be269e + - 08256557922f - 5da9a0e2fb2d - - 920677cd220f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - 4a53b89fa703 - - 82398ba86ba7 - 37d88f41c810 + - 82398ba86ba7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko @@ -544,8 +545,8 @@ tools: - name: yahs owner: iuc revisions: - - 39495e107274 - 425e63adcc5d + - 39495e107274 - ff4031bfaa22 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 9328b582b..547e4d06c 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -3,17 +3,17 @@ tools: owner: iuc revisions: - 4768f7f8e93f - - bfd290fe1588 - 392f100eebcd + - bfd290fe1588 - 1ae00120dd24 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - ded48b36f3b7 - - 8e8dc9a1e3e5 - 31812e7a1315 + - 8e8dc9a1e3e5 + - ded48b36f3b7 - 1f5641a52664 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu @@ -21,7 +21,7 @@ tools: owner: nml revisions: - 24a7a95867b0 - - 5c8ff92e38a9 - 17fcac7ddf54 + - 5c8ff92e38a9 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index 7c0bc3986..3f5e704eb 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,13 +2,13 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 1c427e24fb79 + - 204a131e47db - d58c27d2c5a7 - - d1f62024a08b - 7beb76ffbc0f - - a9c9d768b751 - - 204a131e47db + - 1c427e24fb79 - 0840ba83860c + - d1f62024a08b + - a9c9d768b751 - 159b04e36791 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu @@ -22,7 +22,7 @@ tools: - name: bbtools_tadpole owner: iuc revisions: - - 0ddf147d1897 - ce13b4678f18 + - 0ddf147d1897 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index 03f53c7d3..36ef0ebd3 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - 64e2edfe7a2c - - ce3c7f062223 - - e19bebe96cd2 - - 0a5c785ac6db - - 07e8b80f278c - - a68aa6c1204a - dde39ba9c031 - - 87ee588b3d45 - - b28e0cfa7ba1 - 589e7e57fd6d + - e19bebe96cd2 + - b28e0cfa7ba1 - a8eabd2838f6 + - ce3c7f062223 + - 07e8b80f278c + - 64e2edfe7a2c + - 0a5c785ac6db - a1a923cd89e8 + - a68aa6c1204a + - 87ee588b3d45 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 58b0749a3..3d5644862 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,30 +8,30 @@ tools: - name: diamond owner: bgruening revisions: + - f921014aba5a - 54f751e413f4 - - 62c9df8382c2 - e8ac2b53f262 - - f921014aba5a + - 62c9df8382c2 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - acf4e47b734c - - a52d2d93e595 - - d999e774072a - - e25d3acf6e68 - - 2889433c7ae1 - 6f386c5dc4fb - - 0e3cf9594bb7 - 5edc472ec434 + - 2889433c7ae1 - cbf3f518b668 + - a52d2d93e595 + - acf4e47b734c + - 0e3cf9594bb7 + - d999e774072a + - e25d3acf6e68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart owner: crs4 revisions: - - 1334cb4c6b68 - e9005d1f3cfd + - 1334cb4c6b68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index ba9f81fc6..9565d4856 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 710301bc46fa - - 095ad4d096d1 - 6ca543ec1bf8 - - c8cdde00b105 - - da6bd1975a71 - 27ee142314a9 + - 095ad4d096d1 + - 710301bc46fa - f4230f116196 + - c8cdde00b105 + - da6bd1975a71 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -130,31 +130,31 @@ tools: - name: gmx_editconf owner: chemteam revisions: + - 0fac8e2afc13 - 88076940fa94 + - 3b8a9d5ced85 - 79cfd9ead848 - - 0fac8e2afc13 - bfb65cb551d8 - - 3b8a9d5ced85 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - eb6564a60136 - - d532b7e5f64b - b46d4b4d995c + - d532b7e5f64b - 55918daa5651 - - 715cd0e87781 - f5d979cb4b54 + - eb6564a60136 + - 715cd0e87781 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - d2f955aea23a - f26afd1b7104 - - fdf2cc80adb5 - 5579659312e6 + - d2f955aea23a + - fdf2cc80adb5 - dae135dfd519 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -162,16 +162,16 @@ tools: owner: chemteam revisions: - bc31d02be922 - - d1d0efda35c0 - 319a28774da9 + - d1d0efda35c0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - ed736e6eee39 - 2c349b027a01 - cac1886249a2 + - ed736e6eee39 - 070e3ecc3fda - 4da9ee404eab tool_panel_section_label: ChemicalToolBox @@ -179,25 +179,25 @@ tools: - name: gmx_sim owner: chemteam revisions: + - c0c9a5024177 + - 73008ef1f487 - f197e34c33a9 + - d1f803b5943c + - 807aa4c9293d - 2e219a2d9327 - - da8753545526 - 525ca7c8065f - - 807aa4c9293d - - 73008ef1f487 - - d1f803b5943c - - c0c9a5024177 + - da8753545526 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 27ea4e1a3f95 - 2c8ed1b52bf7 - - c4fbab8e03c5 - 61094e01eff9 - - 7568ae18908a + - 27ea4e1a3f95 - 1809414a9454 + - c4fbab8e03c5 + - 7568ae18908a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -209,18 +209,18 @@ tools: - name: md_converter owner: chemteam revisions: + - d7ec25187599 - ba83f0923369 + - ccfbd956a2d3 - 79e8ab8f1e81 - - d7ec25187599 - 730ef07b90ae - - ccfbd956a2d3 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: mdanalysis_dihedral @@ -268,10 +268,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - b59c91adeac1 - e2c36f62e22f - - e6011617c748 - 4242b4d68e9c + - b59c91adeac1 + - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -351,9 +351,9 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - bf99565cec1f - - 85fad59f8168 - d4c67ced6abc + - 85fad59f8168 + - bf99565cec1f - 9b48456a96fe tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 065091000..0fc871a1e 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,11 +2,11 @@ tools: - name: diffbind owner: bgruening revisions: - - 2605cbdaa7d8 - fa56d93f7980 - - f907216064f6 - - 163688bb8f73 - c97a786e8fb5 + - 163688bb8f73 + - 2605cbdaa7d8 + - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -18,17 +18,17 @@ 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: - - f5d67c722d67 + - 86e2413cf3f8 - 495a4173006f - 640d3af5d833 - - 86e2413cf3f8 + - f5d67c722d67 - 424aefbd7777 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -42,7 +42,7 @@ tools: - name: sicer owner: devteam revisions: - - 5c2cc3b58c7d - 74c9214cc8e6 + - 5c2cc3b58c7d 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 db98c6b38..2070c8b75 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -2,17 +2,17 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - - 90981f86000f - - 830961c48e42 - 33151a38533a - 25136a2b0cfe + - 90981f86000f + - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -31,10 +31,10 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 2dae863c8f42 - - 0046692724f9 - 6cbe2f30c2d7 - baabc30154cd + - 0046692724f9 + - 2dae863c8f42 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 e0784a3ee..762534516 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -16,32 +16,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - 5e1240a87bcb - - 0b3c3ad92827 - a3b86937ead6 + - f3a19509108a + - 6ef0b5664c69 - 4a6ee918c13a + - 5e1240a87bcb + - 0b3c3ad92827 + - ab9350a8ab4d - 3b6f97e7094c - - f3a19509108a - 367b1ed91207 - - ab9350a8ab4d - e3cbd2287f63 - - 6ef0b5664c69 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - bd46669113b9 - 54ccb7e1f49a - - 1b5fc03380d4 - - 72ed72122deb - - 584008e574b2 + - e177a8ea0bf1 - 501c21cce614 - 33c99804a32f - - e177a8ea0bf1 + - 1b5fc03380d4 + - 584008e574b2 + - 72ed72122deb - 091bb5922a82 - - d4d4e9febf5c + - bd46669113b9 - e525f9ffb9ac + - d4d4e9febf5c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -67,23 +67,23 @@ tools: owner: devteam revisions: - 8979c288aefb - - 186b8d913e6c - 77b41c89d856 + - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 4b347702c4aa - 614a63f14adf + - 4b347702c4aa - 43807a65369f tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa owner: iuc revisions: - - e33c82b63727 - 8e9d604e92f4 + - e33c82b63727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -95,9 +95,9 @@ tools: - name: gffread owner: devteam revisions: - - 154d00cbbf2d - 3e436657dcd0 - 4dea02886337 + - 154d00cbbf2d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -122,8 +122,8 @@ tools: - name: samtools_bam_to_cram owner: iuc revisions: - - b9ea85dfaf45 - 18dbde5680c0 + - b9ea85dfaf45 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta @@ -143,34 +143,34 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: + - 19e45916daf9 + - 92ac8e086317 + - b9b385097f13 - 63769c4217a7 - 26c6706bfb07 - - b9b385097f13 - - 92ac8e086317 - - 19e45916daf9 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf owner: iuc revisions: - - a40dd4fd3096 - 3c19c84fbce2 + - a40dd4fd3096 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_twobittofa owner: iuc revisions: - 8067dfa00ed2 - - 3c6f9e8a4c17 - e9bbe2f71784 + - 3c6f9e8a4c17 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_wigtobigwig owner: iuc revisions: - fa49730d1d4b - - a2f83a375bf2 - 98704d357ede + - a2f83a375bf2 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 4c95fbd4a..93b79be5a 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,205 +2,205 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 5f6d123679f4 - - 29451af70c52 - a1ca9bccc7f2 - de72ba3ed6f2 + - 29451af70c52 - e821645ef8fc - c929a006727f - 268e91e540ee + - 5f6d123679f4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 5d11599b8a7d - - 12af64f93288 - - bb1e4f63e0e6 + - 0e143b4c3987 - 7a7fd0f5f15d - 0e49b109abc2 + - bb1e4f63e0e6 + - 5d11599b8a7d - 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- 7fda5607e777 - - 3b9d990a0a0e - 4e12ea27f788 - - 56bce3c82278 - - 7e361d147872 + - 3b9d990a0a0e - 231994413f89 - 9368fbc49c8b + - 7fda5607e777 + - 7e361d147872 + - 56bce3c82278 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - e65d16fb2724 + - 94ca68515826 - c03c3384cd81 - ce4ce3316f74 + - b1779366c8e9 - d9114ef1c8a5 - 4431f39ede55 - - 94ca68515826 - - b1779366c8e9 + - e65d16fb2724 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - 23f7c5f1fdaf - 2da482e408b8 - - 4ed32329e0ed - f8fc4e5aff9d - - b88ebb3672a1 - - 793665fff0f8 - - 23f7c5f1fdaf - d57251071381 + - 793665fff0f8 + - b88ebb3672a1 + - 4ed32329e0ed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - 010e58e9d822 - - ba6efa77fb79 - - e4c7985d4585 - a4dfb122e52b + - 010e58e9d822 - 512155688d98 - - 25d830337d31 - c60570fa602f + - ba6efa77fb79 + - 25d830337d31 - a7849312d328 + - e4c7985d4585 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: + - c899e0ccff8c - 69264da0ce77 - - 443d9a9d6d11 + - 38e3f226248b - 00d869ea03a1 - - 4d678170d29b - - c899e0ccff8c + - 443d9a9d6d11 - aa200e4f3939 - - 38e3f226248b + - 4d678170d29b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - c361b12d207a - - a2d70c4fd406 - - 10301d137111 - - aac8444d6681 - - d806504e96d9 - 6662b1a8d326 + - d806504e96d9 + - aac8444d6681 + - 10301d137111 + - a2d70c4fd406 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 b4957b080..67c0f2dc3 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -23,22 +23,22 @@ tools: - name: obi_grep owner: iuc revisions: - - e9e49cf06b42 - 02bab5ff7c37 + - e9e49cf06b42 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend owner: iuc revisions: - - 94f412098ac8 - 8cb6bd511879 + - 94f412098ac8 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter owner: iuc revisions: - - 91a1ed0b486f - 76e69de726b2 + - 91a1ed0b486f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort @@ -51,8 +51,8 @@ tools: - name: obi_stat owner: iuc revisions: - - 39320fee9d70 - 5f4544915893 + - 39320fee9d70 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index caecd371d..9e65a9209 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - dba489bfcd62 - ce385837c160 - 832c20329690 + - dba489bfcd62 - 63dd26468588 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 9ba532992..b1d163d61 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -9,10 +9,10 @@ tools: owner: iuc revisions: - 29bdbc353f20 - - 62f5fab76dfb - - d82648ad25a3 - 6da3972210ee - cf1322aeb137 + - d82648ad25a3 + - 62f5fab76dfb 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 8cd49ab4a..04d539c16 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -10,40 +10,40 @@ tools: revisions: - c4b82dce8335 - 8665bcc8b847 - - fe74900d6dc7 - - 093678460093 - - 5915ea1ec9b1 - - 48f587c13075 - - 288f97432497 - - 5eb7e84243f2 - - 135b80fb1ac2 + - 660cffd8d92a - 4e5056fefd88 + - 093678460093 - 8c0175e03cee - c5e2e5902201 - - e4691e1589d3 - - 44e2cc14f75b - - b1c926deaa2d - - 660cffd8d92a - - 64172f1c1202 - de6cebe3c043 - c053d4cad713 + - 5eb7e84243f2 + - 48f587c13075 - 49370cb85f0f + - e4691e1589d3 + - 288f97432497 + - 44e2cc14f75b + - 64172f1c1202 + - b1c926deaa2d + - 135b80fb1ac2 + - 5915ea1ec9b1 + - fe74900d6dc7 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 owner: devteam revisions: - 7d37cfda8e00 - - de2db1bdfbf8 - 5cbde03c1103 + - de2db1bdfbf8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -62,8 +62,8 @@ tools: owner: devteam revisions: - 9457a20156db - - 516b97a23d7e - 859422bcb689 + - 516b97a23d7e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences @@ -76,55 +76,55 