diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index e5359c8a0..f3f4bed40 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -8153,3 +8153,30 @@ Update 222 04/12/24 01:38:59 krakentools_alpha_diversity False Tests failed iuc Update 222 04/12/24 01:39:44 phyloseq_from_dada2 False Installed iuc 40ebae5bbe51 40ebae5bbe51 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_222/install_log.txt Update 222 04/12/24 01:53:31 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_222/install_log.txt Update 222 04/12/24 02:16:45 ucsc_fatovcf False Installed iuc a40dd4fd3096 a40dd4fd3096 2/2 Convert Formats toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_222/install_log.txt +Install 1708 09/12/24 01:09:31 anndata_ops False Installed ebi-gxa 7ebc22f77d86 7ebc22f77d86 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1708/install_log.txt +Install 1708 09/12/24 01:20:23 anndata_ops False Installed ebi-gxa 890fb06a2893 890fb06a2893 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1708/install_log.txt +Install 1708 09/12/24 01:21:13 scanpy_compute_graph False Installed ebi-gxa 6417cccad133 6417cccad133 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 01:21:59 scanpy_compute_graph False Installed ebi-gxa bc9e8de21efb bc9e8de21efb 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 01:22:52 scanpy_filter_cells False Installed ebi-gxa 55ccc0a121bc 55ccc0a121bc 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 01:23:41 scanpy_filter_cells False Installed ebi-gxa e9283529cba1 e9283529cba1 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 01:24:29 scanpy_filter_genes False Installed ebi-gxa 474a69c47184 474a69c47184 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 01:25:20 scanpy_filter_genes False Installed ebi-gxa da611a744112 da611a744112 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 01:26:11 scanpy_find_cluster False Installed ebi-gxa 2ccd9f9e2cd0 2ccd9f9e2cd0 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 01:27:00 scanpy_find_cluster False Installed ebi-gxa ad6995afd2e6 ad6995afd2e6 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 01:27:52 scanpy_find_markers False Installed ebi-gxa 49653e680ea4 49653e680ea4 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 01:28:42 scanpy_find_markers False Installed ebi-gxa 81c34e67f262 81c34e67f262 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 01:29:44 scanpy_find_variable_genes False Installed ebi-gxa 2861ca3bfe4d 2861ca3bfe4d 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 01:30:42 scanpy_find_variable_genes False Installed ebi-gxa 4667fe07bd68 4667fe07bd68 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 01:32:58 scanpy_normalise_data False Installed ebi-gxa 6b97ffba31da 6b97ffba31da 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 01:33:48 scanpy_normalise_data False Installed ebi-gxa 8d9c22419c56 8d9c22419c56 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 01:34:41 scanpy_plot_embed False Installed ebi-gxa 35f6611fb8c3 35f6611fb8c3 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 01:35:36 scanpy_plot_embed False Installed ebi-gxa 56d22aa6cb3b 56d22aa6cb3b 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 01:36:29 scanpy_regress_variable False Installed ebi-gxa 36daab33aecf 36daab33aecf 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 01:37:21 scanpy_run_pca False Installed ebi-gxa 3ee74b58c72d 3ee74b58c72d 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 01:38:14 scanpy_run_pca False Installed ebi-gxa 59028945c857 59028945c857 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 01:39:07 scanpy_run_tsne False Installed ebi-gxa 181d61d2f3cd 181d61d2f3cd 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 01:39:56 scanpy_run_tsne False Installed ebi-gxa 8b0d6f6f44c8 8b0d6f6f44c8 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 01:40:47 scanpy_run_umap False Installed ebi-gxa bd4a244faeb8 bd4a244faeb8 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 01:41:38 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 diff --git a/requests/singlecells.yml b/requests/singlecells.yml deleted file mode 100644 index b36759184..000000000 --- a/requests/singlecells.yml +++ /dev/null @@ -1,98 +0,0 @@ -tools: -- name: scanpy_filter_cells - owner: ebi-gxa - revisions: - - 55ccc0a121bc - - e9283529cba1 - tool_panel_section_label: HCA Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: scanpy_filter_genes - owner: ebi-gxa - revisions: - - da611a744112 - - 474a69c47184 - tool_panel_section_label: HCA Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: scanpy_normalise_data - owner: ebi-gxa - revisions: - - 8d9c22419c56 - - 6b97ffba31da - tool_panel_section_label: HCA Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: scanpy_find_variable_genes - owner: ebi-gxa - revisions: - - 4667fe07bd68 - - 2861ca3bfe4d - 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 - tool_panel_section_label: HCA Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: scanpy_run_pca - owner: ebi-gxa - revisions: - - 59028945c857 - - 3ee74b58c72d - tool_panel_section_label: HCA Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: scanpy_compute_graph - owner: ebi-gxa - revisions: - - 6417cccad133 - - bc9e8de21efb - tool_panel_section_label: HCA Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: scanpy_run_tsne - owner: ebi-gxa - revisions: - - 181d61d2f3cd - - 8b0d6f6f44c8 - tool_panel_section_label: HCA Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: scanpy_run_umap - owner: ebi-gxa - revisions: - - bd4a244faeb8 - - fe562424a0a6 - tool_panel_section_label: HCA Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: scanpy_find_cluster - owner: ebi-gxa - revisions: - - ad6995afd2e6 - - 2ccd9f9e2cd0 - tool_panel_section_label: HCA Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: anndata_ops - owner: ebi-gxa - revisions: - - 890fb06a2893 - - 7ebc22f77d86 - tool_panel_section_label: Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: scanpy_find_markers - owner: ebi-gxa - revisions: - - 49653e680ea4 - - 81c34e67f262 - tool_panel_section_label: HCA Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: scanpy_plot_embed - owner: ebi-gxa - revisions: - - 56d22aa6cb3b - - 35f6611fb8c3 - tool_panel_section_label: HCA Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu -- name: scanpy_regress_variable - owner: ebi-gxa - revisions: - - 36daab33aecf - tool_panel_section_label: HCA Single-cell - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index 33386f610..4a179745e 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,54 +2,54 @@ tools: - name: abricate owner: iuc revisions: - - 4efdca267d51 - - 78c75f134c16 - 3f3e247c053d - - c2ef298da409 + - 78c75f134c16 - 6e9aea89e388 + - 4efdca267d51 + - c2ef298da409 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 owner: iuc revisions: - - 1dd7adc21b6d - 8dc7512c9dc9 + - 1dd7adc21b6d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_locuspocus owner: iuc revisions: - - 1fdc517743e6 - c4ac24510b55 + - 1fdc517743e6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_parseval owner: iuc revisions: - - d6c074a93c51 - 1b52f0c8ad7f + - d6c074a93c51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - 3e1f6f6d557e - - 44018dd6b447 + - a79ee60b6926 - 4f2967b27e67 - cd2480f35935 - - b5d8e5475247 - - 133f36c29579 + - 44018dd6b447 - fe3ca740a485 + - 133f36c29579 - f29602ae449e - - a79ee60b6926 - 1aae04680c4b + - b5d8e5475247 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -64,26 +64,26 @@ tools: revisions: - 6519ebe25019 - dc027fa56d55 - - 7be22100e5e1 - f1e653756174 + - 7be22100e5e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 28433faa6e42 + - 09855551d713 - bd0e53f3a891 + - 28433faa6e42 - ca6d970d931c - - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - d77802fe76f7 - - 728dacaf08a9 - - da5f1924bb2e - 92eee5f31117 + - da5f1924bb2e + - 728dacaf08a9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap @@ -103,8 +103,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 8bd92f2404dd - 1b9a9409831d + - 8bd92f2404dd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -116,16 +116,16 @@ tools: - name: cpat owner: bgruening revisions: - - 8e9e228c54c4 - 7ccc6234b54e + - 8e9e228c54c4 - 1ac12c0cc7a0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - - d9c3016f7283 - 9d1fbff733cf + - d9c3016f7283 - 63662ae295d6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -156,61 +156,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - b6b5cd37f2a2 - 756376aeb1ae + - 14f588312c56 - 3bbe70fef6df + - 582fd74dc2a1 + - b6b5cd37f2a2 - 9c15ca7e764e - 9f2455341fac - - 14f588312c56 - - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 8e1ace8f77c6 - - 30fb23d4c31c - 989f7c061f35 + - 8e1ace8f77c6 - 0ffe5be70caf - a230ea445788 - - 1691af4a0d17 - 73428a792541 + - 30fb23d4c31c + - 1691af4a0d17 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 494f0bb4a993 - 5a5ae61da69c - - 30f08d74024f - - 563a19373357 + - 57c6718cbfcc - 0418d28136de + - 563a19373357 + - 494f0bb4a993 - e94187d661df - - 57c6718cbfcc + - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - f31125bb85ea - - 1bc5a03faf2e - f77d7b685bb3 - - d6c7106b7b2e + - 1bc5a03faf2e + - f31125bb85ea - 2bba2ff070d9 - - 7abc5f6dd595 - 4b96ced19f75 + - 7abc5f6dd595 + - d6c7106b7b2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - 520e30695ec3 - fed64e676186 - - 54961e026fe4 - b3cf4684e9c7 - - d3af38b9c7e1 + - 54961e026fe4 - d77fdcca400e - 52af33194019 + - d3af38b9c7e1 + - 520e30695ec3 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: - - 07d7991bf205 - 2aea122fbd25 + - 07d7991bf205 - 79261884facd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -236,10 +236,10 @@ tools: - name: goseq owner: iuc revisions: - - ef2ad746b589 - - 8b3e3657034e - 43798b4caee0 + - 8b3e3657034e - 602de62d995b + - ef2ad746b589 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -270,9 +270,9 @@ tools: - name: interproscan owner: bgruening revisions: - - 74810db257cc - - c55643c3d813 - 98cafcbd2578 + - c55643c3d813 + - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -305,11 +305,11 @@ tools: - name: mitos2 owner: iuc revisions: - - 