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - f81d4362b6c1 - ec0b5076173a + - f81d4362b6c1 - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: - - cd0874854f51 - - 0dbb995c7d35 - - 56022eb50bbd - 9c620a950d3a + - 56022eb50bbd + - 0dbb995c7d35 + - cd0874854f51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - d60c3f704da0 - - dbf9c561ef29 - - a626e8c0e1ba - - ecb9f4854617 - 1d8fe9bc4cb0 - 65b93b623c77 + - d60c3f704da0 + - dbf9c561ef29 - dbfc505896e9 + - a626e8c0e1ba - c59d48774d03 + - ecb9f4854617 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - 9115b978ce10 + - b05e39b9c170 - f1dc2a761c30 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: + - 10b75444feae - '144275714590' - 81a9090d6df3 - - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer owner: devteam revisions: - 47e5dbc3e790 - - e9f8633db0a2 - 8611b80a14d6 + - e9f8633db0a2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation @@ -139,15 +139,15 @@ tools: owner: devteam revisions: - 9dfda4e310ed - - 4e1d64e6385f - 9282652e7234 + - 4e1d64e6385f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - f3936d0632cb - 03d57fea6482 + - f3936d0632cb - 523c2aff0376 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -155,33 +155,33 @@ tools: owner: devteam revisions: - 3e396e702cea - - b41c2c1bcfbf - 2ccb8dcabddc + - b41c2c1bcfbf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner owner: devteam revisions: - - 8d958759cf2a - 09a2199cd356 + - 8d958759cf2a - 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 - 397dc333436b + - 249c8393f2d4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: - - 74db4cffab1f - 54053ea6c77e - 045f0e1043f7 + - 74db4cffab1f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats @@ -195,24 +195,24 @@ tools: - name: fastq_trimmer owner: devteam revisions: - - b63b2bfb3ea3 - f0b18efb97f1 - 33794bdb7fe0 + - b63b2bfb3ea3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta owner: devteam revisions: - - 297962e79f39 - ac3fed111eb6 + - 297962e79f39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter owner: devteam revisions: - - d5e9e83cd3d8 - - 529bccd5e4a1 - 567d5b3c52b1 + - 529bccd5e4a1 + - d5e9e83cd3d8 - 09070cacefd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -220,15 +220,15 @@ tools: owner: devteam revisions: - 8abdedf55101 - - 0b7ec11b3c7c - 4bedca26c133 + - 0b7ec11b3c7c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - - 90858c306551 - bdf1ce174e39 + - 90858c306551 - cb1e251cac37 - 736b8f6ee456 tool_panel_section_label: FASTA/FASTQ @@ -236,9 +236,9 @@ tools: - name: fastx_collapser owner: devteam revisions: + - 7ce1891db6f5 - 421f0af4ee95 - 07497255281e - - 7ce1891db6f5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -255,17 +255,17 @@ tools: revisions: - 177f0621c266 - e246088b6e34 - - 6027ef51ef91 - 0c2907307ba4 + - 6027ef51ef91 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - - 547e8d00f11c - 73194cdd4f57 - 61b4cedc8934 - 377ac2829eac + - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -278,24 +278,24 @@ tools: owner: iuc revisions: - 037f0acc7830 - - f69501361cec - 2f804526f5fd - b4c6f054210a + - f69501361cec tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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: seqkit_sort owner: iuc revisions: + - 29ef2c5ec205 - fdc21382376d - 61eb4cfc7313 - - 29ef2c5ec205 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats @@ -310,34 +310,34 @@ tools: owner: iuc revisions: - 3da72230c066 - - a019807f4e67 - 4b494533146a + - a019807f4e67 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic owner: pjbriggs revisions: - - dfa082f84068 - 51b771646466 + - dfa082f84068 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - - 71f649c23021 - d3f58a0dc09d - bf04bd405d5b + - 71f649c23021 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - 71ad4a56c40c - - 8250ea3a1501 - - b557acca0b56 - - a535cf1e5da4 - e654095ab143 - 24013bf85a6f + - a535cf1e5da4 + - b557acca0b56 + - 8250ea3a1501 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup @@ -350,14 +350,14 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 9fa7803d1c51 + - 7a7e33d28f62 - 015cf18f4a15 - - 6a675c3aa610 - 27ac32a22ad2 - 7accf7407811 - - 7a7e33d28f62 - f3759eec3018 + - 9fa7803d1c51 - 828dba98cdb4 + - 6a675c3aa610 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group @@ -370,8 +370,8 @@ tools: - name: umi_tools_whitelist owner: iuc revisions: - - 4c8a1c7d3608 - 953b4821b183 - e4e12f0b3af1 + - 4c8a1c7d3608 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastq_quality_control.yml b/usegalaxy.org.au/fastq_quality_control.yml index e04b128de..730928ab4 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,30 +2,30 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 7b4468117008 + - ce9cd02d5b88 - 64e9a6afdd0c + - 7b4468117008 - e41385662e5e - - ce9cd02d5b88 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - 8050e091e99b - c64d534a763c + - 8050e091e99b tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - - 5ec9f6bceaee - - e7b2202befea + - f2e8552cf1d0 - 9da02be9c6cc - - 3d0c7bdf12f5 - 2c64fded1286 - - f2e8552cf1d0 - 2b0c9d9fc6ca - ff9530579d1f + - 3d0c7bdf12f5 + - 5ec9f6bceaee + - e7b2202befea tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -39,47 +39,47 @@ tools: - name: fastx_nucleotides_distribution owner: devteam revisions: - - 18a51655db17 - - ad116ae3f4d9 - b6b54ba71bd8 + - ad116ae3f4d9 + - 18a51655db17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - cc0fd298cc17 - - 7306ec78632a - 59003d0543cd + - 7306ec78632a tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - 8880fb74ef56 - - 1f296803dfa3 - a72af9de6bf5 + - 1f296803dfa3 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - abfd8a6544d7 - - f7e2f1eb3a16 - - 75c93c70d094 - - 1c2db0054039 - 9a913cdee30e + - 5e33b465d8d5 + - 75c93c70d094 + - bf675f34b056 - b2f1f75d49c4 + - f7e2f1eb3a16 - 3d93dd18d9f8 - - bf675f34b056 + - 1c2db0054039 - c1a4b5f3b432 - - 5e33b465d8d5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - cd7e644cae1d - - 949f01671246 - 084bbd8ba7b8 + - 949f01671246 + - cd7e644cae1d tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fetch_alignmentssequences.yml b/usegalaxy.org.au/fetch_alignmentssequences.yml index 0dfc5355c..c01999d90 100644 --- a/usegalaxy.org.au/fetch_alignmentssequences.yml +++ b/usegalaxy.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 19f42b3ea391 - 9e776e7fab4f + - 19f42b3ea391 tool_panel_section_label: Fetch Alignments/Sequences 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 b329fac45..b2d46f1a1 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: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs @@ -17,7 +17,7 @@ tools: owner: peterjc revisions: - 85ef5f5a0562 - - 141612f8c3e3 - 83a19df00eab + - 141612f8c3e3 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index 8a5dad66d..bddfa34e4 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -16,30 +16,30 @@ tools: - name: gemini_annotate owner: iuc revisions: - - f2f3bc622a16 - 0c8f7322f8fc + - f2f3bc622a16 - 8f53b238a360 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 owner: iuc revisions: - - 62647e2637f6 - 7cf9bc210044 + - 62647e2637f6 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 @@ -59,8 +59,8 @@ 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 @@ -94,15 +94,15 @@ tools: - name: gemini_lof_sieve owner: iuc revisions: - - 2969a1f43b7d - 90021fffff70 + - 2969a1f43b7d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors owner: iuc revisions: - - 00c2734b3bea - 61343646155c + - 00c2734b3bea tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways @@ -122,16 +122,16 @@ 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 owner: iuc revisions: - - 05124dc72dba - 86f3aac4418d + - 05124dc72dba tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region @@ -144,8 +144,8 @@ tools: - name: gemini_roh owner: iuc revisions: - - 93967598e18e - 345d41f3f574 + - 93967598e18e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 62d2c91e4..dd5bc64db 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -2,15 +2,15 @@ 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 owner: iuc revisions: - - b946929d31c4 - d46e36492bff + - b946929d31c4 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle @@ -30,7 +30,7 @@ tools: - 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/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index c3525cc69..1cf560c0a 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - e9df53a75f3c + - b39347891609 - c1b437242fee + - e9df53a75f3c - 983bf725dfc2 - - b39347891609 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,44 +17,44 @@ tools: - 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: - - e08a7ad4378b + - 6ea73833cf67 - 516a54ddf218 - - 6591f049cf7e - - 9a776b080193 - - f5ea3ce9b9b0 - - 1790dcf3c32d - - ba931a59dd59 + - 653e89d73fc4 + - aad3885b3216 - f8054ea1c365 - - c441583adae5 + - 6591f049cf7e + - 5e6237d58b0c - 4317d3cb6cba - - 734abc7ac21d - - 653e89d73fc4 - - 83c7d564b128 - - 1ec814014652 - - 4df8de2d0e48 - - 7068f48d0ef9 + - 1790dcf3c32d - 8848455c0270 - - e407b9da183a - 69ebb7f46e45 - - 6ea73833cf67 - - aad3885b3216 - - 5e6237d58b0c + - 4df8de2d0e48 + - e407b9da183a + - e08a7ad4378b + - 7068f48d0ef9 + - 734abc7ac21d + - 9a776b080193 + - 1ec814014652 + - 83c7d564b128 + - ba931a59dd59 + - c441583adae5 + - f5ea3ce9b9b0 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - 75b3b3d0adbf - - 21a560af5913 - 9aaa46d45472 + - 21a560af5913 - 34758ab8aaa4 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -63,8 +63,8 @@ tools: revisions: - 468c71dac78a - bfdc6a7ffd3a - - 95fb5712344f - af5eccf83605 - 054483e27a35 + - 95fb5712344f 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 2fa627162..5b29ebc6f 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: - - fd59d783248a + - c4bde687c846 + - 740057a5126d + - ae9994cf526f + - 4b519282a05b - 7f13dc906cb9 + - fd59d783248a - 290a11559985 - - c4bde687c846 - a64dc31ab7f2 - - 4b519282a05b - df7356989ac1 - - ae9994cf526f - - 740057a5126d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,9 +28,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: + - 7cf5b1d072b5 - 867ab348287d - f95284aa2946 - - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -42,24 +42,24 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 3b37b1b1c3a7 - - 51c6ccaace7e - - 48b42ee61bc5 - '566197475670' - - 374e9062d874 - 53460afd5115 + - 374e9062d874 - ca7cb0eaad62 + - 51c6ccaace7e + - 3b37b1b1c3a7 + - 48b42ee61bc5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: + - da4c086cff5b + - 3d059e9c2fba - 391a4cc45fea - 10515715c940 - d3a9e32672ec - - 3d059e9c2fba - 1a72f938213e - - da4c086cff5b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -79,19 +79,19 @@ tools: - name: ggplot2_point owner: iuc revisions: - - d0fc8b746d57 - 5fe1dc76176e + - d0fc8b746d57 - e3a675da7fd0 - - 5298e06f14f9 - 1acf88921176 + - 5298e06f14f9 - 299307abd804 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - - 0e7290688b50 - 17b666467c32 + - 0e7290688b50 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -103,15 +103,15 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - 97e3b735ed22 + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan owner: iuc revisions: - - 6e8eb0c0d91f - 8f62f666dcb6 + - 6e8eb0c0d91f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -129,17 +129,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 6cd09d7b5f37 - - fd5dbf0f732e - 1cfc579079a6 - a6e57ff585c0 - - 17359b808b01 + - 4542035c1075 - 836d1aa3e89a + - fd5dbf0f732e - 112eb40ba6cf - ca2def38369c - 2bb2e07a7a21 - 667e17248bfe - - 4542035c1075 + - 17359b808b01 + - 6cd09d7b5f37 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -157,9 +157,9 @@ 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 @@ -179,10 +179,10 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - f234e2e59d76 - - 85da91bbdbfb - 62e3a4e8c54c - 1c5dcef5ce0f + - f234e2e59d76 + - 85da91bbdbfb tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -201,10 +201,10 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 6c571966cfb9 - 44c66e8d21e6 - - 26f2fe7e53a1 - 7c9417381ad5 + - 26f2fe7e53a1 + - 6c571966cfb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -216,23 +216,24 @@ tools: - name: pygenometracks owner: iuc revisions: - - a1abfa420d9d - - 36b848d5f3ec - - 2824d77cd8f8 - 360df4999907 - - 326a3db8d9d1 - 4ac4e7083b7e + - 326a3db8d9d1 - 7dd841a32245 - 14e7c35f3d00 + - 36b848d5f3ec + - 2824d77cd8f8 + - a1abfa420d9d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - 2f557f6abbfb + - ab01e379d29e + - 73b8cb5bddcd - 44608d0193ed - 83c573f2e73c - - 73b8cb5bddcd - - 2f557f6abbfb 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 3c6815952..9f6c59651 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 @@ -28,55 +28,55 @@ tools: - name: scanpy_compute_graph owner: ebi-gxa revisions: + - 6417cccad133 + - 22bd5861706d - bc9e8de21efb - 7779b9dcf040 - - 22bd5861706d - - 6417cccad133 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells owner: ebi-gxa revisions: - - 55ccc0a121bc - - e9283529cba1 - - bf1e0bdec1db - 361608369dda + - bf1e0bdec1db + - e9283529cba1 + - 55ccc0a121bc tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes owner: ebi-gxa revisions: - 23d838d1569d - - cc64914b0cf4 - da611a744112 + - cc64914b0cf4 - 474a69c47184 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster owner: ebi-gxa revisions: - - 36735850e461 - - 2ccd9f9e2cd0 - fc4b3b46dc9d + - 2ccd9f9e2cd0 - ad6995afd2e6 + - 36735850e461 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers owner: ebi-gxa revisions: + - 0a8e527d1517 - d8f5224005bb - - 81c34e67f262 - 49653e680ea4 - - 0a8e527d1517 + - 81c34e67f262 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes owner: ebi-gxa revisions: + - 2861ca3bfe4d + - 4667fe07bd68 - 64dd8bb151e1 - 79da59a0b180 - - 4667fe07bd68 - - 2861ca3bfe4d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn @@ -96,32 +96,32 @@ tools: - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - c354af93f567 - 6903bc865d63 + - c354af93f567 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - 9a2f72d7dbd2 - - 94697510d55f - ff6decc0f432 + - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet owner: ebi-gxa revisions: - - 53ce0e336840 - 70cb0596ffef + - 53ce0e336840 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalise_data owner: ebi-gxa revisions: + - 28b1546857b0 - 8d9c22419c56 - - 3027cb62adbd - 6b97ffba31da - - 28b1546857b0 + - 3027cb62adbd tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator @@ -134,17 +134,17 @@ tools: - name: scanpy_plot_embed owner: ebi-gxa revisions: - - 35f6611fb8c3 - - 7d5c97823f8b - 56d22aa6cb3b - 1be0fc4d8654 + - 35f6611fb8c3 + - 7d5c97823f8b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet owner: ebi-gxa revisions: - - 6f5509cf3176 - 4a74b45c1ce4 + - 6f5509cf3176 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory @@ -157,16 +157,16 @@ tools: - name: scanpy_read_10x owner: ebi-gxa revisions: - - 287503c35cb4 - 078aa23c9374 + - 287503c35cb4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable owner: ebi-gxa revisions: - d18ed15697bb - - 36daab33aecf - 0bab2ae44e7a + - 36daab33aecf tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap @@ -193,34 +193,34 @@ tools: - name: scanpy_run_paga owner: ebi-gxa revisions: - - 6d4f88995e40 - b2768cae00a1 + - 6d4f88995e40 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_pca owner: ebi-gxa revisions: - - 3ee74b58c72d - - 4428dba93375 - 0cf90e01d9f8 + - 3ee74b58c72d - 59028945c857 + - 4428dba93375 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne owner: ebi-gxa revisions: - 8b0d6f6f44c8 - - 181d61d2f3cd - - 3fb53f5e46ea - abdb61e4afa3 + - 3fb53f5e46ea + - 181d61d2f3cd tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: - - 0f98603d0116 - 767a675b5254 - fe562424a0a6 + - 0f98603d0116 - ea91cfd0444e - bd4a244faeb8 tool_panel_section_label: HCA Single-cell @@ -228,9 +228,9 @@ tools: - name: scanpy_scale_data owner: ebi-gxa revisions: - - e2d0dc8a50ca - - f86b2c3bc459 - 5605f8452eb3 - 4cc9362782b4 + - e2d0dc8a50ca + - f86b2c3bc459 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index d0a954c22..430f0a65d 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,55 +2,60 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 29f66c353bcb + - 0f611e7d7858 - a4c13ddcc8ee + - ed2cca6b5de4 + - d9967770de96 - 9edf8894a22d - 921a2da49a0c - - 0f611e7d7858 - - ed2cca6b5de4 + - 29f66c353bcb tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - 755df866ad0c - 5746d61f0a91 - - 78fb5e286609 - ec4b948dc6f0 + - 78fb5e286609 - d404277cc87a - 11de0d28ab30 - - 755df866ad0c + - 478aacfbaa37 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 977dc15add20 - 4d511437b1e5 + - 9e357a8b2ec3 - 11fa44ee0603 + - 9d93c8fbe0a6 - f72063d9426b - - 9e357a8b2ec3 + - 977dc15add20 - 03dd3c16ae4e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: + - 41dbf4d162a2 - 0ba4f56a3613 + - 1da5f169b491 + - f86ca478c6af + - 3b5b54ed6392 - 77919cc3618e - - 41dbf4d162a2 - c3e5e2cf12b7 - - 3b5b54ed6392 - - 1da5f169b491 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: + - 7babd8a46fe0 + - 025a128652dc - b63363075c2e - - f741330d4a71 - 9939786dd9c9 - - 7babd8a46fe0 - 12d51d7be66f + - f741330d4a71 - 5308ca68ef3d 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 b929f1429..61b8da74c 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,29 +2,29 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 699a5e9146b3 - - 3df9f0a4bf34 - - 8bccb36e055a - - 81f0cbca04a7 - 0c777d708acc - 7db4fc31dbee + - 8bccb36e055a + - 699a5e9146b3 + - 81f0cbca04a7 + - 3df9f0a4bf34 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5791a7f65275 - - 0a53256b48c6 - - 2436a8807ad1 - 5bc8cdc17fd0 + - 2436a8807ad1 + - 0a53256b48c6 + - 5791a7f65275 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - 6ad1d3cfdea1 - - e576b73a2e2f - 9d47aabda459 + - e576b73a2e2f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization @@ -38,9 +38,9 @@ tools: - name: 2d_simple_filter owner: imgteam revisions: - - f70b215d155c - - d51310ab328a - dba87c4b32d3 + - d51310ab328a + - f70b215d155c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_split_binaryimage_by_watershed @@ -52,26 +52,26 @@ tools: - name: bfconvert owner: imgteam revisions: - - f3360fbeda64 + - 10eed33aa9b2 - 85edbb7a436b - fcadded98e61 - - 10eed33aa9b2 + - f3360fbeda64 - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 6e65fd971e13 - 984358e43242 + - 6e65fd971e13 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - - b58447a2eed2 - - 664232d2a3f7 - 5bf8eb50b280 + - 664232d2a3f7 + - b58447a2eed2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler @@ -85,32 +85,32 @@ tools: - name: cp_color_to_gray owner: bgruening revisions: - - bad171ed1e96 - e8f822eeb9fd + - bad171ed1e96 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - 670975e92458 - - e7273daa5ae2 - 6070780813d9 + - e7273daa5ae2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - ef4aed1d34c4 - cdf8e3c57dae - df3ad3ba5c6f + - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: + - 2484086dee41 - 5d28ac336861 - 6a7da2e5f696 - - 2484086dee41 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features @@ -124,17 +124,17 @@ tools: - name: cp_export_to_spreadsheet owner: bgruening revisions: - - f8fa0f6718a3 - - d0178bdcd00e - f24c370e5ea4 + - d0178bdcd00e + - f8fa0f6718a3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: + - 31d195bedf6d - 3245681b2f6d - ad271f78a87a - - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects @@ -149,15 +149,15 @@ tools: owner: bgruening revisions: - ff1a86a87364 - - 6100a22bf4f2 - c09dcda1143f + - 6100a22bf4f2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - 3a05117669cf - b178453ea8d1 + - 3a05117669cf - 667a513e67e4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -165,8 +165,8 @@ tools: owner: bgruening revisions: - 2564f461de62 - - a1a961c46d4b - ac5bea85a391 + - a1a961c46d4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied @@ -180,17 +180,17 @@ tools: - name: cp_measure_image_intensity owner: bgruening revisions: - - 5499dc6f8ac1 - 8536b1ae0254 + - 5499dc6f8ac1 - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - 6f4715b8540a - e972e07c7845 - d3890df07463 + - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity @@ -205,38 +205,38 @@ tools: owner: bgruening revisions: - d85f11570109 - - 79e10d12d90a - acf3aa487283 + - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - 035a58c7f54a - 80b200ae516b - b76841ee5560 + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines owner: bgruening revisions: - - 91560258e972 - b44b081bcf37 + - 91560258e972 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_relate_objects owner: bgruening revisions: + - 3a3033222f61 - 8083a87d2fdf - 48102a685037 - - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 33f4fa1413fb - 4ecf93628f97 + - 33f4fa1413fb - 27edbb90ab2b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -271,7 +271,7 @@ tools: - name: overlay_images owner: imgteam revisions: - - ca362a9bfa20 - 8dc02c854048 + - ca362a9bfa20 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index c43a6e5ed..c2b6fadef 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: + - 3e4f434a69c6 + - 78bbd17d0703 - f362150bef41 - - a38934e303b9 - - e319b5b65879 - - 1069f6db0a0e - - 3a72fede57ce + - e4ee04da1c19 - d6e72da3ec35 - - 78bbd17d0703 + - 3a72fede57ce + - 1069f6db0a0e + - e319b5b65879 - 40737febe339 - - 3e4f434a69c6 - - e4ee04da1c19 + - a38934e303b9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 618297d23022 - - 7fe36019c073 - - 8f8df367470d - - f91cfb73d369 - - fcbeda41d0ac + - c88553ec696e - 2b95d5c04908 + - f91cfb73d369 - 0135f1d487a0 - - 72ddd32392cd - - c88553ec696e + - 8f8df367470d - 9537184d421f + - 618297d23022 + - 7fe36019c073 + - 72ddd32392cd + - fcbeda41d0ac tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - 2cf4a1cafc16 - - d7e79eb3bcb3 - - ad0dc9f4c9e2 - fafb3d685fa9 + - ad0dc9f4c9e2 + - d7e79eb3bcb3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 94df24c6bc00 - - 7f1cfa4c0e32 - - 5dc33613c288 - 8d36959b000d - - 43aac8d29685 - a1c2aecd7a0d - - 28a6f1908fcc - - bd2a7d1316b9 - 8c05afb547fa - - ee29337f905c - - 6a1515bb0687 - - ee2beb764a7b - 3d18f8c3c0f6 - 9eaadf03e0df + - 43aac8d29685 + - 6a1515bb0687 + - ee29337f905c + - 5dc33613c288 + - ee2beb764a7b + - 94df24c6bc00 + - 7f1cfa4c0e32 + - 28a6f1908fcc + - bd2a7d1316b9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: + - cb903c9dc33d - e3bb03cf207a + - 5671e1d3d5ee + - 9f978da6528a + - c092052ed673 - 5d6ed46cc101 + - db536ad45f28 + - d37ede8589b2 + - bcaa0d571ce2 - a250929be21b - - cb903c9dc33d - 364f4ffec275 - - 86a20ae274fc - - bcaa0d571ce2 - - db536ad45f28 - - 5671e1d3d5ee - 8858fa037a15 - - c092052ed673 - - d37ede8589b2 - - 9f978da6528a + - 86a20ae274fc tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 230b05597996 - - 38b91a3190cd - - 3b6a16d82c1b - - 194e3ceee923 - - c5c9f02b6167 - ed28dd32141c + - e1a015876aa9 + - 38b91a3190cd - abbc8041e8ec + - 230b05597996 + - 194e3ceee923 + - 584beffa972b - 49236b03e4fd + - c5c9f02b6167 - f95f403841ad - - 584beffa972b - - e1a015876aa9 + - 3b6a16d82c1b - 12d66d0d05ac 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 c604c60d1..1977394b7 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -11,10 +11,10 @@ tools: - name: datamash_transpose owner: iuc revisions: + - 22c2a1ac7ae3 - 374cb875d38a + - a513e3fbb4c5 - ac092723240d - ba0c40780ecf - - 22c2a1ac7ae3 - - a513e3fbb4c5 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 b24e13e9f..3c55c34a3 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,78 +2,78 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 66d7efc06000 - 772e0e89fc68 - 522137aaa9c4 + - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - 8a794e6d3388 - 4d81e3e2fb63 + - 8a794e6d3388 - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - f1b9a42d6809 - b6ef6d0cb6b7 - - e1317b5502fa + - f1b9a42d6809 - 818f9b69d8a0 - 2af1346e68c9 + - e1317b5502fa tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 05143043ca13 - - c80db5d6fd8c - - 947c2eacccb8 - 8334dc98c48e + - c80db5d6fd8c - 1588f9076e32 + - 947c2eacccb8 + - 05143043ca13 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: + - 25b46af53232 + - 9991c4ddde14 - 83228baae3c5 - - 1552b8cb4a94 - 29e4122c90de - - 9991c4ddde14 - - 25b46af53232 + - 1552b8cb4a94 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 53616c8b0865 - 060ca94ac049 + - 53616c8b0865 - f3dfa4bdf87e + - 1a53edc4b438 - 841a6cc5fc58 - a07ab242b0b5 - - 1a53edc4b438 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 2fc89dcd41c8 - - 91c4e3331208 - - d4808d5b83da - - 927586a18553 - dc4b5fd604a6 + - d4808d5b83da - 40f4447733b2 + - 2fc89dcd41c8 + - 927586a18553 + - 91c4e3331208 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: + - 7626ea9c2e1b - c6ae57f774c6 - - 301e07345c93 - 36e8d6d5d01b - - 7626ea9c2e1b + - 301e07345c93 - 25ab6b4e376e - e5a5ad882f1f tool_panel_section_label: Machine Learning @@ -81,20 +81,20 @@ tools: - name: sklearn_svm_classifier owner: bgruening revisions: + - 02d2be90dedb - 0630258dcf35 - - f9639b488779 - 80852884053f - - 4ed102b922cb - - 02d2be90dedb - b7c3e9a3b954 + - 4ed102b922cb + - f9639b488779 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - caeb57858702 - - 61634a87efc7 - - ec69cbe34b73 - 14180f9c831e + - ec69cbe34b73 + - 61634a87efc7 