033755194fe9 - c8ac28e8ac44 - - e95d52d295d7 - 624606f7c996 + - 033755194fe9 - b815ec682418 + - e95d52d295d7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -353,9 +353,9 @@ tools: revisions: - a17498c603ec - eaee459f3d69 - - 8a22554cdde2 - - bf68eb663bc3 - d643e3b03500 + - bf68eb663bc3 + - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -374,8 +374,8 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -400,14 +400,14 @@ tools: owner: iuc revisions: - cfcf33df7fc0 - - 68693743661e - - c7275bd8b4d6 - - 5c7b70713fb5 - - 268d162b9c49 - - 5b80f544c67f - 5a29ab10dba6 - - 6322be79bd8e - 8f92c2b26e6d + - 268d162b9c49 + - 6322be79bd8e + - 5c7b70713fb5 + - 5b80f544c67f + - 68693743661e + - c7275bd8b4d6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift @@ -427,8 +427,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 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: - - 809dfc93d593 - - 45083d070fb8 - - 8cb134b8c1a5 - - 37213cf56392 - d03af1c7002c - - ba6f87115e13 - - 200c378d85f3 + - ac8250086ac3 - 037a11682176 + - ba6f87115e13 + - 8cb134b8c1a5 + - 37213cf56392 - 4839e590cb26 - - 51dd22484644 - e1a9d6fd258d - - ac8250086ac3 + - 51dd22484644 + - 45083d070fb8 + - 200c378d85f3 + - 809dfc93d593 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 9923dd013..67307ae8a 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -3,43 +3,43 @@ tools: owner: iuc revisions: - 7547fcab5d19 - - d6d5ccc2c581 - - db9b10824c61 + - fa5259cc561b + - 553bfe8bd0b5 - 0e93176640ac - 841084c5fc46 - - 8f1b150a2487 - 0124fce4654a - - 553bfe8bd0b5 + - 8f1b150a2487 - 890b794c997d - a929ce596a34 - - fa5259cc561b + - db9b10824c61 + - d6d5ccc2c581 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - b2860df42e16 - - 94fe43e75ddc + - 21e491ad532a + - 067592b6b312 - b9e31c5c01c7 - ddddce450736 - - 067592b6b312 - - 21e491ad532a + - b2860df42e16 + - 94fe43e75ddc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 25ca5d73aedf - 321347bd0494 + - 25ca5d73aedf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - 5258e18bbe23 - - 3371c5bdc17a - faee8629b460 + - 3371c5bdc17a - 22286dab5aa1 + - 5258e18bbe23 - a7f16f24e9a1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -53,32 +53,32 @@ tools: - name: busco owner: iuc revisions: - - e824f5d958d0 + - 5ecdeca79a0d + - 2babe6d5c561 + - bb935709506a + - ea8146ee148f - 1440ae06552f - - 94170eee0ad8 - - 2dd755c1c6ff - - 41030a6c03b7 + - 46ae58b1d792 - cf13a1e03e5b - - 602fb8e63aa7 - 4048d82f0c88 + - e824f5d958d0 + - 94170eee0ad8 + - 2dd755c1c6ff + - 0d243f458b53 - f18f0b887c31 - - bb935709506a - - 46ae58b1d792 - - ea8146ee148f - e4bd1e99bacf - - 0d243f458b53 - - 5ecdeca79a0d - - 2babe6d5c561 - - 1e62c28ba91d + - 41030a6c03b7 - e5c372c91e46 + - 1e62c28ba91d + - 602fb8e63aa7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - c5b7390290b1 - 86f150c8019d - 5732f959936a - - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -90,14 +90,14 @@ tools: - name: flye owner: bgruening revisions: - - 8d4f03b5fe9d - e27815e82dd4 - - 1ce9b1d72ec3 - cb8dfd28c16f - - 276f5d8712d5 - - 3ee0ef312022 - 3e4f8642c77e + - 3ee0ef312022 - 291923e6f276 + - 1ce9b1d72ec3 + - 276f5d8712d5 + - 8d4f03b5fe9d - 1f0769f0b56b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -105,29 +105,29 @@ tools: owner: iuc revisions: - b2f674562a18 - - 3169a38c2656 - - 01210c4e9144 - 460fad600dce + - 01210c4e9144 + - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - 8b330a577046 - - 06bcf65179fb - - ba88bc5a6446 - 7348b69e5109 + - ba88bc5a6446 + - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 5127a713de83 - - 6ec1b853c8fd - - 690c2caa367e - 3ef480892a9f - f4a3eff8ab85 - 3fba9c77550a + - 6ec1b853c8fd + - 690c2caa367e + - 5127a713de83 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -139,24 +139,24 @@ tools: - name: hifiasm owner: bgruening revisions: - - da9d8bf98802 - - 71740308d412 - - f3c89da3af16 - - 284a1cb82b61 - 5f625c63b8bc - - 60024a528cbd - - 41cea2aa2dce - - 6505bd37670d + - 5bec28269d95 + - 284a1cb82b61 - df25d4fb79b7 - - ec9e21e9c71b + - 366a11d316a7 + - 5161f204ba63 + - 71740308d412 + - da9d8bf98802 - 2061fb3b81b4 - - 045c7c3d8e59 - - 5bec28269d95 + - 6505bd37670d + - f3c89da3af16 - 9ef6920c3089 - - 5161f204ba63 - - 0ee0c3089254 - - 366a11d316a7 + - 41cea2aa2dce + - ec9e21e9c71b - 3f7be05a1597 + - 0ee0c3089254 + - 60024a528cbd + - 045c7c3d8e59 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -174,43 +174,43 @@ tools: - name: megahit owner: iuc revisions: + - de387b2b2803 - 14ddfc8ffb93 - - a96f3ad4e0d8 - 7518ee87b53d - - de387b2b2803 + - a96f3ad4e0d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - f8113c25bc6b - - d7edbc9c3a07 - - 9d79beb19ac3 - 39edec572bae - eb7b00ec347d + - 9d79beb19ac3 + - d7edbc9c3a07 - 09c589057ee8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: + - eadfd71dde37 - 29dabd8db6f2 - 51c2360aa807 - - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - fd128c111ab0 - f369ef5f210b - 606b09cc9860 + - 99ecfdafc64f + - f338e9942b27 - 3ca2d2a9068c + - fd128c111ab0 + - eb7a370f6588 - 2ecf5a570907 - - f338e9942b27 - e731ea24e48d - - 99ecfdafc64f - - eb7a370f6588 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -223,10 +223,10 @@ tools: owner: iuc revisions: - 8dee0218ac7d - - b799a615995d - - a7b889b90140 - 8b6d0d85252b + - b799a615995d - 73a3846701e1 + - a7b889b90140 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -245,8 +245,8 @@ tools: owner: iuc revisions: - 64a1c751d99b - - 7c2f5268d01c - 15200570e926 + - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -258,14 +258,13 @@ tools: - name: pretext_map owner: iuc revisions: + - dfb8a4497339 + - bbe19ef04a74 + - d256a51a656b - 2b16ba799da9 - c6cec5ab35c1 - - bbe19ef04a74 - 8fef980d48b5 - - dfb8a4497339 - 02831bf9e95f - - 79b48f02db49 - - d256a51a656b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups @@ -279,26 +278,26 @@ tools: - name: quast owner: iuc revisions: - - 675488238c96 - - 72472698a2df + - 342a1d1fed7b - ebb0dcdb621a - - 3061c8b029e5 - 875d0f36d66f - - 342a1d1fed7b + - 3061c8b029e5 + - 6fcbee531de6 - 59db8ea8c845 + - 675488238c96 - 7594365c546b - - 6fcbee531de6 + - 72472698a2df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - 39bed8de8017 - - aa39b19ca11e - - 78c533842eeb - - cd06929b224b - - d865b62f501c - a199cd7ac344 + - d865b62f501c + - cd06929b224b + - 78c533842eeb + - aa39b19ca11e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -316,12 +315,12 @@ tools: - name: raven owner: iuc revisions: - - 2b2a352488fa - - f8564b2d7f63 - - 5c55448d0f33 + - f11b994b7eb2 - 33b7d8481a76 + - 5c55448d0f33 - 3edba9afc9bc - - f11b994b7eb2 + - f8564b2d7f63 + - 2b2a352488fa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast @@ -334,13 +333,13 @@ tools: - name: rnaspades owner: iuc revisions: - - 5fc94b3a4704 - ef69617ecb42 + - 5fc94b3a4704 + - e122f9101584 - 53c2bc8c2ae3 - - 1d06c8b38e77 - - 28189050e437 - 378e55aeeb25 - - e122f9101584 + - 28189050e437 + - 1d06c8b38e77 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -352,149 +351,149 @@ tools: - name: shovill owner: iuc revisions: - - ad80238462c1 - - d9f6a00b6db7 - f698c7604b3b - - 865119fcb694 - ee17a294d3a3 + - ad80238462c1 + - 865119fcb694 - 83ead2be47b2 + - d9f6a00b6db7 - 196a599ec43d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 015283de3004 - 5e0825476fb7 + - 015283de3004 - 24e471d13fe9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 604782a8a53a - - 1fc82fe7ebef - - 1bb12736175c - - c33a476f4001 - 7490b213baa9 - - 904bf932cf78 + - c33a476f4001 - 051fd2db8a27 + - 904bf932cf78 + - 1fc82fe7ebef + - 1bb12736175c + - 604782a8a53a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: + - 808b3a0a6716 + - d6e617c4e338 - 9678993ca5bd + - 34305b013402 + - fee85957cebe - ad8b536d1caa - 655fa188c3cc - - 808b3a0a6716 - - fee85957cebe - - 34305b013402 - - d6e617c4e338 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 7e27faaad80e + - e5a3b75a271f - 037f9927c4ff + - b8002c3f7141 - 21da31ed41a1 - 6b5a5842531e - - e5a3b75a271f - 8d4b90bf9caf - - b8002c3f7141 + - 7e27faaad80e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 9de69775f512 + - 328aa71f0f3c + - 2a10645aeadd + - 7922870efcca - 5b26685e5d3b + - 9de69775f512 - 86f66ab58e14 - f1532cb33c75 - - 2a10645aeadd - - 328aa71f0f3c - - 7922870efcca tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - e41dcb0e913b - - 85fb02c43042 - 6aad515a5270 - 340bc17f49cf - 8cc856b935ee + - 85fb02c43042 - 1708851f8804 + - e41dcb0e913b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - d159735a6a9f - - 6357b127161e - - 249f6a28c751 - b3490b036c5a - d5fb354f745d + - 6357b127161e + - d159735a6a9f - b65a43f70b99 - de1260f8a300 + - 249f6a28c751 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 33368fec3b70 - - 9006e5836729 - d2d1df21dfb9 - - d5887ace0dd4 - - dd7ad84f3943 - - 7897763d14ec - - a90db5dbaaf3 + - 33368fec3b70 - b7829778729f + - a90db5dbaaf3 + - 7897763d14ec + - dd7ad84f3943 + - d5887ace0dd4 + - 9006e5836729 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 189e837009c9 - - 505a9833ab5d - - 8f631679571f + - 6f4c8ad6ea01 - 0368ac680e70 + - 505a9833ab5d - ced385aa976d - - 6f4c8ad6ea01 + - 189e837009c9 + - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e + - 9ded6109434a + - e59bee4565b3 - 19bdfd1e6fe3 - 356afed970b4 + - d40ed4eb0c0e - a7ed21de23fe - - e59bee4565b3 - - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 6dd935e4984b - - b23249f81bc4 - ebd801e712bc - - 7673a6c920b2 - 4688ae3b49b5 + - 7673a6c920b2 - 80a17897564d + - 6dd935e4984b + - b23249f81bc4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - ed312479d9eb + - 59bd28f6265d + - 937ea677d437 - b64696992ee9 - cb1e3db43020 - - 59bd28f6265d - b5e35a2ca4f3 - - 937ea677d437 + - ed312479d9eb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample @@ -502,41 +501,41 @@ tools: revisions: - 6015aa0303f2 - 05bd7504fdb2 + - b9b0246a2be3 - cb4768eeca3b - 2628f6790eda - 383bb5ad32e2 - - b9b0246a2be3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: + - 3e44ef016b45 - 8f9f06995f98 - - e92675014ac9 + - 0a3a602cd1e3 + - 6e26c9afd301 - e022dff952df - 9e3e80cc4ad4 - - 6e26c9afd301 - - 0a3a602cd1e3 - - 3e44ef016b45 + - e92675014ac9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f - - 5da9a0e2fb2d - 920677cd220f + - 5da9a0e2fb2d + - 08256557922f - 8d09f8be269e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 0e2b4e3f9ca1 - - 82398ba86ba7 - d81360ea69d8 - 4a53b89fa703 + - 82398ba86ba7 - 37d88f41c810 + - 0e2b4e3f9ca1 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 6d738cfa3..9dd4ec51c 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -18,16 +18,16 @@ tools: owner: iuc revisions: - 31812e7a1315 - - ded48b36f3b7 - - 1f5641a52664 - 8e8dc9a1e3e5 + - 1f5641a52664 + - ded48b36f3b7 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 17fcac7ddf54 - - 5c8ff92e38a9 - 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 cd35eb24e..52d5136ee 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: - - 159b04e36791 - - 0840ba83860c - - 204a131e47db + - d58c27d2c5a7 - 7beb76ffbc0f - d1f62024a08b - - d58c27d2c5a7 - - 1c427e24fb79 - a9c9d768b751 + - 204a131e47db + - 0840ba83860c + - 159b04e36791 + - 1c427e24fb79 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 3c93a52cf..38777d513 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: - - e19bebe96cd2 + - a8eabd2838f6 + - a1a923cd89e8 - dde39ba9c031 - - 589e7e57fd6d - 87ee588b3d45 + - a68aa6c1204a + - 589e7e57fd6d + - 0a5c785ac6db + - e19bebe96cd2 + - b28e0cfa7ba1 - ce3c7f062223 - 64e2edfe7a2c - 07e8b80f278c - - a1a923cd89e8 - - a8eabd2838f6 - - a68aa6c1204a - - b28e0cfa7ba1 - - 0a5c785ac6db 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 f26788125..838363517 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: - - f921014aba5a - - e8ac2b53f262 - 54f751e413f4 - 62c9df8382c2 + - e8ac2b53f262 + - f921014aba5a 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: - - 6f386c5dc4fb + - 0e3cf9594bb7 - d999e774072a + - e25d3acf6e68 + - 2889433c7ae1 - 5edc472ec434 - - cbf3f518b668 - - a52d2d93e595 - acf4e47b734c - - 0e3cf9594bb7 - - 2889433c7ae1 - - e25d3acf6e68 + - 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: - - 1334cb4c6b68 - e9005d1f3cfd + - 1334cb4c6b68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/staging.gvl.org.au/checkm_taxon_set.yml b/staging.gvl.org.au/checkm_taxon_set.yml deleted file mode 100644 index e52a6c5f3..000000000 --- a/staging.gvl.org.au/checkm_taxon_set.yml +++ /dev/null @@ -1,7 +0,0 @@ -tools: -- name: checkm_taxon_set - owner: iuc - revisions: - - 407e50329077 - tool_panel_section_label: CheckM taxon_set - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index ca2f972b7..e73bb3709 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - f4230f116196 + - 6ca543ec1bf8 + - 095ad4d096d1 + - c8cdde00b105 - da6bd1975a71 + - f4230f116196 - 27ee142314a9 - 710301bc46fa - - 095ad4d096d1 - - c8cdde00b105 - - 6ca543ec1bf8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -131,73 +131,73 @@ tools: owner: chemteam revisions: - 79cfd9ead848 - - 3b8a9d5ced85 - 0fac8e2afc13 - - 88076940fa94 - bfb65cb551d8 + - 3b8a9d5ced85 + - 88076940fa94 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - eb6564a60136 - - f5d979cb4b54 - 55918daa5651 - - b46d4b4d995c - 715cd0e87781 + - f5d979cb4b54 + - eb6564a60136 - d532b7e5f64b + - b46d4b4d995c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - f26afd1b7104 - 5579659312e6 + - d2f955aea23a - fdf2cc80adb5 + - f26afd1b7104 - 97872d87ba80 - - d2f955aea23a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - 319a28774da9 - d1d0efda35c0 - bc31d02be922 + - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 070e3ecc3fda - - ed736e6eee39 - 4da9ee404eab - - cac1886249a2 - 2c349b027a01 + - ed736e6eee39 + - cac1886249a2 + - 070e3ecc3fda tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - f197e34c33a9 + - 807aa4c9293d + - 73008ef1f487 + - 2e219a2d9327 - d1f803b5943c + - f197e34c33a9 - c0c9a5024177 - - 525ca7c8065f - da8753545526 - - 73008ef1f487 - - 2e219a2d9327 - - 807aa4c9293d + - 525ca7c8065f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - c4fbab8e03c5 - - 27ea4e1a3f95 - - 7568ae18908a - 1809414a9454 - - 61094e01eff9 + - 7568ae18908a + - 27ea4e1a3f95 - 2c8ed1b52bf7 + - 61094e01eff9 + - c4fbab8e03c5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -210,17 +210,17 @@ tools: owner: chemteam revisions: - d7ec25187599 + - ccfbd956a2d3 - 730ef07b90ae - 79e8ab8f1e81 - - ccfbd956a2d3 - ba83f0923369 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 - e6011617c748 - - 1400d1977e7b - 4242b4d68e9c - - b59c91adeac1 + - 1400d1977e7b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -291,7 +291,6 @@ tools: owner: recetox revisions: - 89b026d67e9f - - 53dce0e49af7 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_neutral_run @@ -304,7 +303,6 @@ tools: - name: qcxms_production_run owner: recetox revisions: - - e97bfe7ac906 - 356f7916ac07 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -341,10 +339,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - bf99565cec1f - - 9b48456a96fe - d4c67ced6abc - 85fad59f8168 + - 9b48456a96fe + - bf99565cec1f 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 6308eadd7..db5e6e4e8 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: + - c97a786e8fb5 - 163688bb8f73 - - f907216064f6 - fa56d93f7980 - - c97a786e8fb5 + - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -23,18 +23,18 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 4124781932db - 11cf21ee4242 + - 4124781932db tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - - 424aefbd7777 - 86e2413cf3f8 - 640d3af5d833 - - 495a4173006f - f5d67c722d67 + - 495a4173006f + - 424aefbd7777 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -53,8 +53,8 @@ tools: - name: sicer owner: devteam revisions: - - 74c9214cc8e6 - 4a14714649b4 + - 74c9214cc8e6 - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/collection_operations.yml b/staging.gvl.org.au/collection_operations.yml index bc51fb7f2..bd0b0a56b 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -9,17 +9,17 @@ tools: - name: collapse_collections owner: nml revisions: - - 25136a2b0cfe - 33151a38533a - 90981f86000f + - 25136a2b0cfe - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,10 +31,10 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - baabc30154cd - - 6cbe2f30c2d7 - 0046692724f9 - 2dae863c8f42 + - baabc30154cd + - 6cbe2f30c2d7 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index d42be1eca..c07d9d58a 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -2,8 +2,8 @@ tools: - name: agat owner: bgruening revisions: - - e7449b2c14bf - abba05ead5d7 + - e7449b2c14bf - d6ede73082da tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -16,32 +16,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: + - 0b3c3ad92827 + - ab9350a8ab4d + - f3a19509108a - 3b6f97e7094c - - a3b86937ead6 - e3cbd2287f63 - - 5e1240a87bcb - 4a6ee918c13a - - 367b1ed91207 - - ab9350a8ab4d - - f3a19509108a - 6ef0b5664c69 - - 0b3c3ad92827 + - 5e1240a87bcb + - a3b86937ead6 + - 367b1ed91207 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 72ed72122deb - - e525f9ffb9ac - - e177a8ea0bf1 - - bd46669113b9 + - 1b5fc03380d4 + - 501c21cce614 + - d4d4e9febf5c - 54ccb7e1f49a + - bd46669113b9 - 33c99804a32f - - 501c21cce614 + - e177a8ea0bf1 - 584008e574b2 - - 1b5fc03380d4 - 091bb5922a82 - - d4d4e9febf5c + - 72ed72122deb + - e525f9ffb9ac tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -60,15 +60,15 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - 7e801ab2b70e - e7ed3c310b74 + - 7e801ab2b70e tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: - - 77b41c89d856 - 186b8d913e6c + - 77b41c89d856 - 8979c288aefb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -89,8 +89,8 @@ tools: - name: gfa_to_fa owner: iuc revisions: - - 8e9d604e92f4 - e33c82b63727 + - 8e9d604e92f4 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -102,9 +102,9 @@ tools: - name: gffread owner: devteam revisions: + - 4dea02886337 - 154d00cbbf2d - 3e436657dcd0 - - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -129,8 +129,8 @@ 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 @@ -143,19 +143,19 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 78fb18899c99 - - 68f57cc8fad0 - 2dcfbbf9071a + - 68f57cc8fad0 + - 78fb18899c99 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - - b9b385097f13 - 19e45916daf9 - 63769c4217a7 - 26c6706bfb07 - 92ac8e086317 + - b9b385097f13 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf @@ -177,8 +177,8 @@ tools: owner: iuc revisions: - 98704d357ede - - fa49730d1d4b - a2f83a375bf2 + - fa49730d1d4b tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index 3f811f3d6..f28522915 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,34 +2,34 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 268e91e540ee - - 5f6d123679f4 + - de72ba3ed6f2 - e821645ef8fc + - 5f6d123679f4 + - 268e91e540ee + - 29451af70c52 - c929a006727f - - de72ba3ed6f2 - a1ca9bccc7f2 - - 29451af70c52 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - bb1e4f63e0e6 - 0e143b4c3987 - - 0e49b109abc2 - 12af64f93288 - - 7a7fd0f5f15d - - 2d2cf5c1ea8a - 5d11599b8a7d + - bb1e4f63e0e6 + - 2d2cf5c1ea8a + - 7a7fd0f5f15d + - 0e49b109abc2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 81b1e3e1fc6c - - 195e98217334 - c06951d10364 + - 81b1e3e1fc6c - dc059492a995 + - 195e98217334 - 1d848bc4585f - 7c1beb6d6eca tool_panel_section_label: DeepTools @@ -37,146 +37,146 @@ tools: - name: deeptools_bigwig_compare owner: bgruening revisions: - - 26e7304d6737 + - 3d211717a775 + - a67ac707496a - 93eb012d9eed - bfff7454b59a - - 3d211717a775 - - 07418a30ed01 - 71aa86af6762 - - a67ac707496a + - 07418a30ed01 + - 26e7304d6737 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 26983857c91a - 56d5b797ce84 + - 2bc10a9ca58b + - 29fcfd36e90a + - b8858746dc1f - dd0b7398bb96 - 5be24eba848d - - b8858746dc1f - - 29fcfd36e90a - - 2bc10a9ca58b + - 26983857c91a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 9384cd033f30 - 7ef978dc1b8a - - ee3a1b0f45f1 - 7e6bcd2e5128 + - 72bfafe3330b - c3e012dfe21f + - 9384cd033f30 + - ee3a1b0f45f1 - e6d0bff01239 - - 72bfafe3330b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - b73e213add0c - - 167788df3b46 - - fd1275e01605 - d9a637e83828 - 514fa53b5efb + - b73e213add0c + - 167788df3b46 - 9470f29702f8 - - a60c359ec43c - fb9cf9c97ec4 + - fd1275e01605 + - a60c359ec43c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - ca0616bb2cdf - - a02cfa31e9cb - - c34d11ea4ba6 - e479c7ca5570 - - 5bffaa8354a1 - 2c37ce318bc3 + - 5bffaa8354a1 + - a02cfa31e9cb + - ca0616bb2cdf - 86febdcc4283 + - c34d11ea4ba6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 1fcb7adc39b8 - 004aea905d4d - - 192ef85c0b0b - - 01fb6a7654e6 - - 2d466b530754 - - 78f405266706 - 69a8621ca2f0 + - 1fcb7adc39b8 + - 78f405266706 + - 2d466b530754 + - 01fb6a7654e6 + - 192ef85c0b0b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 2f9e4843f480 - - d580d6acd1df - - 9ecba5e225a6 + - 459cfa861f0b - 137c4beed34b + - d9ce4897dbb2 + - d580d6acd1df - 3c9f0c486cca - - 459cfa861f0b + - 2f9e4843f480 + - 9ecba5e225a6 - db940c262830 - - d9ce4897dbb2 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 - - 2c66e43f1c86 - - bd7db9e2f2cb - 32e451def88c - - bad3ca889618 - fbe773640707 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 231994413f89 - - 56bce3c82278 - 9368fbc49c8b + - 56bce3c82278 - 7fda5607e777 - - 3b9d990a0a0e - 7e361d147872 + - 231994413f89 - 4e12ea27f788 + - 3b9d990a0a0e tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - ce4ce3316f74 + - e65d16fb2724 + - d9114ef1c8a5 - b1779366c8e9 + - ce4ce3316f74 + - 94ca68515826 - 4431f39ede55 - - d9114ef1c8a5 - c03c3384cd81 - - 94ca68515826 - - e65d16fb2724 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - 793665fff0f8 - 4ed32329e0ed - - f8fc4e5aff9d - - d57251071381 - - b88ebb3672a1 - 23f7c5f1fdaf - - 793665fff0f8 + - f8fc4e5aff9d - 2da482e408b8 + - b88ebb3672a1 + - d57251071381 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - 512155688d98 - - 010e58e9d822 - - a7849312d328 - - ba6efa77fb79 - 25d830337d31 + - ba6efa77fb79 - c60570fa602f + - 010e58e9d822 + - a7849312d328 + - 512155688d98 - e4c7985d4585 - a4dfb122e52b tool_panel_section_label: DeepTools @@ -185,22 +185,22 @@ tools: owner: bgruening revisions: - 38e3f226248b + - 443d9a9d6d11 + - 69264da0ce77 - 4d678170d29b + - c899e0ccff8c - aa200e4f3939 - 00d869ea03a1 - - 69264da0ce77 - - 443d9a9d6d11 - - c899e0ccff8c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - 6662b1a8d326 - - a2d70c4fd406 + - aac8444d6681 - c361b12d207a - - 10301d137111 - d806504e96d9 - - aac8444d6681 + - 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 7148ee113..61f922109 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: - - e328ced6cf0a - 4d705e3443a7 + - e328ced6cf0a tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep @@ -30,8 +30,8 @@ tools: - 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 @@ -58,8 +58,8 @@ tools: - name: obi_tab owner: iuc revisions: - - 3299c7d5268f - 4cf47c504672 + - 3299c7d5268f 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 c87ebd957..c20dc3f9c 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - 63dd26468588 - - dba489bfcd62 - 832c20329690 - 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 64123eae0..18bf4bfca 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: - - d82648ad25a3 - 62f5fab76dfb + - cf1322aeb137 - 6da3972210ee - 29bdbc353f20 - - cf1322aeb137 + - d82648ad25a3 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 23693468f..2355b7e6e 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: + - 48f587c13075 + - 4e5056fefd88 - 64172f1c1202 - - 8665bcc8b847 - - 660cffd8d92a - - b1c926deaa2d - - 8c0175e03cee - - 44e2cc14f75b - - 5915ea1ec9b1 - - 093678460093 - - 5eb7e84243f2 - c4b82dce8335 - - 49370cb85f0f + - c5e2e5902201 + - e4691e1589d3 + - 44e2cc14f75b - fe74900d6dc7 + - 49370cb85f0f + - 5eb7e84243f2 + - 288f97432497 + - 660cffd8d92a + - c053d4cad713 - 135b80fb1ac2 - - 48f587c13075 + - 8665bcc8b847 - de6cebe3c043 - - e4691e1589d3 - - c053d4cad713 - - 288f97432497 - - c5e2e5902201 - - 4e5056fefd88 + - 8c0175e03cee + - 093678460093 + - b1c926deaa2d + - 5915ea1ec9b1 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: + - 8889eb864cef - 9db07fd39f85 - f666895cbebd - - 8889eb864cef tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -54,8 +54,8 @@ tools: owner: devteam revisions: - de2db1bdfbf8 - - 5cbde03c1103 - 7d37cfda8e00 + - 5cbde03c1103 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length @@ -87,9 +87,9 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 859422bcb689 - - 9457a20156db - 516b97a23d7e + - 9457a20156db + - 859422bcb689 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -109,8 +109,8 @@ tools: owner: devteam revisions: - f81d4362b6c1 - - f773e98b26cf - 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: - - 9c620a950d3a + - 56022eb50bbd - 0dbb995c7d35 + - 9c620a950d3a - cd0874854f51 - - 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: - - 1d8fe9bc4cb0 + - a626e8c0e1ba - dbfc505896e9 + - 1d8fe9bc4cb0 + - ecb9f4854617 + - 65b93b623c77 + - dbf9c561ef29 - c59d48774d03 - d60c3f704da0 - - dbf9c561ef29 - - 65b93b623c77 - - a626e8c0e1ba - - ecb9f4854617 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -156,9 +156,9 @@ tools: - name: fastq_combiner owner: devteam revisions: + - 9115b978ce10 - f1dc2a761c30 - b05e39b9c170 - - 9115b978ce10 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -170,8 +170,8 @@ tools: - name: fastq_filter owner: devteam revisions: - - 81a9090d6df3 - '144275714590' + - 81a9090d6df3 - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -185,8 +185,8 @@ tools: owner: devteam revisions: - 8611b80a14d6 - - e9f8633db0a2 - 47e5dbc3e790 + - e9f8633db0a2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -212,9 +212,9 @@ tools: - name: fastq_masker_by_quality owner: devteam revisions: + - 4e1d64e6385f - 9dfda4e310ed - 9282652e7234 - - 4e1d64e6385f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality @@ -227,8 +227,8 @@ tools: owner: devteam revisions: - 03d57fea6482 - - 523c2aff0376 - f3936d0632cb + - 523c2aff0376 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -254,9 +254,9 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: - - 09a2199cd356 - - 8d958759cf2a - 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: - - e39cc71d3ed6 - - 397dc333436b - 35e38452bb3f + - e39cc71d3ed6 - 249c8393f2d4 + - 397dc333436b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -283,9 +283,9 @@ tools: - name: fastq_quality_converter owner: devteam revisions: - - 54053ea6c77e - - 74db4cffab1f - 045f0e1043f7 + - 74db4cffab1f + - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -297,9 +297,9 @@ tools: - name: fastq_stats owner: devteam revisions: - - f0e7deab6518 - - f86c27295151 - b1cea1b2fcd0 + - f86c27295151 + - f0e7deab6518 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats @@ -311,9 +311,9 @@ tools: - name: fastq_trimmer owner: devteam revisions: + - f0b18efb97f1 - 33794bdb7fe0 - b63b2bfb3ea3 - - f0b18efb97f1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer @@ -332,9 +332,9 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 567d5b3c52b1 - d5e9e83cd3d8 - 09070cacefd8 + - 567d5b3c52b1 - 529bccd5e4a1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -348,8 +348,8 @@ tools: owner: devteam revisions: - 4bedca26c133 - - 8abdedf55101 - 0b7ec11b3c7c + - 8abdedf55101 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -362,9 +362,9 @@ tools: owner: devteam revisions: - 90858c306551 + - cb1e251cac37 - 736b8f6ee456 - bdf1ce174e39 - - cb1e251cac37 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -376,8 +376,8 @@ tools: - name: fastx_collapser owner: devteam revisions: - - 7ce1891db6f5 - 07497255281e + - 7ce1891db6f5 - 421f0af4ee95 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -391,9 +391,9 @@ tools: owner: devteam revisions: - 3599f5451ee2 - - 02f8a17a4ebd - - f984bb114520 - 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: - - 177f0621c266 - - e246088b6e34 - 6027ef51ef91 - 0c2907307ba4 + - e246088b6e34 + - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -421,9 +421,9 @@ tools: owner: devteam revisions: - 73194cdd4f57 - - 547e8d00f11c - 377ac2829eac - 61b4cedc8934 + - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -447,10 +447,10 @@ tools: - name: pear owner: iuc revisions: - - 037f0acc7830 - 2f804526f5fd - - f69501361cec - b4c6f054210a + - 037f0acc7830 + - f69501361cec tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -462,16 +462,16 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 3b0a14722175 - 8e1a90917fa7 + - 3b0a14722175 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_sort owner: iuc revisions: - - fdc21382376d - - 29ef2c5ec205 - 61eb4cfc7313 + - 29ef2c5ec205 + - fdc21382376d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats @@ -485,9 +485,9 @@ tools: - 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 @@ -506,16 +506,16 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - 51b771646466 - dfa082f84068 + - 51b771646466 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - - d3f58a0dc09d - bf04bd405d5b - 71f649c23021 + - d3f58a0dc09d 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: - - 8250ea3a1501 + - 71ad4a56c40c - b557acca0b56 + - a535cf1e5da4 - e654095ab143 + - 8250ea3a1501 - 24013bf85a6f - - 71ad4a56c40c - - a535cf1e5da4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -544,21 +544,21 @@ tools: - name: umi_tools_dedup owner: iuc revisions: - - c5a2ee07c4e1 - f1d33e4c7bd8 + - c5a2ee07c4e1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract owner: iuc revisions: - - 7a7e33d28f62 - - 9fa7803d1c51 - - 27ac32a22ad2 + - f3759eec3018 - 828dba98cdb4 - 015cf18f4a15 - - f3759eec3018 + - 27ac32a22ad2 - 7accf7407811 + - 9fa7803d1c51 - 6a675c3aa610 + - 7a7e33d28f62 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract @@ -570,15 +570,15 @@ tools: - name: umi_tools_group owner: iuc revisions: - - d6255614afd7 - 428735be9764 + - d6255614afd7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_whitelist owner: iuc revisions: - - 4c8a1c7d3608 - - e4e12f0b3af1 - 953b4821b183 + - e4e12f0b3af1 + - 4c8a1c7d3608 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index 83e8ce18c..16d6bb3f3 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,9 +2,9 @@ tools: - name: fastq_quality_filter owner: devteam revisions: + - 64e9a6afdd0c - e41385662e5e - 7b4468117008 - - 64e9a6afdd0c - ce9cd02d5b88 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu @@ -18,14 +18,14 @@ tools: - name: fastqc owner: devteam revisions: - - f2e8552cf1d0 - - 2c64fded1286 - - 5ec9f6bceaee - - 3d0c7bdf12f5 - - ff9530579d1f + - 9da02be9c6cc - 2b0c9d9fc6ca - e7b2202befea - - 9da02be9c6cc + - 3d0c7bdf12f5 + - ff9530579d1f + - f2e8552cf1d0 + - 5ec9f6bceaee + - 2c64fded1286 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -38,47 +38,47 @@ tools: - name: fastx_nucleotides_distribution owner: devteam revisions: - - b6b54ba71bd8 - - 18a51655db17 - 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: + - 59003d0543cd - 7306ec78632a - cc0fd298cc17 - - 59003d0543cd 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: - - f7985e0479b9 - - 75c93c70d094 + - bf675f34b056 + - abfd8a6544d7 - 5e33b465d8d5 - - 9a913cdee30e - - f7e2f1eb3a16 - 3d93dd18d9f8 - b2f1f75d49c4 + - f7985e0479b9 + - f7e2f1eb3a16 - 1c2db0054039 - - bf675f34b056 - - abfd8a6544d7 + - 9a913cdee30e + - 75c93c70d094 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 084bbd8ba7b8 - - cd7e644cae1d - 949f01671246 + - cd7e644cae1d + - 084bbd8ba7b8 tool_panel_section_label: FASTQ Quality Control 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 9243d596c..ab23c208f 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: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 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: - - 141612f8c3e3 - - 85ef5f5a0562 - 83a19df00eab + - 85ef5f5a0562 + - 141612f8c3e3 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 0439730c4..3b4f18f40 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -2,8 +2,8 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 3630a6e624d4 - 142d95ab942e + - 3630a6e624d4 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend @@ -17,15 +17,15 @@ tools: owner: iuc revisions: - f2f3bc622a16 - - 8f53b238a360 - 0c8f7322f8fc + - 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 @@ -38,29 +38,29 @@ tools: - name: gemini_db_info owner: iuc revisions: - - 7d75673f4d6f - 4c5f4e9b1931 + - 7d75673f4d6f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo owner: iuc revisions: - - d5b01cc263be - 9db3e299b1c8 + - d5b01cc263be tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump owner: iuc revisions: - - 40f85b45e472 - 96a2d270bf0f + - 40f85b45e472 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions owner: iuc revisions: - - 91d53f89ca54 - 8151a5a0e4f6 + - 91d53f89ca54 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise @@ -86,9 +86,9 @@ tools: - name: gemini_load owner: iuc revisions: - - cf61daf064fe - - b2c25142267e - 45296e47d565 + - b2c25142267e + - cf61daf064fe tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -108,8 +108,8 @@ tools: - name: gemini_pathways owner: iuc revisions: - - 6b09debcfc49 - 9199331c3421 + - 6b09debcfc49 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -122,9 +122,9 @@ tools: - name: gemini_query owner: iuc revisions: + - da74170c55c7 - 666f60a9331a - 840fb4850be3 - - da74170c55c7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -137,8 +137,8 @@ tools: - name: gemini_region owner: iuc revisions: - - 33efe43c1dbb - 601b70d10d92 + - 33efe43c1dbb tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh @@ -165,7 +165,7 @@ tools: - name: gemini_windower owner: iuc revisions: - - 8f04952b8882 - 0c58ba91d018 + - 8f04952b8882 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 2a6e45eeb..301093442 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -2,22 +2,22 @@ tools: - name: mageck_count owner: iuc revisions: - - 3edbd1ff5602 - e329d44424d7 + - 3edbd1ff5602 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 owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index 942851da2..cc088c9e5 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - b39347891609 - - 983bf725dfc2 - - c1b437242fee - e9df53a75f3c + - c1b437242fee + - 983bf725dfc2 + - b39347891609 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 - - 1c58de56d587 - 28587613264f + - 1c58de56d587 + - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - f5ea3ce9b9b0 + - 6591f049cf7e + - aad3885b3216 + - e407b9da183a + - f8054ea1c365 - 69ebb7f46e45 - - e08a7ad4378b - - c441583adae5 - - 516a54ddf218 - - 734abc7ac21d + - 1ec814014652 + - 4df8de2d0e48 - 83c7d564b128 - - aad3885b3216 - - 9a776b080193 - - 6ea73833cf67 - 5e6237d58b0c + - 6ea73833cf67 - 7068f48d0ef9 - - ba931a59dd59 + - 4317d3cb6cba + - e08a7ad4378b + - 9a776b080193 + - 734abc7ac21d + - c441583adae5 + - f5ea3ce9b9b0 - 653e89d73fc4 - - 1790dcf3c32d - 8848455c0270 - - f8054ea1c365 - - 4df8de2d0e48 - - e407b9da183a - - 1ec814014652 - - 4317d3cb6cba - - 6591f049cf7e + - 516a54ddf218 + - ba931a59dd59 + - 1790dcf3c32d tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 9aaa46d45472 - - 75b3b3d0adbf - - 34758ab8aaa4 - 21a560af5913 + - 34758ab8aaa4 + - 75b3b3d0adbf + - 9aaa46d45472 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - bfdc6a7ffd3a - - 054483e27a35 - 468c71dac78a + - 054483e27a35 + - bfdc6a7ffd3a - af5eccf83605 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 ebf64259a..eb3fca8c6 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: - - df7356989ac1 + - ae9994cf526f - fd59d783248a - - 4b519282a05b - - 7f13dc906cb9 - - 290a11559985 - - 740057a5126d + - df7356989ac1 - a64dc31ab7f2 - - ae9994cf526f - c4bde687c846 + - 740057a5126d + - 7f13dc906cb9 + - 290a11559985 + - 4b519282a05b 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: - - 7cf5b1d072b5 - - f95284aa2946 - 867ab348287d + - f95284aa2946 + - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -48,56 +48,56 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: + - '566197475670' + - 3b37b1b1c3a7 + - 374e9062d874 + - ca7cb0eaad62 - 51c6ccaace7e - 53460afd5115 - - ca7cb0eaad62 - - 374e9062d874 - - 3b37b1b1c3a7 - 48b42ee61bc5 - - '566197475670' tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 10515715c940 + - 3d059e9c2fba - 1a72f938213e + - 391a4cc45fea + - 10515715c940 - da4c086cff5b - d3a9e32672ec - - 3d059e9c2fba - - 391a4cc45fea tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram owner: iuc revisions: - - b0d96516e6a5 - 6fc8bab811da + - b0d96516e6a5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_pca owner: iuc revisions: - - b1268b7544d3 - ae344ccf9d62 + - b1268b7544d3 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 1acf88921176 - d0fc8b746d57 - - 5298e06f14f9 - - 299307abd804 + - 1acf88921176 - 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: - - 0e7290688b50 - 17b666467c32 + - 0e7290688b50 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: - - 8f62f666dcb6 - 6e8eb0c0d91f + - 8f62f666dcb6 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: + - fd5dbf0f732e - 1cfc579079a6 - - 836d1aa3e89a - - 112eb40ba6cf - - ca2def38369c - 17359b808b01 - - a6e57ff585c0 - - 2bb2e07a7a21 - 6cd09d7b5f37 - 667e17248bfe - - fd5dbf0f732e + - 112eb40ba6cf + - 2bb2e07a7a21 + - 836d1aa3e89a + - ca2def38369c - 4542035c1075 + - a6e57ff585c0 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 - - fe154a7af404 - f1691de443a7 + - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -188,9 +188,9 @@ tools: owner: bgruening revisions: - f234e2e59d76 + - 62e3a4e8c54c - 85da91bbdbfb - 1c5dcef5ce0f - - 62e3a4e8c54c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -209,11 +209,10 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 326098bc19cc - 26f2fe7e53a1 + - 44c66e8d21e6 - 7c9417381ad5 - 6c571966cfb9 - - 44c66e8d21e6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -225,23 +224,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 326a3db8d9d1 + - 36b848d5f3ec - 360df4999907 - - 7dd841a32245 - - a1abfa420d9d - 4ac4e7083b7e + - 326a3db8d9d1 + - 7dd841a32245 - 2824d77cd8f8 - - 36b848d5f3ec + - a1abfa420d9d - 14e7c35f3d00 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - 83c573f2e73c - 73b8cb5bddcd - 2f557f6abbfb - 44608d0193ed - - 83c573f2e73c 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 439f27bfb..00aa36029 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.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 @@ -29,40 +29,52 @@ tools: owner: ebi-gxa revisions: - 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: - - 361608369dda - 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 - cc64914b0cf4 + - da611a744112 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster owner: ebi-gxa revisions: - - 36735850e461 - fc4b3b46dc9d + - ad6995afd2e6 + - 2ccd9f9e2cd0 + - 36735850e461 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 + - 81c34e67f262 - 0a8e527d1517 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 - 79da59a0b180 - 64dd8bb151e1 tool_panel_section_label: HCA Single-cell @@ -70,44 +82,46 @@ tools: - name: scanpy_integrate_bbknn owner: ebi-gxa revisions: - - c9da9192eee5 - 9d76c3d6dff6 + - c9da9192eee5 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 3c47bc560688 - 352cdf3b2f75 + - 3c47bc560688 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 - ff6decc0f432 + - 9a2f72d7dbd2 - 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: - - 3027cb62adbd - 28b1546857b0 + - 6b97ffba31da + - 8d9c22419c56 + - 3027cb62adbd tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator @@ -120,22 +134,24 @@ tools: - name: scanpy_plot_embed owner: ebi-gxa revisions: - - 1be0fc4d8654 - 7d5c97823f8b + - 35f6611fb8c3 + - 56d22aa6cb3b + - 1be0fc4d8654 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 owner: ebi-gxa revisions: - - d3df472a21dc - cb1992d1804b + - d3df472a21dc tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x @@ -149,49 +165,54 @@ tools: owner: ebi-gxa revisions: - 0bab2ae44e7a + - 36daab33aecf - d18ed15697bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap owner: ebi-gxa revisions: - - 6a6364b488db - 79cc06a557b0 + - 6a6364b488db tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt owner: ebi-gxa revisions: - - 03921aa8b29c - 12f67b0c1a94 + - 03921aa8b29c tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_fdg owner: ebi-gxa revisions: - - 65c3ec07502b - be019b069e31 + - 65c3ec07502b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_paga owner: ebi-gxa revisions: - - b2768cae00a1 - 6d4f88995e40 + - b2768cae00a1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_pca