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 40a17e786..fd5cee815 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -4,15 +4,15 @@ tools: revisions: - 03e9b2fbc005 - cd659e8cc5fa + - f6877ad76b00 - a6d65b0c67af - - 749c918495f7 - - d5ceb9f3c25b + - 17062a0decb7 + - 937aa69e715f - 0d4acadabb04 - 017aba02828d - - 937aa69e715f + - d5ceb9f3c25b + - 749c918495f7 - 3ba8d4563129 - - 17062a0decb7 - - f6877ad76b00 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -24,19 +24,19 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - bfaa0d22c2e4 - b4a22d90cce9 + - bfaa0d22c2e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - 2477830927ec - - 53646aaaafef - - 64f11cf59c6e - - dfd8b7f78c37 - e188dc7a68e6 + - dfd8b7f78c37 + - 53646aaaafef - 3fe632431b68 + - 64f11cf59c6e tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,46 +48,47 @@ tools: - name: lastz owner: devteam revisions: - - 60afcc2c1d05 - - e7f19d6a9af8 + - 2ff111fac1d7 - 3e1ea2facca6 - 37b497aa133f - - 2ff111fac1d7 + - e7f19d6a9af8 + - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: + - 11a0d50a54e6 + - b3eab4b67562 - 09b53c1d4ab1 - - 8c6cd2650d1f - - 53c0b7a1a0c3 - - 037c6e54df11 + - 3f4d6399997b - be1d967337e4 - - 11a0d50a54e6 - - 6b1e195506a3 + - 53c0b7a1a0c3 - f54f5baedfdd - - c0c2d0941de8 - - 3f4d6399997b - - b3eab4b67562 - - 77b2770508f6 - 5cc34c3f440d + - 77b2770508f6 + - c0c2d0941de8 + - 037c6e54df11 + - 8c6cd2650d1f + - 6b1e195506a3 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 5ef7ec16b04f - b8f5f6e87f5c - - 9ee34ba73ebf - - 178bdbdb6d24 - - ec9cbd6b9a49 + - e403d27e8f24 + - 381a32c51141 + - 5ef7ec16b04f - 45795f582ae9 - 79b885ce78d7 + - ec9cbd6b9a49 + - 1cd2511a396e + - 9ee34ba73ebf + - 178bdbdb6d24 + - 13022c3d3076 - 42ce70172b72 - 00fbfac99d39 - - 13022c3d3076 - - e403d27e8f24 - - 1cd2511a396e tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/usegalaxy.org.au/metabolomics.yml b/usegalaxy.org.au/metabolomics.yml index e4c48b68a..5cb5d5d2a 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -57,8 +57,8 @@ tools: - name: isolib owner: recetox revisions: - - 6b0fef8a77c0 - 2b1118bce0b1 + - 6b0fef8a77c0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: lcmsmatching @@ -76,8 +76,8 @@ tools: - name: matchms_convert owner: recetox revisions: - - b9cc12600553 - 9e83636da9d3 + - b9cc12600553 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering @@ -90,15 +90,15 @@ tools: - name: matchms_fingerprint_similarity owner: recetox revisions: - - fd890f162ce6 - 84af792d3a78 + - fd890f162ce6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter owner: recetox revisions: - - 1b09315a3f87 - a5a5b147da70 + - 1b09315a3f87 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export @@ -156,8 +156,8 @@ tools: - name: matchms_split owner: recetox revisions: - - ea6c5636c0cf - 0cf68b536cd1 + - ea6c5636c0cf tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting @@ -225,82 +225,82 @@ tools: - name: ramclustr owner: recetox revisions: - - da7722f665f4 - 9b716db0a786 + - da7722f665f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_align_features owner: recetox revisions: - - 79ad928a0dae + - ec196e27a61a - 7b42ee54d757 + - 79ad928a0dae - c53a97599181 - - ec196e27a61a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - 149b9cc7499b - - f3a18e020cdd - 59c393d35e0e - 18ec7635bac6 + - f3a18e020cdd tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - - dfebc82ba1f0 - - 134be5abb208 - 50b9918aeff2 + - 134be5abb208 - 481d769e2f7a + - dfebc82ba1f0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - - a82db010c53e - - 02c772a49998 - 501a232f3cd5 - - 9064aecc78a7 - 51332c2520c7 - 30bf4e35da3e + - a82db010c53e + - 9064aecc78a7 + - 02c772a49998 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - 89178a72388a - - b341cfd4baf8 - b3413f335327 + - b341cfd4baf8 + - 89178a72388a - e7305ba0dd38 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - 17a48d0a80f4 - - dd7bbc2b99d1 - - b7c8a44b9cc1 - cf061712a184 + - b7c8a44b9cc1 + - dd7bbc2b99d1 + - 17a48d0a80f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - f92b1b64da93 - 99d118321d5f - d7f5878a98c3 - 24278c6b6d1c + - f92b1b64da93 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - ffbabefbd2e2 - - d90187b0f247 - ea0758b41473 - 7acd11ddc061 + - d90187b0f247 + - ffbabefbd2e2 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -312,8 +312,8 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 6b5dec818827 - 2c6fa447f6a0 + - 6b5dec818827 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index 4440ad3b2..8f30c59ad 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -9,8 +9,8 @@ tools: - name: cat_bins owner: iuc revisions: - - 18676df0cb3a - 0094893f5001 + - 18676df0cb3a - 0e63d03c8790 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -90,50 +90,50 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 63f86089423e - 5b5a7af9fbb4 - - 65db807336bc - - 76d3d2b10738 + - 3a89c3f99f3d - 7c2100246a2f + - 76d3d2b10738 + - 63f86089423e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 00f5005840fa - 84fd33a60b35 - - 1c35dadbe76f - - 18a502a9d287 - 96336c6a2bb7 + - 18a502a9d287 + - 00f5005840fa + - 1c35dadbe76f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - e8fba04706d3 - - a9f4a217dcd6 - addaf9d22850 - - f732237754fc + - a9f4a217dcd6 + - e8fba04706d3 - 34e55239e68b + - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 0776d824d896 - - 8c202e741d68 - - 5fe3edf19b9c - 75403243703a + - 8c202e741d68 - 04c15826a0b8 + - 0776d824d896 + - 5fe3edf19b9c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - 1c9b3bcd4261 + - e96bbb9e24ea - 75c8945b0da2 - 43c99742158b - - e96bbb9e24ea - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -141,29 +141,29 @@ tools: owner: iuc revisions: - 1d75bd0595e2 - - 35176674168c + - 5c865a382933 - 306a40d4bb8f - 84743da21318 - - 5c865a382933 + - 35176674168c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - ac72310b038a - - 32c9ea835770 - 555ccac8a4c5 - 8daf4564ccda - 78faebd0879c + - 32c9ea835770 + - ac72310b038a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - a58e4a43f49c - 7b8cb2b02978 - - f947b4bb5107 - d60df8727f59 + - f947b4bb5107 + - a58e4a43f49c - cae017b76acb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -171,40 +171,40 @@ tools: owner: iuc revisions: - 04144473e59e - - 7136e9ab70db - - 073608a50ac3 - 7f3b59dee073 + - 1770d188f72d + - 7136e9ab70db - 1bc3657cd694 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 0a1224c4b781 - 19299bb1c6af - d943081510da - a7817705348e + - 0a1224c4b781 - 9058d8943303 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - c7e73acfa3eb - e005e659ae21 + - c7e73acfa3eb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: - - 5c7ba3d85a01 - - 4d9445dff47b - - c4db8c4de66f - b907a3c0434f - - 65d52c693b8e - dbf1798c0dcc - - f8f56dd6449f + - c4db8c4de66f + - 65d52c693b8e + - 5c7ba3d85a01 - a68b985913ab + - 4d9445dff47b + - f8f56dd6449f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -217,8 +217,8 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 6c84982ee6f7 - 6d364c65c946 + - 6c84982ee6f7 - 654548ae1357 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -231,24 +231,24 @@ tools: - name: humann2_regroup_table owner: iuc revisions: + - e66ab198ec15 - 6aad8ca3918b - bd7a9c6efb10 - - e66ab198ec15 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - c6676a890f50 - b084117133af - d77397f09da1 + - c6676a890f50 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - 7f208f1eb64f - 9704f1a3b32d + - 7f208f1eb64f - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -267,54 +267,54 @@ tools: - name: humann_barplot owner: iuc revisions: - - 523ae8314ef5 - 5fea25ee6275 + - 523ae8314ef5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_join_tables owner: iuc revisions: - - 6bf703133209 - f01ca38fb6c5 + - 6bf703133209 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_reduce_table owner: iuc revisions: - - 6552df6efe6b - 60749924ad62 + - 6552df6efe6b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_regroup_table owner: iuc revisions: - - e88b731dad59 - - c409a495841f - 8237a0f225db - - 79706f10d680 + - c409a495841f + - e88b731dad59 - 31c6d107e7a5 + - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 714d5a28cc5c - - 71ea608ddfa3 - - d24841f5c3d2 - - 094ad9c068af - aabf8cfb8fef + - 094ad9c068af - 172920f67a84 + - d24841f5c3d2 + - 71ea608ddfa3 + - 714d5a28cc5c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - a293a742194f - - d7e9a3c41657 + - 12fb63b5f63f - 4137b492233e + - a293a742194f - a4d7148ccee4 + - d7e9a3c41657 - 2bdd84912a2b - - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -326,20 +326,20 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - 6fcb8ac37a3e - - 64bc7acc22a9 + - cf87759761eb - e2c71b852aba + - 64bc7acc22a9 - a92c06a3afa7 - - 75bedfb2078b - - cf87759761eb - 97f7bb0851e7 + - 75bedfb2078b + - 6fcb8ac37a3e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - e9d12c223a80 - 81c5dd1c777f + - e9d12c223a80 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler @@ -351,21 +351,21 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - c82508e76ad1 - 080ea153677c + - 4033827c76b8 + - 2d35528d2141 + - c82508e76ad1 - 5e5a999ffaa9 - 4e5e73d03f0d - - 2d35528d2141 - - 4033827c76b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 6b7622dda516 - 2cd76b089570 - - fc6c328c292f - 95bf7479d53c + - fc6c328c292f + - 6b7622dda516 - c2803012bbb3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -378,8 +378,8 @@ tools: - name: jellyfish owner: iuc revisions: - - dcd30574a456 - 11658afb8c87 + - dcd30574a456 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution_single @@ -392,8 +392,8 @@ tools: - name: khmer_abundance_distribution owner: iuc revisions: - - e699e2747356 - 7624945cacd3 + - e699e2747356 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_count_median @@ -406,15 +406,15 @@ tools: - name: khmer_extract_partitions owner: iuc revisions: - - 1061711538c6 - adb3dd5a899f + - 1061711538c6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_abundance owner: iuc revisions: - - b86562b4f3fd - 29a4d6e2ae9c + - b86562b4f3fd tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_below_abundance_cutoff @@ -434,8 +434,8 @@ tools: - name: khmer_partition owner: iuc revisions: - - 5a0fa29951ae - 8388fe31d604 + - 5a0fa29951ae tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kmc @@ -447,10 +447,10 @@ tools: - name: kraken2 owner: iuc revisions: - - 20e2f64aa1fe + - 4a9da2b6c2e3 - 328c607150ff - cdee7158adf3 - - 4a9da2b6c2e3 + - 20e2f64aa1fe tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -469,8 +469,8 @@ tools: - name: kraken_filter owner: devteam revisions: - - 67236d921e83 - 5bee9adae474 + - 67236d921e83 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report @@ -483,8 +483,8 @@ tools: - name: kraken_taxonomy_report owner: iuc revisions: - - 27d65c78863c - bfae8da6082c + - 27d65c78863c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -496,8 +496,8 @@ tools: - name: kraken owner: devteam revisions: - - 766d5f63b0f4 - 8ba2174315aa + - 766d5f63b0f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_alpha_diversity @@ -509,15 +509,15 @@ tools: - name: krakentools_beta_diversity owner: iuc revisions: - - c254d75b8b67 - 4505d7643673 + - c254d75b8b67 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_combine_kreports owner: iuc revisions: - - 073c867c5244 - 3d2cffa2c4ab + - 073c867c5244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -530,9 +530,9 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 88d274322340 - - 02bbace216f2 - 2deaada69b14 + - 02bbace216f2 + - 88d274322340 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa @@ -569,22 +569,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: + - 27250f92a01a - 2cff76cf35c6 - - 0270541aaf46 - - 327d9f4cc95f - - e073891b2afc - 3cc4a60615c0 - 4fd3b5d8706b - - 27250f92a01a + - 327d9f4cc95f + - 0270541aaf46 - 7f5d7b0e9884 + - e073891b2afc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - eb50e7eca3dc - 708abf08a626 - 76bc4efa1aeb + - eb50e7eca3dc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -650,33 +650,33 @@ 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: + - ef65b083bd0c + - b89b0765695d + - 2131d7dca455 + - a92a632c4d9b - 1a037928504c - ec368db926f4 - - b89b0765695d - 289b3807e80c + - 6dee4abadccb - fd69c607b43f - - 1a6cdf55390f - - 2131d7dca455 + - a16313517e55 - ff8f55893e7d - 740fd2d16a28 - - a16313517e55 - - a92a632c4d9b - - ef65b083bd0c - - 6dee4abadccb + - 1a6cdf55390f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning owner: galaxy-australia revisions: - - e3a64a1d2a6e - 2a8bc1d26d06 + - e3a64a1d2a6e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -707,36 +707,36 @@ tools: - name: picrust2_hsp owner: iuc revisions: - - 3b133b8d578a - 6eafc1e01a8c + - 3b133b8d578a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 415cb5d91168 - 709adbfcf308 + - 415cb5d91168 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline owner: iuc revisions: - - f53beb324696 - 6077821e8ae7 + - f53beb324696 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline owner: iuc revisions: - - 540aedfc81c7 - d6bb2e3febda + - 540aedfc81c7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs owner: iuc revisions: - - 73b56418e7f4 - 680fb3eb574c + - 73b56418e7f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions @@ -793,34 +793,34 @@ tools: - name: polypolish owner: iuc revisions: - - 915637bd1d1a - f355085dd2aa + - 915637bd1d1a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: recentrifuge owner: iuc revisions: - - d4fbfd31696c - 591175c0f051 + - d4fbfd31696c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: staramr owner: nml revisions: - - 4b9a8031ab74 - - aeaa20b96ef2 - - 4d83eccf5f81 + - 141afacabcfa + - be818ae858e4 - 3b22de20bd4b + - 4d83eccf5f81 + - 4b9a8031ab74 - 2fd4d4c9c5c2 - - be818ae858e4 - - 141afacabcfa + - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - - 576963db5f1b - - b3c7199d8786 - 9495df9dd6ef + - b3c7199d8786 + - 576963db5f1b 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 bc3ed5768..524ad9f69 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - 7238968f58f7 - ab12df91b47f + - 7238968f58f7 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -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 c90e866be..47d82442a 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,38 +2,38 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 94b8c6013083 + - 8b67dd48fec1 + - bdfbaf0c10aa + - 80f03df2e2ce + - 098506c54016 - 9eeb13a92d79 - - 9422c5a87ee2 - 2263989660f5 - - 098506c54016 - - cd07731e4434 - - 80f03df2e2ce - - bdfbaf0c10aa - 9baa871cb1d1 - - 6ae5a7b5a0a2 + - 94b8c6013083 + - cd07731e4434 - a74dbfee5a86 - - 8b67dd48fec1 + - 9422c5a87ee2 - 48c13389050d + - 6ae5a7b5a0a2 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - f14193ec1f50 - - f0af8936ed41 - - c44f824c051a - - 5abf2c2249aa - - be78f13134e2 + - aaa0d6a8b808 - '764845535798' - - d390fe1567dc - - c18157c68134 - - bc3831dd65c1 + - be78f13134e2 - 4a60927aaca5 - - aaa0d6a8b808 + - 5abf2c2249aa + - f14193ec1f50 + - f0af8936ed41 - fc2e49f91e52 + - d390fe1567dc + - c44f824c051a - 2e093badc689 - d7ce0ec78e51 + - c18157c68134 + - bc3831dd65c1 - 3ff17bad4006 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -53,75 +53,75 @@ tools: - name: clustalw owner: devteam revisions: - - d6694932c5e0 - 5b097fde95dd + - d6694932c5e0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko owner: iuc revisions: - - 5efbd15675ca - 1de657a3198d + - 5efbd15675ca tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mafft owner: rnateam revisions: - - f1a5908ea2cb - - bf28a8cff401 - - 15974dd17515 - - 6f28e90db932 - - 8e649f27aa0d - - f0d493f8f84f - a65296ffb4a0 - c5908940967d + - 8e649f27aa0d + - 6f28e90db932 + - f0d493f8f84f + - bf28a8cff401 + - f1a5908ea2cb + - 15974dd17515 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - b3acbb3a6af0 - - fbca557a4847 - e8fdceffea4c + - fbca557a4847 + - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - 60698466facd - - c9685bc0407c - 5561a1193611 + - c9685bc0407c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - 57f042937ba7 - 48823c9635a4 - bcd65de9725b + - 57f042937ba7 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - fb43e8887350 - 4fc0cb2ac8ae - ebe3b0f84de9 + - fb43e8887350 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - 636b049e6141 - - e18267f90096 - 7cd7a55a678d + - e18267f90096 + - 636b049e6141 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - b4124df98b26 - - 959c1f8dae95 - cf3c9489c088 + - 959c1f8dae95 + - b4124df98b26 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 e6c2d5591..3429e0d92 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -8,10 +8,10 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 7c47b3c9e493 - - 9aa9d92c3c51 - 28928576e1ea + - 7c47b3c9e493 - 18a8d140ec6f + - 9aa9d92c3c51 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado_trimming @@ -23,30 +23,30 @@ tools: - name: dorado owner: galaxy-australia revisions: + - 6942f170cc43 - fc5b6491cf78 - 63d8ecfcfab1 - 99c9427219d3 - - 6942f170cc43 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus_pipeline owner: iuc revisions: + - a7228a7ea146 - 79e9a869f40e + - 72b5e9dda577 - 0e9e7fcdd543 - - a7228a7ea146 - cb34f00cc10f - fc8804320156 - - 72b5e9dda577 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - d6cddc06aeae - 18505fe2bdb1 - - db25ec99c3ea - fa11aa8103b2 + - db25ec99c3ea + - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -58,15 +58,15 @@ tools: - name: medaka_variant owner: iuc revisions: - - 0f5f4a208660 - - eb746fa6f514 - - ec699520444c - edf6d4003fad - - cc36773a3681 - - 2bf63b38ee9b - - 222669c4afb6 - 19f3b583a9b3 + - 2bf63b38ee9b + - cc36773a3681 + - ec699520444c - 43815fa60f3a + - 0f5f4a208660 + - 222669c4afb6 + - eb746fa6f514 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -85,53 +85,53 @@ tools: - name: nanoplot owner: iuc revisions: - - 645159bcee2d - - 7b379e98b9a9 + - a3c4fe6f49ab + - 0f1c34698076 - a38bdcec9e4c + - 7b379e98b9a9 - a02b8b3f5a0c - edbb6c5028f5 - - a3c4fe6f49ab - - 0f1c34698076 + - 645159bcee2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - 3b6f94fc7e1d - - d219b6d8158a - 85a394edc247 + - d219b6d8158a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - a8d4be409446 - be95355fef8d - 90a922f32523 + - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - 449e9aeded2d - - 4857d5bcce52 - d376944466bf + - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: + - a3afc5f0a96c - bec636361cfd - de5b3d8f5b90 - - a3afc5f0a96c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 5f76b20953e5 - 543cbeef3949 - 93d623d9979c + - 5f76b20953e5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events @@ -150,8 +150,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - d1805f9c4c82 - 47936349f3e9 + - d1805f9c4c82 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -163,8 +163,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 336791b5665f - 0433aad600e9 + - 336791b5665f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -176,15 +176,15 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 2e22ebec211a - 626b6c2be5c2 + - 2e22ebec211a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle owner: iuc revisions: - - 26e6c9362b7b - ce8af9373061 + - 26e6c9362b7b tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats @@ -214,8 +214,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - 64a83664b814 - c5c5a3e84989 + - 64a83664b814 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 9b71bc881..b42cf64c8 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -2,8 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - 592ef3959907 - a5921c09b7b7 + - 592ef3959907 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -27,10 +27,10 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - 97b1b5ad1cda - - adfd6bf710bd - 3e73c97f025d - baceff842902 + - 97b1b5ad1cda + - adfd6bf710bd - d74850cf4e42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -38,8 +38,8 @@ tools: owner: devteam revisions: - 1586b111d2a3 - - 83da94c0e4a6 - 9dd107db92c2 + - 83da94c0e4a6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -51,20 +51,20 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: + - 1e34d2e3d285 - 19b6a2f0dbe2 - - e4b4837f06f5 - e9ee4d074d5d - - 2f27f3b86827 - - 13851aefa67a - - 1e34d2e3d285 - ed1518ce2237 + - e4b4837f06f5 + - 13851aefa67a + - 2f27f3b86827 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -83,9 +83,9 @@ tools: - name: data_manager_dada2 owner: iuc revisions: + - 5711fc06a63e - 38ccd4589990 - 48a42ca61006 - - 5711fc06a63e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -112,8 +112,8 @@ tools: - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - b1bc53e9bbc5 - 4d3eff1bc421 + - b1bc53e9bbc5 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -125,17 +125,17 @@ 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: - - 27a6a256cd23 + - b4b2b284230a - 172815da3d41 - 52b6a4d98009 - - b4b2b284230a + - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -147,8 +147,8 @@ 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 @@ -160,9 +160,9 @@ 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 @@ -194,12 +194,12 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 2c61c30a57e7 - d8dc037e3c13 - - 0cb27ea69dc1 - 4ba60cb14cb0 - - 5fe20c915fa6 - 9c43baa60906 + - 0cb27ea69dc1 + - 2c61c30a57e7 + - 5fe20c915fa6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -212,18 +212,18 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - aec831b54a5b - 9d09724f2bf1 + - aec831b54a5b - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - 6e24e79d3d69 - 29c738066906 - df30a2f1db55 - ed7a967cb11b + - 6e24e79d3d69 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -241,16 +241,16 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - ad90c2da4f38 - 3e4d45aca422 - 1865e693d8b2 + - ad90c2da4f38 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - d107d20dc6bd - def511e8e005 + - d107d20dc6bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -263,6 +263,7 @@ tools: owner: iuc revisions: - 64deddb6a8ec + - 71c994a11f71 - c520a52b5174 - d63c1442407f tool_panel_section_label: None @@ -270,9 +271,9 @@ tools: - name: data_manager_twobit_builder owner: devteam revisions: - - 94a50db37d1a - 9946bc39c834 - 625fd9476402 + - 94a50db37d1a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -783,8 +784,8 @@ 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 @@ -797,10 +798,10 @@ tools: owner: iuc revisions: - 58a870ef434c + - ab5b7f6b7198 - 9a22227bb6d0 - ba7b0f11e470 - f77f7a7f3b83 - - ab5b7f6b7198 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index 0b5a386c4..73f5b3ef3 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -34,65 +34,65 @@ tools: owner: iuc revisions: - a6619171428e - - 3f59ebfbfe3d + - 8834daeb9892 - '841557158611' - - 107d3ba7024a - - 5a7c56a5cc08 + - 26de3a7b1cb9 + - d033ffc1c161 - f04a1264e2a2 - - f73435dc282b - 3b8b5bde0bd9 - 81e66674859e + - 3f59ebfbfe3d + - c78f3d7dd1db - cce7b18495e4 - - 26de3a7b1cb9 + - 5a7c56a5cc08 + - f73435dc282b - b89cac5156ec - - 8834daeb9892 - - c78f3d7dd1db - d7c7ef3353fe - - d033ffc1c161 + - 107d3ba7024a - 6a457678efcb tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 3b96e92e8ec3 - - 5b777002c2de - - df47d4845b62 - - 7a2092844346 - - aa8cc71438cf - - 02b8758214b0 - - a185b079b095 + - b0af57c1a968 - 4755f52427c4 - 6223845127ea - - 88c4aa435ded - - 659517798cc4 - - b0af57c1a968 + - df47d4845b62 - e75442c7f4da + - 88c4aa435ded + - 02b8758214b0 + - 7a2092844346 + - 5b777002c2de + - aa8cc71438cf + - 3b96e92e8ec3 - 6283babe736e - - 5fcd1ece3a6e - 6a726db04d4b + - 659517798cc4 + - a185b079b095 + - 5fcd1ece3a6e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - d1c340a5664b - - 24d024316465 - f97743d52b87 + - 111bd54f6bc4 - f87ac61981f0 - - b8476e82ac20 + - d1c340a5664b - c1d53e95327f + - 24d024316465 - 70acec670c30 - - 111bd54f6bc4 + - b8476e82ac20 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - daddf188c13f - - 9e10ba792be2 - feb40665d7cd + - 9e10ba792be2 - 4f6349228462 + - daddf188c13f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -104,33 +104,33 @@ tools: - name: pangolin owner: iuc revisions: - - 81804a978fc0 - - 7bb8726be37c + - 03ed9524dcd1 - 2f1019071464 - - ca337cce3888 - - 42a174224817 - - ca0d8cf80567 - - 14ae456b8cc5 + - 83a69484cb87 + - a2099fb98cdb - 9d61d3fa046c - - b7e297c2ede6 - 2fa9d4f1b48f - - abf6dbe8c9d7 - - 03ed9524dcd1 - b6abccb1f25b + - ca337cce3888 + - 36912871ccdc + - 7bb8726be37c + - ca0d8cf80567 - 5f8727ff21e7 - - 83a69484cb87 - - a2099fb98cdb - - 3a43c3982401 - 437e28791761 - - 36912871ccdc + - abf6dbe8c9d7 - 8ad84c5753ea + - 3a43c3982401 + - 42a174224817 + - 14ae456b8cc5 + - 81804a978fc0 + - b7e297c2ede6 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 2bf47d57ebb5 - 7157a5b34a68 + - 2bf47d57ebb5 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -142,23 +142,23 @@ tools: - name: raxml owner: iuc revisions: - - 73a469f7dc96 - - 29ff6a849eac - - a4b71be30c3c - ea30d3089354 - b1e68bbe4cef + - 73a469f7dc96 + - 29ff6a849eac - ba29b5e2a4be + - a4b71be30c3c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 809e42326fc2 - - 9b2b122d0415 - e88a7de55d6e - dbe2b2204555 - - 91887494eb97 + - 809e42326fc2 - f1ccc8a6eb05 + - 9b2b122d0415 + - 91887494eb97 - 15ac71df11a0 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 