owner: ebi-gxa revisions: + - 59028945c857 - 0cf90e01d9f8 - 4428dba93375 + - 3ee74b58c72d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne owner: ebi-gxa revisions: - - abdb61e4afa3 - 3fb53f5e46ea + - abdb61e4afa3 + - 181d61d2f3cd + - 8b0d6f6f44c8 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap @@ -199,13 +220,17 @@ tools: revisions: - 767a675b5254 - 0f98603d0116 + - bd4a244faeb8 - ea91cfd0444e + - fe562424a0a6 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - 4cc9362782b4 + - f86b2c3bc459 + - 5605f8452eb3 - e2d0dc8a50ca + - 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 73ec83f07..31eb96f5a 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,56 +2,56 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - a4c13ddcc8ee + - 9edf8894a22d - 29f66c353bcb + - 0f611e7d7858 + - a4c13ddcc8ee - 921a2da49a0c - ed2cca6b5de4 - - 9edf8894a22d - - 0f611e7d7858 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - 5746d61f0a91 + - ec4b948dc6f0 - d404277cc87a - 755df866ad0c - - ec4b948dc6f0 - - 5746d61f0a91 - - 78fb5e286609 - 11de0d28ab30 + - 78fb5e286609 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 11fa44ee0603 - - f72063d9426b - 977dc15add20 + - 11fa44ee0603 + - 03dd3c16ae4e - 9e357a8b2ec3 + - f72063d9426b - 4d511437b1e5 - - 03dd3c16ae4e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 3b5b54ed6392 - 1da5f169b491 + - 0ba4f56a3613 - 77919cc3618e - c3e5e2cf12b7 + - 3b5b54ed6392 - 41dbf4d162a2 - - 0ba4f56a3613 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - f741330d4a71 - - 5308ca68ef3d - 9939786dd9c9 - - b63363075c2e - 7babd8a46fe0 + - b63363075c2e - 12d51d7be66f + - 5308ca68ef3d 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 7849adca6..e3fc944ff 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,213 +2,213 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 0c777d708acc - - 3df9f0a4bf34 - - 699a5e9146b3 - 81f0cbca04a7 - - 8bccb36e055a + - 699a5e9146b3 - 7db4fc31dbee + - 3df9f0a4bf34 + - 8bccb36e055a + - 0c777d708acc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 2436a8807ad1 - 0a53256b48c6 - - 5791a7f65275 + - 2436a8807ad1 - 5bc8cdc17fd0 + - 5791a7f65275 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - 6ad1d3cfdea1 - - 9d47aabda459 - e576b73a2e2f + - 9d47aabda459 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: - - 70316d792fc9 - b1c2c210813c - 77f7159d775a + - 70316d792fc9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - dba87c4b32d3 - d51310ab328a - f70b215d155c + - dba87c4b32d3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - - f3360fbeda64 + - fcadded98e61 + - b07f4839ca77 - 10eed33aa9b2 + - f3360fbeda64 - 85edbb7a436b - - b07f4839ca77 - - fcadded98e61 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: - - 5bf8eb50b280 - b58447a2eed2 + - 5bf8eb50b280 - 664232d2a3f7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - e917a2424690 - eb6c08714244 + - e917a2424690 - 0e4dccaafef5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - 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 + - 670975e92458 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - cdf8e3c57dae - ef4aed1d34c4 - df3ad3ba5c6f + - cdf8e3c57dae tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 6a7da2e5f696 - - 5d28ac336861 - 2484086dee41 + - 5d28ac336861 + - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - bace5a93a97c - - f2ed92b011a9 - 11f177b1a59e + - f2ed92b011a9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - d0178bdcd00e - - f8fa0f6718a3 - f24c370e5ea4 + - f8fa0f6718a3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - - 3245681b2f6d - - 31d195bedf6d - ad271f78a87a + - 31d195bedf6d + - 3245681b2f6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: + - b6eec6087271 - 993faa34333b - 87d4d92d7487 - - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - ff1a86a87364 - - 6100a22bf4f2 - c09dcda1143f + - 6100a22bf4f2 + - ff1a86a87364 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - b178453ea8d1 - 667a513e67e4 - 3a05117669cf + - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity 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 owner: bgruening revisions: + - a32c3f810ade - 91e03287f285 - 20dbb1f7ec7b - - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - 5499dc6f8ac1 - 8536b1ae0254 - b64af54c5c09 + - 5499dc6f8ac1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - d3890df07463 - - e972e07c7845 - 6f4715b8540a + - e972e07c7845 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: - - acf3aa487283 - d85f11570109 + - 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 @@ -220,17 +220,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 48102a685037 - 3a3033222f61 + - 48102a685037 - 8083a87d2fdf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 33f4fa1413fb - 4ecf93628f97 - 27edbb90ab2b + - 33f4fa1413fb tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -242,23 +242,23 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 1fd453cd757b - 972d2c365739 + - 1fd453cd757b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: idr_download_by_ids owner: iuc revisions: - - f92941d1a85e - 4b794652dcdc + - f92941d1a85e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info owner: imgteam revisions: - - f8b4eada923c - - 236ec78b2e53 - 7b6d9412c7f8 + - 236ec78b2e53 + - f8b4eada923c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index c07f7df97..1427db5a8 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -3,30 +3,30 @@ tools: owner: iuc revisions: - f362150bef41 - - 78bbd17d0703 - - d6e72da3ec35 - 3e4f434a69c6 - - 40737febe339 - 1069f6db0a0e + - 3a72fede57ce + - 40737febe339 - e4ee04da1c19 - - a38934e303b9 - e319b5b65879 - - 3a72fede57ce + - a38934e303b9 + - d6e72da3ec35 + - 78bbd17d0703 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 7fe36019c073 - f91cfb73d369 - - fcbeda41d0ac + - c88553ec696e + - 9537184d421f + - 7fe36019c073 - 2b95d5c04908 + - 72ddd32392cd - 0135f1d487a0 - 618297d23022 - - c88553ec696e + - fcbeda41d0ac - 8f8df367470d - - 9537184d421f - - 72ddd32392cd tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked @@ -41,54 +41,54 @@ tools: - name: ivar_removereads owner: iuc revisions: - - 8c05afb547fa - - ee2beb764a7b - ee29337f905c + - 43aac8d29685 + - 5dc33613c288 + - ee2beb764a7b - 7f1cfa4c0e32 - - bd2a7d1316b9 - - 94df24c6bc00 - - 3d18f8c3c0f6 + - 28a6f1908fcc + - 8c05afb547fa - a1c2aecd7a0d - 8d36959b000d - - 5dc33613c288 - 9eaadf03e0df - - 28a6f1908fcc + - 3d18f8c3c0f6 + - bd2a7d1316b9 - 6a1515bb0687 - - 43aac8d29685 + - 94df24c6bc00 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: + - 364f4ffec275 + - 8858fa037a15 + - 5d6ed46cc101 + - 5671e1d3d5ee - cb903c9dc33d - - db536ad45f28 - - e3bb03cf207a - - d37ede8589b2 - - 86a20ae274fc - bcaa0d571ce2 - c092052ed673 - - 5d6ed46cc101 - - 364f4ffec275 - - 8858fa037a15 - - a250929be21b + - d37ede8589b2 - 9f978da6528a - - 5671e1d3d5ee + - db536ad45f28 + - 86a20ae274fc + - e3bb03cf207a + - a250929be21b tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 584beffa972b + - 3b6a16d82c1b + - ed28dd32141c + - e1a015876aa9 + - 12d66d0d05ac + - f95f403841ad + - 49236b03e4fd + - c5c9f02b6167 - 194e3ceee923 - 230b05597996 - - f95f403841ad - - e1a015876aa9 - - 3b6a16d82c1b + - 584beffa972b - 38b91a3190cd - - c5c9f02b6167 - - 12d66d0d05ac - abbc8041e8ec - - ed28dd32141c - - 49236b03e4fd 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 c5e46d293..c40dd66b7 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: - - f198773344e4 - - b8a457820315 - 17e3b698dd52 - 0f1724dd59d2 + - f198773344e4 + - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - ac092723240d - - ba0c40780ecf - - 374cb875d38a - a513e3fbb4c5 + - 374cb875d38a + - ba0c40780ecf - 22c2a1ac7ae3 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 ca8b7279f..7c20d8272 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,99 +2,99 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 772e0e89fc68 - 522137aaa9c4 + - 772e0e89fc68 - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 2af1346e68c9 - - b6ef6d0cb6b7 - - e1317b5502fa - 818f9b69d8a0 - f1b9a42d6809 + - b6ef6d0cb6b7 + - e1317b5502fa + - 2af1346e68c9 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - 1588f9076e32 - - 05143043ca13 - - 947c2eacccb8 - c80db5d6fd8c - 8334dc98c48e + - 05143043ca13 + - 947c2eacccb8 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: + - 25b46af53232 + - 83228baae3c5 + - 1552b8cb4a94 - 9991c4ddde14 - 29e4122c90de - - 1552b8cb4a94 - - 83228baae3c5 - - 25b46af53232 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 841a6cc5fc58 - - f3dfa4bdf87e - 060ca94ac049 - - 1a53edc4b438 + - 841a6cc5fc58 - a07ab242b0b5 - 53616c8b0865 + - f3dfa4bdf87e + - 1a53edc4b438 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - dc4b5fd604a6 - - d4808d5b83da - 40f4447733b2 - 2fc89dcd41c8 - - 927586a18553 + - dc4b5fd604a6 + - d4808d5b83da - 91c4e3331208 + - 927586a18553 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 7626ea9c2e1b - - 25ab6b4e376e - - 36e8d6d5d01b - - e5a5ad882f1f - 301e07345c93 + - 25ab6b4e376e - c6ae57f774c6 + - 7626ea9c2e1b + - e5a5ad882f1f + - 36e8d6d5d01b tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - b7c3e9a3b954 - - 80852884053f + - 0630258dcf35 - 4ed102b922cb - 02d2be90dedb - f9639b488779 - - 0630258dcf35 + - 80852884053f + - b7c3e9a3b954 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 - - 61634a87efc7 - - ec69cbe34b73 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 f096df26c..bab5e04f2 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: - - f6877ad76b00 + - 749c918495f7 + - 937aa69e715f - 0d4acadabb04 - - d5ceb9f3c25b + - 03e9b2fbc005 + - f6877ad76b00 - 17062a0decb7 - - a6d65b0c67af + - cd659e8cc5fa + - d5ceb9f3c25b - 3ba8d4563129 - - 937aa69e715f - - 749c918495f7 + - a6d65b0c67af - 017aba02828d - - 03e9b2fbc005 - - cd659e8cc5fa tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -31,12 +31,12 @@ tools: - name: bwa owner: devteam revisions: - - e188dc7a68e6 - - dfd8b7f78c37 - 53646aaaafef - - 2477830927ec - - 64f11cf59c6e - 3fe632431b68 + - dfd8b7f78c37 + - 64f11cf59c6e + - 2477830927ec + - e188dc7a68e6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: + - e7f19d6a9af8 - 