eb13b3b88..44d182bd3 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - 881d7645d1bf - - a1f0b3f4b781 - - 7d34178f2812 - fc288950c3b7 + - 7d34178f2812 - 1aac2a13842a - - 3f254c5ced1d - f6ced08779c4 - - b502c227b5e6 - f9242e01365a + - 881d7645d1bf + - b502c227b5e6 + - a1f0b3f4b781 + - 3f254c5ced1d 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 60fab0b79..41efd6fc8 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,18 +2,18 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: + - 3f188450ca4f + - e4a053d67e24 + - a58f7eb0df2c + - d00e15139065 - c0e71cb2bd1b - - ca90d17ff51b - eb085b3dbaf8 - - 6ab1a261520a - - d00e15139065 - - 3bd420ec162d + - 7fbec959cf2b - 2f7702fd0a4c + - 6ab1a261520a - e7f1b552a695 - - e4a053d67e24 + - ca90d17ff51b - 5b85006245f3 - - a58f7eb0df2c - - 3f188450ca4f - - 7fbec959cf2b + - 3bd420ec162d 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 49cc9b524..693b7aee7 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,23 +2,23 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - 277dc652246e - - 0a18ac48ac53 - - b18329a8ac14 - f28ad96b76dc - - ece627528a78 - 4c177985028a + - b18329a8ac14 + - 277dc652246e - b574b84afc4d + - ece627528a78 + - 0a18ac48ac53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - a9a28e46d54a - - bf06d196e23d - e215f71d7983 - e988563cc6e5 - 525f201b86c1 + - bf06d196e23d - b41107d8fe89 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -26,70 +26,70 @@ tools: owner: galaxyp revisions: - 56da27be956a - - 4fbffddde8cd - - 8da3511c9467 - bb6397b94018 + - 8da3511c9467 + - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - 528fb09022be - - a8157342d9a3 - - 890845926d4b - f23d67e28cc8 - b8c79e70516d + - 528fb09022be + - 890845926d4b + - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 59e85306eae5 - - ae304a72db7b - - 25b83cbd596a - a95a82eb4d50 + - ae304a72db7b - a69865da6f80 + - 59e85306eae5 + - 25b83cbd596a - 80600735685d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: + - e0669b1854b1 - 83aac7741200 - - 798da6bdff3d - 611d80c0e29d - - e0669b1854b1 - - f1897eb07081 - ed9ed1e6cca2 + - 798da6bdff3d + - f1897eb07081 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 5a35e3a8d013 - 74b61bf5bc4b - d426a9107a6c + - 5a35e3a8d013 - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - cc430977c8ff - 91f0f5922011 - - df2187f9013b - 82f6c2f4332d + - df2187f9013b + - cc430977c8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: + - c5aa9fca18c6 + - 043f9c91f686 - d2483487e077 - 10566783d718 - - 1693b2126f30 - ba92b59cd529 - - c5aa9fca18c6 - - 043f9c91f686 + - 1693b2126f30 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -108,9 +108,9 @@ tools: owner: galaxyp revisions: - bf0728e000cd - - 9fa3dbf06f17 - - ff8c9e0e8a7b - ae4dc0c041f9 + - ff8c9e0e8a7b + - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -122,16 +122,16 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - eac99effe86f - d0ea7589e95f - d263296cd73e + - eac99effe86f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: - - 4081e4faa4ab - 0fa397f4f40b + - 4081e4faa4ab - 1c5cbf8f79ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -145,9 +145,9 @@ tools: - name: encyclopedia_walnut owner: galaxyp revisions: + - ce1a157a41bd - 0d2e93e01e68 - d6a4dfdad269 - - ce1a157a41bd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -159,16 +159,16 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - d286ff4600dd - - 160538a890a6 - e66f552a3c47 + - 160538a890a6 + - d286ff4600dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 71411ac28268 - 60ee8c592b13 + - 71411ac28268 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -181,16 +181,16 @@ tools: - name: maxquant owner: galaxyp revisions: - - 7f432d87c82c - - 37d669de2828 + - 1f39c833f65f - 4d17fcdeb8ff - - 97a7f34fcb6a - - 9c52362ae7bb - - e42225f8a659 - - 837224ad1694 - f522c08e900c - - 1f39c833f65f - 2133b0be850a + - 7f432d87c82c + - e42225f8a659 + - 97a7f34fcb6a + - 837224ad1694 + - 9c52362ae7bb + - 37d669de2828 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -203,27 +203,27 @@ tools: owner: galaxyp revisions: - 85b8866f06d7 - - a72ac2c7cc5b - e63db1aa82ee - 0ed07016d668 + - a72ac2c7cc5b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - 352b37c66d97 - - 767c1d761aaf - 1974224d63c2 - 990b4560ead7 + - 767c1d761aaf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 35cc7ca0bdc7 - - deaf035bbe9f - 4f359549383c - 99450519d727 + - 35cc7ca0bdc7 + - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample @@ -238,19 +238,19 @@ tools: - name: metaquantome_stat owner: galaxyp revisions: - - d2eac53666f0 + - d46d64e7964d - b9d453dca8d3 + - d2eac53666f0 - da986f83631b - - d46d64e7964d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 9bf325045235 - - 1199751329b0 - 944b43462104 - 8bd7734309f6 + - 1199751329b0 + - 9bf325045235 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -271,9 +271,9 @@ tools: owner: galaxyp revisions: - 593839e1f2c3 - - 28434abe6c5c - - de7593c29499 - 8212e342e482 + - de7593c29499 + - 28434abe6c5c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -286,46 +286,46 @@ tools: - name: openms_consensusid owner: galaxyp revisions: - - 01dbaf6a57e0 - - 8960fb791701 - f4be248c3d47 + - 8960fb791701 + - 01dbaf6a57e0 - 4e77b8f12cd3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 370141bc0da3 - - 25529df60a81 - 06cca574e337 + - 25529df60a81 + - 370141bc0da3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - c9eff69a7c62 - - 6ccbf9a2072c - - 518b1730cf2a - 9cdf15d3cfc8 + - 6ccbf9a2072c - f7fef900f5b2 + - 518b1730cf2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - 9876bda3ec53 - - ca88bd28f116 - - 5e948629bc73 - dff6c756eee5 + - 5e948629bc73 + - ca88bd28f116 + - 9876bda3ec53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - 658494a2cb00 - - 1595601708ec - 890025d6e426 - 41859bbdc16e + - 1595601708ec tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter @@ -333,8 +333,8 @@ tools: revisions: - 9b7977080f6d - 2a93a25f0599 - - 6634cad7d797 - 5ad0b5bf1deb + - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter @@ -349,37 +349,37 @@ tools: - name: openms_fileinfo owner: galaxyp revisions: - - 52ba9695e752 - 5ad830edc021 - febd569ad26f - 4af67edd5aef + - 52ba9695e752 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: + - 39e8fde08881 - 92352a475eed - - 27cba4c5fc42 - b2fc8da99bcc - - 39e8fde08881 + - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - 9e26f5c770f8 - - d413dc49d650 - d3546bb9fd8e + - d413dc49d650 - 0efbc235f314 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - c28f13cab67a - - 8a04ed1c1d1b - 3720e349ba2a + - 8a04ed1c1d1b - ca1740533b59 + - c28f13cab67a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter @@ -388,27 +388,27 @@ tools: - c55dddc5844a - c427a8628cbe - ca799a7246e7 - - 382cde407f81 - a5d785af0ad8 + - 382cde407f81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - 8ddb7bab1138 - - adca857b4884 - b5d0905419da - 39caaa778d2e + - adca857b4884 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 1c5f31b8d632 - - 8d4db262964c - 18f93351f8b6 - - f817513840a9 - 34e7afee141d + - 1c5f31b8d632 + - f817513840a9 + - 8d4db262964c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability @@ -423,26 +423,26 @@ tools: - name: openms_idscoreswitcher owner: galaxyp revisions: - - 0e52c85f3b15 + - 476b5e296979 - be74a8cd7d66 + - 0e52c85f3b15 - 4204882495f2 - - 476b5e296979 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - - 2b2a7551a857 - c18d8efa4474 - f5ec766d80cf - a407b6790342 + - 2b2a7551a857 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - - 021fdb80f204 - 4e66c4e73909 + - 021fdb80f204 - d0304fb829c0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -450,41 +450,41 @@ tools: owner: galaxyp revisions: - 8098330f6d91 - - ee860980edc6 - 2735db4dd8d9 + - ee860980edc6 - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - - 0ced5bc9f4dd - 08488066d588 - a2a6e9551046 + - 0ced5bc9f4dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - - de7a553552a6 - - 2a9ff56cb279 - 8c01da82292c + - 2a9ff56cb279 + - de7a553552a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: + - e8f64a7dc470 - 1bf940c18d93 - c1809c05ae8c - - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - f861ec9fbe59 - 9f505cd4428f - 496cf619e311 + - f861ec9fbe59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring @@ -498,93 +498,93 @@ tools: - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 8b814eafce2c - - 4bb198c0bd3e - 89254095cbf6 + - 4bb198c0bd3e + - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - f82b320ceb90 - f9ed7e074900 - 05ec9fb05ed1 + - f82b320ceb90 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - d31426ef20f6 - 6e8cc5ed2a9b - 18826fb8e5db + - d31426ef20f6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - - 2aebe58de46e - - 4a7b96835140 - bc63b4d12779 + - 4a7b96835140 + - 2aebe58de46e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - 3d8d4ada5405 - 6b01678ec2fc - - 5ae104d0da6e - decc397c3b7e + - 5ae104d0da6e + - 3d8d4ada5405 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - dd173849c3d8 - - d6aca689dd48 - - 5182338d5e7c - e039cc5c7aed + - d6aca689dd48 - 539a3a4dcc9e + - 5182338d5e7c + - dd173849c3d8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - d426affe977c - - 16026cdb1330 - 8a45fd5a608a + - 16026cdb1330 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: + - dd71e020e2aa - 43b9ed22e8ce - 9c70a651a53e - - dd71e020e2aa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: - 9020199dba0a - - 1b03536aa3c9 - d063e2fe4ba4 + - 1b03536aa3c9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - 78c080d36945 - f036e8cf1a55 - ad2ba3a95a02 + - 78c080d36945 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - c8b225c69a7f + - 7f6a1f27553e - 5c2a97a234d6 - fb52e95a370c - - 7f6a1f27553e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -610,13 +610,13 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - 3ec27b4cee7c - - 07ff622ec007 - a72c48001f7c - - 3634c90301af + - 1beff3ddce58 - da885ca16cb2 + - 07ff622ec007 - 7fdd9119cc4f - - 1beff3ddce58 + - 3634c90301af + - 3ec27b4cee7c - 943a34df6047 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -677,9 +677,9 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: + - 1a5690a5eedc - 265c35540faa - a371252a2cf6 - - 1a5690a5eedc - 12692567c7f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/qiime_2.yml b/usegalaxy.org.au/qiime_2.yml index 52697721b..bf015d3f9 100644 --- a/usegalaxy.org.au/qiime_2.yml +++ b/usegalaxy.org.au/qiime_2.yml @@ -962,7 +962,7 @@ tools: - name: qiime2_core__tools__import owner: q2d2 revisions: - - 18c6b2b6740f - 10447a4b0cc3 + - 18c6b2b6740f tool_panel_section_label: QIIME 2 tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index ba560f6ae..4cbc1ec5e 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,132 +2,132 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: + - cd5f98911089 + - 289b7d6b69a4 - 110a346daf36 + - 42201b90e3f4 - e345aadf914f - - cd5f98911089 - 2f1d464ebfd2 - - 42201b90e3f4 - - 289b7d6b69a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: + - 8501601a118d + - fcce77c09289 - 42d9087b4789 + - c207119ba5f6 - 0345dbaaa79b - 0cd2df8af811 - - 8501601a118d - - c207119ba5f6 - - fcce77c09289 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - 421c33b8bf17 - - 33486216eec0 - - ad5ab22ffe24 - - 04db7fd6b238 - 405a212b32ab + - ad5ab22ffe24 - 89eb29319bf4 + - 04db7fd6b238 + - 421c33b8bf17 + - 33486216eec0 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - eb784fa07f80 - - f6e91108b7b1 - - 7b72fde3d27e - 7370bb65bad4 + - 7b72fde3d27e - fa51dc5e8386 - 1d839ead7ad3 + - f6e91108b7b1 + - eb784fa07f80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - - a3e86cd9cac7 - - 8a55d29c8fcf + - 1544278c272e - 3d70c2996730 - - d30e36c48c93 + - 8a55d29c8fcf - c9b77ced9a78 - - 1544278c272e + - a3e86cd9cac7 + - d30e36c48c93 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - b242deb58952 - - e2db212d64ad - - 887cf585cafc - 564c33e5c3e3 - 7b881f5f5ad5 - a5969aa9347e + - 887cf585cafc + - e2db212d64ad + - b242deb58952 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - 9a171f9a450b - - 8cff84759bf6 + - e897c74a48bb - bd5ff77e2036 - b4bab607eb05 - - e897c74a48bb + - 8cff84759bf6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - adc7a7610d4f - - 4f65e343ecdf - - 5e10f396979e - - 6dafad990086 - 33f0793edf93 - 887e0991eb24 + - 6dafad990086 + - 4f65e343ecdf + - adc7a7610d4f + - 5e10f396979e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - 43e3eeb2e0ec - - 4e280b27a831 - c5d7050e4ad7 - 97575d01f06b - - c287418eb288 - 17d39bf0a63a + - c287418eb288 + - 43e3eeb2e0ec + - 4e280b27a831 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - 9586f08634c0 - cd034465d4a4 - d9bf483266a1 - - 09b8edb56d80 - a819ec3b362d - 0b8c84a7fdb5 + - 09b8edb56d80 + - 9586f08634c0 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - - a9c34a289493 - 69842dd5aa48 - - a4b4bd84f69e - - 95351dd0fd3f - bf0e43ab0416 - 2645575d1bf2 + - 95351dd0fd3f + - a4b4bd84f69e + - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - d033e1ccb386 - - d1fda11e602f - cfb504394ae1 - - bb0475c884ff - 912f904a6e1e + - bb0475c884ff - 8a35a3bc6752 + - d1fda11e602f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -195,8 +195,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 563af4497055 - 96de7538bf0c + - 563af4497055 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 6f29d6272..43aadf541 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -3,26 +3,26 @@ tools: owner: iuc revisions: - 7acb00fc980a - - 2d4e3aff9dc7 - cf01dd6c6b1f - 31f8063eedea + - 2d4e3aff9dc7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 703a2cb3fb38 - 32e542c2a773 - 125d20cb23d7 - 7a5a2d28c539 + - 703a2cb3fb38 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 3d61a698e5e1 - - 45c2ec061cf9 - 01ccd366690d + - 45c2ec061cf9 + - 3d61a698e5e1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -90,34 +90,34 @@ tools: owner: devteam revisions: - ad5d061fbdf2 - - e66b9b5b8580 - f648e5180e40 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: - e04dbae2abe0 - - 6926716bbfb5 - d080005cffe1 + - 6926716bbfb5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - 86285ddd4512 - - cf747d1bd79a - - 04adc9db1581 - 22cf48ad7b16 + - cf747d1bd79a - 6a6717a5f421 + - 04adc9db1581 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: - 9a854107dbb2 - - 28b94cfbfdb9 - 6cbfede05833 + - 28b94cfbfdb9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -143,55 +143,55 @@ tools: owner: iuc revisions: - 3b36efd62b3e + - 0693ccd171c4 - 8f0181aacb7a - e3b16fd7dd08 - - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - 24a09ca67621 - - d027d1f4984e - - 6a3a025714d3 - cd9874cb9019 + - 6a3a025714d3 - 8fe98f7094de - 0696db066a5b - 9a882d108833 + - d027d1f4984e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - b47c006d90c5 - - 9a7c5b6d8f1e + - 62adf13b86ea - df929f257179 + - 9a7c5b6d8f1e - 2872c633f07e - - 62adf13b86ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 5bf899c13979 - - 0cb907a2a810 - - 6e53e565fc6a - - df0c8d0a5992 - 3d89af8a44f0 - - 555659de7321 - 070900306913 + - 6e53e565fc6a + - 555659de7321 + - 9bdff28ae1b1 - 334ce9b1bac5 + - df0c8d0a5992 + - ae2aad0a6d50 + - 0cb907a2a810 + - 5bf899c13979 - f2843df56434 - a8305cf0c951 - - 9bdff28ae1b1 - - ae2aad0a6d50 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea owner: iuc revisions: - - 31ea4992b948 - fba1660fb717 + - 31ea4992b948 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: express @@ -203,18 +203,18 @@ tools: - name: featurecounts owner: iuc revisions: - - a56fbe2d6ba7 - - 7db9d3ea71c9 - - 90d16db017d7 - a37612abf7f9 - - 38b6d12edc68 - - af814359d244 + - a56fbe2d6ba7 + - e6a2a912677a - f9d49f5cb597 - - 6f66ae7c5f7a - 1b851f87fbe0 - - f3a5f075498f + - af814359d244 + - 38b6d12edc68 + - 6f66ae7c5f7a + - 90d16db017d7 - ea04b737afa0 - - e6a2a912677a + - 7db9d3ea71c9 + - f3a5f075498f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -238,9 +238,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 3c97c841a443 - - 0f710191a66d - 3c5e024a18cf + - 0f710191a66d + - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -252,21 +252,21 @@ tools: - name: hisat2 owner: iuc revisions: - - 6c19daec423d - 26371a1df031 - - f4af63aaf57a - 3fb01a8c902d - - a86e80d3c09c + - f4af63aaf57a - d4b55e2beb12 + - 6c19daec423d + - a86e80d3c09c - 6ab42baa56e9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - - 916cb26bd9d3 - 4418229c501e - 67b0b160903a + - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -278,33 +278,33 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 5ae5c312d718 - - 1c75aa5de15e - ce5d418183c5 - 87c11c05d238 - 01247aaf0a10 + - 5ae5c312d718 + - 1c75aa5de15e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - 10c98fab6c5a - 40985510cd98 - - c971db6f0fe5 - 4f9c4e6566e5 + - 10c98fab6c5a + - c971db6f0fe5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 0921444c832d - e827f9aae031 - - 119b069fc845 - 97e06a4c7c75 - - 708348a17fa1 - - 58c35179ebf0 - - 32511f586472 - d6f5fa4ee473 + - 0921444c832d + - 32511f586472 + - 58c35179ebf0 + - 119b069fc845 + - 708348a17fa1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -341,8 +341,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - d696cf0a9622 - 72927fc9e9ed + - d696cf0a9622 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -360,21 +360,22 @@ tools: - name: rgrnastar owner: iuc revisions: - - 3ea5a2a63fa2 + - c772497b2c32 - 980d2a2e1180 - - 4df95e2d7f61 - - c7c55b694974 + - 3ea5a2a63fa2 - 4074fc1940e2 - - c772497b2c32 - - b0f2be869d6d - 5ec75f5dae3c - - b9e04854e2bb - - 7ed2edc1337f - - 79de45b5069b - - 0a563fd2f22e - - 99b17b74a8cd + - c7c55b694974 - 4014de1b6daf + - 79de45b5069b + - 7ed2edc1337f - e132e7d02a3e + - b9e04854e2bb + - 53255f6eecfc + - b0f2be869d6d + - 99b17b74a8cd + - 4df95e2d7f61 + - 0a563fd2f22e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -386,36 +387,36 @@ tools: - name: salmon owner: bgruening revisions: - - e3d32471da11 - - ebab418107f5 - - 2c0ca397d302 - - 49121db48873 - 15cd64d7c58b - - 53e9709776a0 - f4d5237a84f6 + - 53e9709776a0 + - 49121db48873 - cc05793bb896 + - 2c0ca397d302 + - ebab418107f5 + - e3d32471da11 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - - c0fd285eb553 - - 8c28affc7c48 - fab6ff46e019 - 56242ff81c84 + - 8c28affc7c48 + - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - cef79931dda5 - - ae618321f34a - 76d290331481 - 914cfcba0ec8 - - cbf488da3b2c - 258d696dbd7e + - cef79931dda5 - dd4df992d93d + - ae618321f34a - 1ebd14235b92 + - cbf488da3b2c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -445,90 +446,90 @@ tools: - name: transdecoder owner: iuc revisions: - - d0d4cef4f967 - - 0db979fead3a - ffd1300599a1 - c6334cb383ff + - 0db979fead3a + - 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 - - bcc5f03f1900 - d6a479fd4281 - 74217fbfba4d + - ba3720d7e68b + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 478f36effca1 - - 56162e446004 - c2b82a94493e - 2fb4ee002432 + - 478f36effca1 + - 56162e446004 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: - 3f4094b6a565 - - 9ff3765e7172 - fab23c3b5258 + - 9ff3765e7172 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: + - 870ac06dff8e - 4687ecf0eb2d - 34a018cbee9c - be3f26533209 - - 870ac06dff8e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 5192f657f305 - - 65e7dea767ea - - 33406f5a445c - c5fbddcac63a + - 33406f5a445c - 05ab8d5e04a2 + - 5192f657f305 + - 65e7dea767ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: + - 1fdb25a8384d - e406ac71165d - - a35cba31d904 - 6f0fb35b799c - - 1fdb25a8384d + - a35cba31d904 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - - 37a1129c89d2 - - 7c7fbf13aadd - c2c039e421af + - 37a1129c89d2 - 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 - eafea3083352 - 24e94d84adc9 - 047c22569787 - - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: + - 3a4ac03d1266 - 04bb8bb7c198 - 9871104ea630 - - 3a4ac03d1266 - 1812dbc5bb7b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -547,15 +548,15 @@ tools: - name: trinity owner: iuc revisions: - - 9fa24d5aac68 - - db1f362cca3e - d84caa5a98ad - - cee61b3fcf78 + - 48636f857c4b - 32b86cd8eb50 + - db1f362cca3e + - 9fa24d5aac68 + - 8f1c3df4dd49 + - cee61b3fcf78 - c9cfec002f71 - d2bc35f3d1c5 - - 8f1c3df4dd49 - - 48636f857c4b 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 44ba177fb..53b800e78 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: - - 1a052c827e88 - - 27e16a30667a - 473382134e56 + - 27e16a30667a + - 1a052c827e88 - 080fd5739bb4 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 5f73eaa62..3c2800c12 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -10,10 +10,10 @@ tools: - name: bamtools_filter owner: devteam revisions: + - cb20f99fd45b + - 1dfd95ee241e - 108db6635177 - 993b19f20c76 - - 1dfd95ee241e - - cb20f99fd45b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_mapped @@ -25,8 +25,8 @@ tools: - name: bamtools_split_paired owner: iuc revisions: - - 5325e44297b9 - 75d5afa09972 + - 5325e44297b9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_tag @@ -76,16 +76,16 @@ tools: owner: iuc revisions: - 5f8e69cc4c6e + - 19ece8afbaab - e7fd6754d093 - 30a201c9c310 - - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc owner: iuc revisions: - - e38af83df163 - 17b35d23731f + - e38af83df163 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam2interval @@ -103,15 +103,15 @@ 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 owner: devteam revisions: - - cf1ffd88f895 - 0e60e2dd20af + - cf1ffd88f895 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sambamba @@ -123,26 +123,26 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - 649a225999a5 - 56c31114ad4a + - 649a225999a5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - 9149ad20699a + - 12749212f61b - 46c6639921f1 - 6856f8a01905 - - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - 33208952b99d + - 92ec40abcdcf - 26b4f9f98aca - 06dc50b7b711 - - 92ec40abcdcf + - 33208952b99d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_coverage @@ -160,65 +160,65 @@ tools: - name: samtools_fastx owner: iuc revisions: - - b906586a6596 - - b3d99709fe1a - a8d69aee190e + - b3d99709fe1a - 66e23b11feae - 720217c23995 + - b906586a6596 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fixmate owner: iuc revisions: - - e5ece8fa99de - d2df79922531 + - e5ece8fa99de tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - fefd89ab563c - - cc61ade70eb8 - db17d5321bad - - fe34990e5ce7 - 22970df7a40e + - cc61ade70eb8 + - fe34990e5ce7 + - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - 7a6034296ae9 - - 811fc2d75ad4 - - 7def34e6cf4d - 88b8c2916784 + - 7def34e6cf4d - fa5d3e61e429 + - 811fc2d75ad4 + - 7a6034296ae9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_markdup owner: iuc revisions: - - 40fa6c240105 - a389f74c3630 + - 40fa6c240105 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - b40e2d865d52 - - 65a38e8c8e2a - - cae2794d2deb - 36677f429310 - 740ce0a18f0d + - cae2794d2deb + - b40e2d865d52 + - 65a38e8c8e2a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - b61f5d6a7f25 - 9da0311ab1dd - 8da515fbc1bf - - 329deb17a9f7 - 583abf29fc8e + - b61f5d6a7f25 + - 329deb17a9f7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -231,8 +231,8 @@ tools: - name: samtools_reheader owner: devteam revisions: - - bb8cfc6f6e0c - 30388d878f81 + - bb8cfc6f6e0c - 85e38b31e8b3 - db000c6007a0 tool_panel_section_label: SAM/BAM @@ -247,53 +247,53 @@ tools: owner: devteam revisions: - b8beef827165 - - 344fc91e1bfd - a4a10c7924d1 + - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - e613c1ad4c4c - - d54a4df48867 - - cab3f8d35989 - 6c2c1836728b + - cab3f8d35989 + - d54a4df48867 + - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - bcedabb53ddf - - 5d9ae78f34d3 - - 818030fa6bbf - - b7f7826ef1cd - bd850490c7f1 + - b7f7826ef1cd + - 818030fa6bbf - 135c85f4cfaf + - bcedabb53ddf + - 5d9ae78f34d3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 3a0efe14891f + - 5a08c09b9311 - 541082d03bef - - 24c5d43cb545 - 145f6d74ff5e - - 5a08c09b9311 + - 3a0efe14891f - 1cc79f49b8d5 + - 24c5d43cb545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - 0dbf49c414ae + - 5826298f6a73 - b72793637686 - - 6be888be75f9 - 2dce91e11ca7 - - bf328cec6a42 - - c370440f901e - 350bbc5c2ffd - - 5826298f6a73 - b01db2684fa5 + - 6be888be75f9 + - 0dbf49c414ae + - bf328cec6a42 - 32dc5f781059 + - c370440f901e 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 42a3138a9..e627643e0 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -8,13 +8,13 @@ tools: - name: ena_upload owner: iuc revisions: + - 4aab5ae907b6 - 6f6537780379 - a62c4a11a67d - - 4aab5ae907b6 + - 480d9e9d156b - ea5e944f447d - - 5cb6146337d8 - 59bb6d34fca6 - d147d6455873 - - 480d9e9d156b + - 5cb6146337d8 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 6d20fb847..738915cfe 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -8,102 +8,102 @@ tools: - name: alevin owner: bgruening revisions: - - e4c01dcece8b - e32b215b7c04 - ecb9ea6269ee - b0fe3e482cb7 - f2000bc73102 + - e4c01dcece8b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - 7a6655aa6eb2 + - c0b037b12765 - 707023fa62fe + - 7a6655aa6eb2 - e1c3c2f2a834 - - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 6f143dfe902a - - 93dd15e13e6a - 32e547223c9e + - 00712416fdaa - cfc3f5a57dc6 + - 6f143dfe902a + - 93dd15e13e6a - 55e35e9203cf - - 00712416fdaa - fb9e030ffae4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 14c576ea6148 - - 6f0d0c784f09 - - ee98d611afc6 - - 39e945f0b2c1 - 038e32885fec - b9fac48532eb + - 14c576ea6148 + - 39e945f0b2c1 + - 6f0d0c784f09 - 688357ad5e61 + - ee98d611afc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - 3d748954434b - d4af736e7b83 - - 43cb7b5a6fe7 - c4209ea387d4 - - ed4996a16f7f - - b85871dd69f9 + - 3d748954434b + - 43cb7b5a6fe7 - 9bd945a03d7b + - b85871dd69f9 + - ed4996a16f7f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - - 890fb06a2893 - - 7ebc22f77d86 + - a4774b7b2e85 - fe75d2414dc0 + - 7ebc22f77d86 + - 890fb06a2893 - 2e8022f1923c - - a4774b7b2e85 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - 02b1fe7aed76 - - 0e70b2dfe4be - 769d815e4b0d - 4fff5a293013 + - 0e70b2dfe4be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - c29e7bb492bf - - aa4a6f0916b4 - 344c2af50552 - a90f8efe08b4 + - aa4a6f0916b4 + - c29e7bb492bf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: + - b13d3e4c48e1 + - 5b7c81b35b89 - 050cf43887d3 - c32347702e12 - - 5b7c81b35b89 - - b13d3e4c48e1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: + - 02fc39c8610d + - 1d77986f9ddc - ae969fdb8442 - 239193b96d72 - - 1d77986f9ddc - - 02fc39c8610d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -139,11 +139,11 @@ tools: - name: dropletutils owner: iuc revisions: - - a9caad671439 - - 8855361fcfc5 - - cdf4443d5625 - cfe1e6c28d95 + - 8855361fcfc5 + - a9caad671439 - 2c1200fba922 + - cdf4443d5625 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: episcanpy_build_matrix @@ -173,39 +173,44 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - fb7068d30ec9 - 01c37e54e86e + - c3ffb2c1e314 + - fb7068d30ec9 - 952abbc4b1de tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: + - f1c35f3f310d - 57aeaf6b237d - 9d42a6133690 - - f1c35f3f310d + - 45828071edc3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 23b8d6b8960c + - 1a31e75e979e - cab616fe7e64 + - 23b8d6b8960c - 163fd744e235 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: + - '920526260066' + - 013e53ccc7ac - f47ac4a0b337 - b9ab56aecd18 - - 013e53ccc7ac tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - a63e9713c39d + - f6a169b5e43b - b892fa1fcaec - 9ea228a9afc8 tool_panel_section_label: Single-cell @@ -215,21 +220,24 @@ tools: revisions: - 640e0e45518a - f8320df1866b + - ff1af7bac1cb - 45a386d18509 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: + - 6f8debcf2ac9 - f963c251ac77 - - c354255ff705 - 9d02f1819e81 + - c354255ff705 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint owner: bgruening revisions: - 40fee49bc6c3 + - 37125838e360 - c4ed35f4f77f - f881c94fb3b3 tool_panel_section_label: Single-cell @@ -237,6 +245,7 @@ tools: - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: + - e8760fc0e29b - e06265d204f6 - 782bdcb775fb - 2dccb6bb0add @@ -245,57 +254,64 @@ tools: - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - 63c8377c58b3 - f0216498a666 - b05f662f9f35 + - 63c8377c58b3 + - 30677e95bc89 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions owner: bgruening revisions: + - 8a11d70b6cd8 + - 3240e8a7c54f - fe3aa71590d5 - c72fa6cb8817 - - 8a11d70b6cd8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 4f9305d3bb34 - - e03780179ee5 + - 5dd1aae12f03 - 3ee5332bf57c + - e03780179ee5 + - 4f9305d3bb34 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: + - 4401ed529d2c + - 87eb9c58cd19 - a315574104c6 - 3a6a5381db36 - - 4401ed529d2c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - a83732c79949 - - c0737631eea1 - 2ba6cee8e4db + - c0737631eea1 + - a83732c79949 + - 574f295b5ba4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - 30d7390bc918 - 62b720dceb56 - ea19190ce5e0 + - 937b7b9832d0 + - 30d7390bc918 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - cd40ca76865a - 2786a931cad2 + - 0f5786ffa10d - 2b4d6a8dab36 + - cd40ca76865a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops @@ -303,38 +319,43 @@ tools: revisions: - 0410b6aada45 - ffc33339cd3e + - 4375e25de06a - bf9379529c3e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: + - 5dfba24d7bdd - 07dd436ea686 + - 4977f65da0ff - 77d8e0fd162a - - 5dfba24d7bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - 6c5097f6d41e - f1b3902f8baf - 972dcccb5bbc + - f0b1bd38745a + - 6c5097f6d41e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - 409396ea5cf0 - - 7f7c6ead2d0d + - 3e5c86c2f80d - bb8849fca57c + - 7f7c6ead2d0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo owner: bgruening revisions: - - 51e40e9b6c3c - b0f33533181d + - 7fbd6feba1ca + - 51e40e9b6c3c - e4f8fceab96a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -342,24 +363,27 @@ tools: owner: bgruening revisions: - 55b013e59018 - - 32173084d53f - c261b6b05ee3 + - 32173084d53f + - 908fa330b93b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains owner: bgruening revisions: - 4b194e675916 - - b376ef118807 - b6b8c8672756 + - b376ef118807 + - febfddb0b3e8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: + - 1d9799f4b854 + - ed900cd4a0a9 - 910c6a1c3a27 - 1511a8ebe906 - - ed900cd4a0a9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize @@ -368,27 +392,31 @@ tools: - 2aa5b6b65197 - 6d042c96aceb - f34ab9882252 + - 5e83c077e31d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: - - 9b383d429659 + - 3f1b286a5c34 - ea5d67ec94ab - dd9988943f53 + - 9b383d429659 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - 11f39d7f6c64 - - 6326cd29c1c3 + - 89cfe7de541b - 06ced663d24f + - 6326cd29c1c3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: + - 1602cc5b673c - 337705015ee8 - beb5b5917d2f - b4e780e93c91 @@ -397,25 +425,28 @@ tools: - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: + - 58de3c7c8e89 + - a10fce08c2dc - e285920f8585 - 8d203e74869b - - 58de3c7c8e89 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicquickqc owner: bgruening revisions: + - 5cbd7a902a8d - 21d859ad4502 - ea8fb5e899e8 - - 5cbd7a902a8d + - b13e7a200525 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - f81750434d70 - - 1d6af10874d5 - 36dfa2825a59 + - d74cf4a61d65 + - 1d6af10874d5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -433,27 +464,29 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - 27fe5cd1729c - f36828ebdc54 + - df64cc4dfb4d - 1de2276f633f + - 27fe5cd1729c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 11a3385e03b5 - 1d201e8378b3 + - 11a3385e03b5 - cef9fb4ece1c + - d890828ab02a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: - - e98619de2776 - - eeab712b0b99 - - db575b4c8b22 - 7784821452ac + - eeab712b0b99 + - e98619de2776 - 59be31ac9dc3 + - db575b4c8b22 - 4b0adaa31c95 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -466,23 +499,23 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 2cfd0db49bbc - - 7ffaa0968da3 - 48f0fb3061b1 + - 7ffaa0968da3 + - 2cfd0db49bbc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 56371b5a2da9 - 8cd2ecfa2e61 + - 56371b5a2da9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset owner: bgruening revisions: - - 8c64a2da3869 - fde4c972e7c5 + - 8c64a2da3869 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -500,46 +533,46 @@ tools: - name: raceid_clustering owner: iuc revisions: - - a4b734cd253b - - c4f39bf4a068 - - 7e014059a88d - 49776718ae90 - f911a64454fb + - c4f39bf4a068 + - a4b734cd253b + - 7e014059a88d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: - - 43c146e25a43 + - d45f092caf24 - 7608d5faee41 + - 43c146e25a43 - 8b917923f7d4 - - d45f092caf24 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters owner: iuc revisions: - 2b0d3e2f402a - - c7ddb719554d - 37a47c4fd84d + - c7ddb719554d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory owner: iuc revisions: - - 6e90c8adf84f - 69018f285aa3 + - 6e90c8adf84f - df8e4e54d367 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - - 2bfd55b87af3 - 44b935f2271b - - c92d0f9338c5 - - 72979cac22b2 - e93b008c637a + - 2bfd55b87af3 + - 72979cac22b2 + - c92d0f9338c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: run_sccaf @@ -557,95 +590,95 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - 8983e7a04ba7 - - f9353ee6a0d4 + - 6acb08931836 - 6f83f8fd381f - - 4d8f983cd751 - - 77b91b9bdf52 - - b2df381a6004 + - 8983e7a04ba7 - cb43c5d3acd3 + - 77b91b9bdf52 - aaa5da8e73a9 - - 6acb08931836 + - b2df381a6004 + - 4d8f983cd751 + - f9353ee6a0d4 - 38db3fef7aad tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: + - 277313130da5 + - fc0321c000a3 - d636ce5cde16 - - 64388be6d510 - - b409c2486353 - a03ff8633507 + - 72a6bebab2a5 - a97abb8cd15b - - fc0321c000a3 - 8cb783c81905 - - 72a6bebab2a5 + - 64388be6d510 + - b409c2486353 - 3c86f71498bc - - 277313130da5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: + - d86cb2ce311b - 6bd82ed14acd - - c5d3684f7c4c - - 18262103fa61 - f54f0f0598ad - - 5c3ebe2adc77 - - 6c145a6868cc - 3081ff5c84a3 - 5e9171dc8244 - - d86cb2ce311b + - 6c145a6868cc - c0a80a16560f + - 18262103fa61 + - c5d3684f7c4c + - 5c3ebe2adc77 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - 56c0d4acef02 - - 146ae5d70b47 - c9cb76cf8d6c - - 4bda4412b8c2 - - 94c19fb1281c - - 3bcd5445cd7a - ab55fe8030b6 - - 9f354c7c8c92 - 7b9fafe32c86 + - 146ae5d70b47 + - 4bda4412b8c2 + - 3bcd5445cd7a - a407e7f8bdc1 + - 9f354c7c8c92 + - 94c19fb1281c - d844935c906c + - 56c0d4acef02 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - 1072ce66b426 - - 62acdd96d4a0 - 9b0cdb8cf6be - - 0185bd174ea0 - - 95777145cb92 + - f7446fd8d5e7 - 7647e5cd1b8b - - dbbe1ea8ecb1 + - aa0c474463c2 - 6f5349dd5c49 + - 0185bd174ea0 - 6adf98e782f3 - - aa0c474463c2 - - f7446fd8d5e7 - 40812a65a78b + - 1072ce66b426 + - dbbe1ea8ecb1 + - 62acdd96d4a0 + - 95777145cb92 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: + - f2f6c703da06 + - 215733a383f2 + - d18e7a6e5cd4 - 458e8f43a775 - - fe8f16c594ec - - c65fce500915 - - c5541bfb8feb - - bf2017df9837 - 73ab2ac53d06 - - 215733a383f2 - - 9fb627495ec2 + - bf2017df9837 - a39040ae0a38 - - f2f6c703da06 - - d18e7a6e5cd4 + - 9fb627495ec2 + - c65fce500915 + - c5541bfb8feb + - fe8f16c594ec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -674,8 +707,8 @@ tools: owner: iuc revisions: - 81e5bdff4853 - - ef4c80837bc5 - 2e41b35b5bdd + - ef4c80837bc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_exprs_freq @@ -687,9 +720,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 46fc6751d746 - 9e5c0bb18d08 - c99ba278dfa9 + - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_tsne @@ -918,8 +951,8 @@ tools: - name: sinto_fragments owner: iuc revisions: - - 6f66f523a9b7 - 29e6bfb2cf49 + - 6f66f523a9b7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: slice_image @@ -938,15 +971,15 @@ tools: - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 64fa083411f1 - 588c811fdd48 + - 64fa083411f1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting owner: iuc revisions: - - fecf9664c885 - 05bd4db20227 + - fecf9664c885 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing @@ -965,8 +998,8 @@ tools: - name: velocyto_cli owner: iuc revisions: - - 90e95e9ee190 - 883c33ef3372 + - 90e95e9ee190 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: vitessce_spatial diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index f4345b739..47e1f7975 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -33,9 +33,9 @@ tools: owner: iuc revisions: - 419027d822d6 + - 562f3c677828 - 4c07ddedc198 - 746e8e4bf929 - - 562f3c677828 - 2f3c6f2dcf39 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -71,8 +71,8 @@ tools: 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 @@ -116,41 +116,41 @@ tools: revisions: - 7442b94d6a1e - b1eda492f063 - - 840f29aad145 - 4c4ec859c31a - - 9c3e1d3235c8 - aef56d0e7a61 + - 840f29aad145 + - 9c3e1d3235c8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - 07843f917990 - - d0352e8b4c10 - 375bbd555f4a - 9fda0b82f419 + - 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464b9305180e - - 02026300aa45 - 9cd341095afd - 6595517c2dd8 + - 464b9305180e - 13b6f0007d9e + - 6e8d94597139 - aff5135563c6 + - 02026300aa45 + - be25c075ed54 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -53,8 +53,8 @@ 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 @@ -80,9 +80,9 @@ tools: revisions: - 557ec8d7087d - 9cc411a62277 + - 37cde8134c6a - 34d29339abab - 90f657745fea - - 37cde8134c6a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -113,22 +113,22 @@ tools: - name: query_tabular owner: iuc revisions: - - 83069b38aa85 - - 623f3eb7aa48 - - 1ea4e668bf73 - 2e8f945f7285 + - 1ea4e668bf73 + - 623f3eb7aa48 + - 83069b38aa85 - 33d61c89fb8d - - cf4397560712 - cf34c344508d + 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