2ff111fac1d7 - 37b497aa133f - - 60afcc2c1d05 - 3e1ea2facca6 - - e7f19d6a9af8 + - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: + - 5cc34c3f440d + - c0c2d0941de8 + - 09b53c1d4ab1 - 6b1e195506a3 - 037c6e54df11 - f54f5baedfdd - - 5cc34c3f440d - - 8c6cd2650d1f - - 77b2770508f6 - 53c0b7a1a0c3 - - be1d967337e4 - - 3f4d6399997b - b3eab4b67562 - - 09b53c1d4ab1 + - 77b2770508f6 + - 3f4d6399997b - 11a0d50a54e6 - - c0c2d0941de8 + - 8c6cd2650d1f + - be1d967337e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - 42ce70172b72 - - 00fbfac99d39 - - 79b885ce78d7 - - 1cd2511a396e - 9ee34ba73ebf + - 79b885ce78d7 + - ec9cbd6b9a49 + - 13022c3d3076 - 45795f582ae9 + - 1cd2511a396e + - 00fbfac99d39 + - b8f5f6e87f5c - 178bdbdb6d24 - 5ef7ec16b04f - - ec9cbd6b9a49 - - b8f5f6e87f5c - e403d27e8f24 - - 13022c3d3076 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/staging.gvl.org.au/metabolomics.yml b/staging.gvl.org.au/metabolomics.yml index 618d9d7cd..8f6f2ec58 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -89,61 +89,53 @@ tools: owner: recetox revisions: - a5d41764722d - - 1d10d32fa3b3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_convert owner: recetox revisions: - - 9e83636da9d3 - b9cc12600553 - - c990df6afc24 + - 9e83636da9d3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering owner: recetox revisions: - - a177ac3c752c - - 00e66c401366 - 83c4b4359ac4 + - a177ac3c752c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity owner: recetox revisions: - fd890f162ce6 - - d7b517f2c5fe - 84af792d3a78 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter owner: recetox revisions: - - a5a5b147da70 - - 9e3c83d2afc3 - 1b09315a3f87 + - a5a5b147da70 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export owner: recetox revisions: - - b576ed720711 - - f04610d25411 - 8832425b1ff6 + - f04610d25411 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match owner: recetox revisions: - - 330b0dfae8da - - 1d443ed476a1 - 03bc9b7f40f6 + - 330b0dfae8da tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge owner: recetox revisions: - - 84ead993862c - 1fd950c5586a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -152,13 +144,11 @@ tools: revisions: - 8147d93d372d - f04b378325e5 - - 1d74ae228df3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key owner: recetox revisions: - - 9d1b01d3fedd - fbdb2ae524df tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -166,7 +156,6 @@ tools: owner: recetox revisions: - d50ce2f51fc0 - - fbe335d27d25 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_similarity @@ -180,14 +169,12 @@ tools: revisions: - 9ff95a1a2705 - 7ba589b01dbc - - 7627b40601f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split owner: recetox revisions: - 0cf68b536cd1 - - 500f473df7e4 - ea6c5636c0cf tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -195,7 +182,6 @@ tools: owner: recetox revisions: - 5bbd1a8404f5 - - 6d2f2c565431 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metams_rungc @@ -270,74 +256,74 @@ tools: - name: recetox_aplcms_align_features owner: recetox revisions: - - 7b42ee54d757 - - ec196e27a61a - 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: - - f3a18e020cdd - 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 - - 50b9918aeff2 - 481d769e2f7a + - 50b9918aeff2 - 134be5abb208 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 - - 30bf4e35da3e - - 501a232f3cd5 - 9064aecc78a7 - - a82db010c53e + - 501a232f3cd5 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - 89178a72388a - b3413f335327 - - b341cfd4baf8 - e7305ba0dd38 + - 89178a72388a + - b341cfd4baf8 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - cf061712a184 - b7c8a44b9cc1 - 17a48d0a80f4 - dd7bbc2b99d1 + - cf061712a184 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - d7f5878a98c3 - - 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: - 7acd11ddc061 - - d90187b0f247 - ea0758b41473 + - d90187b0f247 - ffbabefbd2e2 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -350,8 +336,8 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 2c6fa447f6a0 - 6b5dec818827 + - 2c6fa447f6a0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature @@ -401,7 +387,6 @@ tools: owner: recetox revisions: - b3d41b1fcb18 - - e0cac9994a72 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: w4mclassfilter diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index 91f9d36d6..68c8d73e1 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -8,9 +8,9 @@ tools: - name: cat_bins owner: iuc revisions: - - 0094893f5001 - 18676df0cb3a - 0e63d03c8790 + - 0094893f5001 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -22,8 +22,8 @@ tools: - name: cat_summarise owner: iuc revisions: - - a8216def322b - 7f1aaa1932d8 + - a8216def322b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -95,69 +95,69 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 76d3d2b10738 + - 65db807336bc - 5b5a7af9fbb4 - - 63f86089423e - 7c2100246a2f - - 65db807336bc + - 63f86089423e + - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 18a502a9d287 + - 96336c6a2bb7 - 00f5005840fa - 1c35dadbe76f + - 18a502a9d287 - 84fd33a60b35 - - 96336c6a2bb7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: + - a9f4a217dcd6 - f732237754fc - addaf9d22850 - e8fba04706d3 - 34e55239e68b - - a9f4a217dcd6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - 04c15826a0b8 + - 75403243703a - 5fe3edf19b9c - - 8c202e741d68 - 0776d824d896 - - 75403243703a + - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - e96bbb9e24ea - - 1c9b3bcd4261 - - 8470de786d47 - 43c99742158b + - 8470de786d47 - 75c8945b0da2 + - e96bbb9e24ea + - 1c9b3bcd4261 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: + - 1d75bd0595e2 - 306a40d4bb8f - 35176674168c - - 5c865a382933 - 84743da21318 - - 1d75bd0595e2 + - 5c865a382933 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: + - 8daf4564ccda - 555ccac8a4c5 - 32c9ea835770 - - 8daf4564ccda - ac72310b038a - 78faebd0879c tool_panel_section_label: Metagenomic Analysis @@ -165,66 +165,66 @@ tools: - name: dada2_plotqualityprofile owner: iuc revisions: - - cae017b76acb - - f947b4bb5107 - - a58e4a43f49c - - 7b8cb2b02978 - d60df8727f59 + - 7b8cb2b02978 + - a58e4a43f49c + - f947b4bb5107 + - cae017b76acb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 073608a50ac3 - - 7f3b59dee073 + - 1bc3657cd694 - 04144473e59e + - 073608a50ac3 - 7136e9ab70db - - 1bc3657cd694 + - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 9058d8943303 - 0a1224c4b781 - - d943081510da - - 19299bb1c6af + - 9058d8943303 - a7817705348e + - 19299bb1c6af + - d943081510da 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: - - c4db8c4de66f - 4d9445dff47b + - 5c7ba3d85a01 + - c4db8c4de66f - f8f56dd6449f + - 65d52c693b8e + - b907a3c0434f - dbf1798c0dcc - a68b985913ab - - b907a3c0434f - - 5c7ba3d85a01 - - 65d52c693b8e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 213df31ba341 - 15dbb444df71 + - 213df31ba341 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: - 6c84982ee6f7 - - 654548ae1357 - 6d364c65c946 + - 654548ae1357 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -237,8 +237,8 @@ tools: owner: iuc revisions: - bd7a9c6efb10 - - e66ab198ec15 - 6aad8ca3918b + - e66ab198ec15 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table @@ -253,8 +253,8 @@ tools: owner: iuc revisions: - 9704f1a3b32d - - 7f208f1eb64f - cad93abecac9 + - 7f208f1eb64f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -272,8 +272,8 @@ tools: - name: humann_barplot owner: iuc revisions: - - 5fea25ee6275 - 523ae8314ef5 + - 5fea25ee6275 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_join_tables @@ -286,40 +286,40 @@ tools: - 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: - - 79706f10d680 - - c409a495841f - 31c6d107e7a5 - - 8237a0f225db + - c409a495841f - e88b731dad59 + - 8237a0f225db + - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 094ad9c068af - - aabf8cfb8fef - 71ea608ddfa3 - - 172920f67a84 - 714d5a28cc5c + - 094ad9c068af - d24841f5c3d2 + - 172920f67a84 + - aabf8cfb8fef tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - a293a742194f - d7e9a3c41657 - - 2bdd84912a2b - - 4137b492233e - 12fb63b5f63f + - 2bdd84912a2b - a4d7148ccee4 + - 4137b492233e + - a293a742194f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -331,20 +331,20 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: + - 64bc7acc22a9 - a92c06a3afa7 - - 75bedfb2078b + - 6fcb8ac37a3e - cf87759761eb - - 97f7bb0851e7 - - 64bc7acc22a9 - e2c71b852aba - - 6fcb8ac37a3e + - 75bedfb2078b + - 97f7bb0851e7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - 81c5dd1c777f - e9d12c223a80 + - 81c5dd1c777f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler @@ -356,22 +356,22 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 5e5a999ffaa9 - 2d35528d2141 + - 5e5a999ffaa9 - 080ea153677c - - 4033827c76b8 - 4e5e73d03f0d + - 4033827c76b8 - c82508e76ad1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - fc6c328c292f - 95bf7479d53c + - 6b7622dda516 - 2cd76b089570 + - fc6c328c292f - c2803012bbb3 - - 6b7622dda516 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -389,15 +389,15 @@ 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 owner: iuc revisions: - - 65b382bf9b7c - 385a965c6f87 + - 65b382bf9b7c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution @@ -424,8 +424,8 @@ tools: - 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 @@ -438,8 +438,8 @@ tools: - name: khmer_normalize_by_median owner: iuc revisions: - - 4d23ab83ea29 - b1fe2ef3d244 + - 4d23ab83ea29 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition @@ -459,16 +459,16 @@ tools: owner: iuc revisions: - 4a9da2b6c2e3 - - 328c607150ff - cdee7158adf3 - 20e2f64aa1fe + - 328c607150ff tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax owner: devteam revisions: - - f03c7ba8d8bc - 50bd98b3ae5a + - f03c7ba8d8bc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -480,8 +480,8 @@ 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 @@ -541,16 +541,16 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 02bbace216f2 - 2deaada69b14 - 88d274322340 + - 02bbace216f2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa owner: iuc revisions: - - d33cf727ed94 - bb96a1e6583d + - d33cf727ed94 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: lotus2 @@ -580,12 +580,12 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 4fd3b5d8706b - 327d9f4cc95f - 27250f92a01a - 2cff76cf35c6 - - e073891b2afc + - 4fd3b5d8706b - 7f5d7b0e9884 + - e073891b2afc - 3cc4a60615c0 - 0270541aaf46 tool_panel_section_label: Metagenomic Analysis @@ -593,9 +593,9 @@ tools: - name: metabat2 owner: iuc revisions: - - 76bc4efa1aeb - 708abf08a626 - eb50e7eca3dc + - 76bc4efa1aeb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -668,19 +668,19 @@ tools: - name: metaphlan owner: iuc revisions: - - 2131d7dca455 - - ff8f55893e7d - - b89b0765695d + - a92a632c4d9b + - 1a037928504c - ec368db926f4 + - 6dee4abadccb - fd69c607b43f + - 740fd2d16a28 + - 1a6cdf55390f - 289b3807e80c + - b89b0765695d + - ff8f55893e7d - a16313517e55 - - 1a037928504c - - 1a6cdf55390f - - a92a632c4d9b - - 740fd2d16a28 + - 2131d7dca455 - ef65b083bd0c - - 6dee4abadccb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -718,8 +718,8 @@ tools: - name: picrust2_hsp owner: iuc revisions: - - 6eafc1e01a8c - 3b133b8d578a + - 6eafc1e01a8c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline @@ -732,15 +732,15 @@ tools: - name: picrust2_pathway_pipeline owner: iuc revisions: - - 6077821e8ae7 - f53beb324696 + - 6077821e8ae7 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 @@ -753,8 +753,8 @@ tools: - name: picrust2_shuffle_predictions owner: iuc revisions: - - 881f2faa5fe7 - 677f3c8db525 + - 881f2faa5fe7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -766,8 +766,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 0ba7dfaa941d - 8e2ac1b8f70a + - 0ba7dfaa941d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -785,8 +785,8 @@ tools: - name: picrust_normalize_by_copy_number owner: iuc revisions: - - 2e62e32d4f33 - 65e5f9caefcc + - 2e62e32d4f33 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_predict_metagenomes @@ -823,19 +823,19 @@ tools: - 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 - 2fd4d4c9c5c2 - - 4d83eccf5f81 - 3b22de20bd4b + - 4d83eccf5f81 - be818ae858e4 - 141afacabcfa + - 4b9a8031ab74 - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -866,8 +866,8 @@ tools: - name: vsearch owner: iuc revisions: + - 576963db5f1b - b3c7199d8786 - 9495df9dd6ef - - 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 63fd21d8b..334c2c5c3 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - e866e31f6da3 - 67cb43432196 + - e866e31f6da3 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 2344ed181ae6 - 72be09dfd803 + - 2344ed181ae6 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index 9012b1e89..7fc9bd788 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: - - 098506c54016 - 9baa871cb1d1 - - 94b8c6013083 - - 2263989660f5 - 80f03df2e2ce - - 48c13389050d - - cd07731e4434 - - bdfbaf0c10aa - - 6ae5a7b5a0a2 + - 9422c5a87ee2 + - 2263989660f5 - 8b67dd48fec1 + - 098506c54016 - a74dbfee5a86 - - 9422c5a87ee2 - 9eeb13a92d79 + - bdfbaf0c10aa + - 6ae5a7b5a0a2 + - 48c13389050d + - 94b8c6013083 + - cd07731e4434 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - aaa0d6a8b808 + - fc2e49f91e52 + - 2e093badc689 + - bc3831dd65c1 + - c18157c68134 - 3ff17bad4006 - - f0af8936ed41 + - d390fe1567dc + - aaa0d6a8b808 + - c44f824c051a - be78f13134e2 - - '764845535798' + - 4a60927aaca5 - 5abf2c2249aa - d7ce0ec78e51 - - bc3831dd65c1 - - d390fe1567dc - f14193ec1f50 - - c44f824c051a - - fc2e49f91e52 - - 4a60927aaca5 - - c18157c68134 - - 2e093badc689 + - f0af8936ed41 + - '764845535798' tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -53,8 +53,8 @@ tools: - name: clustalw owner: devteam revisions: - - 5b097fde95dd - d6694932c5e0 + - 5b097fde95dd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -67,14 +67,14 @@ tools: - name: mafft owner: rnateam revisions: - - 8e649f27aa0d - - 15974dd17515 - - 6f28e90db932 - f0d493f8f84f - - f1a5908ea2cb + - c5908940967d - a65296ffb4a0 - bf28a8cff401 - - c5908940967d + - f1a5908ea2cb + - 15974dd17515 + - 6f28e90db932 + - 8e649f27aa0d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter @@ -88,40 +88,40 @@ tools: - name: mummer_dnadiff owner: iuc revisions: - - 5561a1193611 - - c9685bc0407c - 60698466facd + - c9685bc0407c + - 5561a1193611 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - 57f042937ba7 - - 48823c9635a4 - bcd65de9725b + - 48823c9635a4 + - 57f042937ba7 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - ebe3b0f84de9 - - 4fc0cb2ac8ae - fb43e8887350 + - 4fc0cb2ac8ae + - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - 7cd7a55a678d - - e18267f90096 - 636b049e6141 + - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - cf3c9489c088 - - 959c1f8dae95 - b4124df98b26 + - 959c1f8dae95 + - cf3c9489c088 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 3b17aceb2..afb02ed16 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,11 +8,10 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 18a8d140ec6f - 7c47b3c9e493 - 28928576e1ea - 9aa9d92c3c51 - - 1145758d2f0b + - 18a8d140ec6f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado_trimming @@ -25,9 +24,8 @@ tools: owner: galaxy-australia revisions: - 6942f170cc43 - - fc5b6491cf78 - 63d8ecfcfab1 - - 090ab4f31074 + - fc5b6491cf78 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: guppy_basecaller @@ -39,21 +37,21 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - fc8804320156 - - a7228a7ea146 - - 0e9e7fcdd543 - cb34f00cc10f + - a7228a7ea146 + - fc8804320156 - 79e9a869f40e - 72b5e9dda577 + - 0e9e7fcdd543 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - db25ec99c3ea - - 18505fe2bdb1 - - d6cddc06aeae - fa11aa8103b2 + - d6cddc06aeae + - 18505fe2bdb1 + - db25ec99c3ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -65,22 +63,22 @@ tools: - name: medaka_variant owner: iuc revisions: - - 19f3b583a9b3 - cc36773a3681 + - 19f3b583a9b3 - 43815fa60f3a + - 222669c4afb6 + - ec699520444c + - edf6d4003fad - 0f5f4a208660 - eb746fa6f514 - - edf6d4003fad - - ec699520444c - - 222669c4afb6 - 2bf63b38ee9b tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - b833eff63b10 - c0fb573c1e8d + - b833eff63b10 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -92,60 +90,60 @@ tools: - name: nanoplot owner: iuc revisions: - - 0f1c34698076 - - a02b8b3f5a0c - a3c4fe6f49ab + - a02b8b3f5a0c - 645159bcee2d + - 7b379e98b9a9 - edbb6c5028f5 + - 0f1c34698076 - a38bdcec9e4c - - 7b379e98b9a9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 3b6f94fc7e1d - d219b6d8158a - 85a394edc247 + - 3b6f94fc7e1d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - be95355fef8d - - 90a922f32523 - a8d4be409446 + - 90a922f32523 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 4857d5bcce52 - 449e9aeded2d - d376944466bf + - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - de5b3d8f5b90 - - a3afc5f0a96c - bec636361cfd + - a3afc5f0a96c + - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 543cbeef3949 - - 93d623d9979c - 5f76b20953e5 + - 93d623d9979c + - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - daf8518d243a - 1d835c691480 + - daf8518d243a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -170,8 +168,8 @@ 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 @@ -183,15 +181,15 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 626b6c2be5c2 - 2e22ebec211a + - 626b6c2be5c2 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 @@ -221,8 +219,8 @@ 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/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index 18896dfe2..50c6a706d 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -28,8 +28,8 @@ tools: - name: bcftools_plugin_frameshifts owner: iuc revisions: - - 96d2000977ab - 58341ad4fb42 + - 96d2000977ab tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -44,6 +44,12 @@ tools: - 344ac3ca7557 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu +- name: checkm_taxon_set + owner: iuc + revisions: + - 407e50329077 + tool_panel_section_label: None + tool_shed_url: toolshed.g2.bx.psu.edu - name: compose_text_param owner: iuc revisions: @@ -59,18 +65,18 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - 3e73c97f025d + - adfd6bf710bd - d74850cf4e42 - 97b1b5ad1cda - - adfd6bf710bd - baceff842902 + - 3e73c97f025d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 1586b111d2a3 - 9dd107db92c2 + - 1586b111d2a3 - 83da94c0e4a6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -83,12 +89,12 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - edacc4bcd3cb - - 1e34d2e3d285 - e4b4837f06f5 + - 1e34d2e3d285 - e9ee4d074d5d - - 2f27f3b86827 + - edacc4bcd3cb - ed1518ce2237 + - 2f27f3b86827 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -107,16 +113,16 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 74af283d8ebd - 472dabcb03bf + - 74af283d8ebd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_dada2 owner: iuc revisions: - - 38ccd4589990 - - 5711fc06a63e - 48a42ca61006 + - 5711fc06a63e + - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -129,8 +135,8 @@ tools: - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - fcb8bdd124f4 - 81a286e4c5a2 + - fcb8bdd124f4 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco @@ -143,8 +149,8 @@ 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 @@ -163,10 +169,10 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 5bcf0e24f42c - - b4b2b284230a - 27a6a256cd23 - 172815da3d41 + - b4b2b284230a + - 5bcf0e24f42c tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -193,8 +199,8 @@ tools: owner: iuc revisions: - 87febc68b45b - - 19bbd19b74b3 - fea85c467896 + - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -226,35 +232,35 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 5fe20c915fa6 - d8dc037e3c13 - 4ba60cb14cb0 - - 0cb27ea69dc1 - 2c61c30a57e7 + - 5fe20c915fa6 + - 0cb27ea69dc1 - 9c43baa60906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - d9339bb8127e - 14785f8a3725 + - d9339bb8127e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite owner: iuc revisions: + - 0db22932bc39 - 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 - ed7a967cb11b - - 6e24e79d3d69 - df30a2f1db55 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -273,9 +279,9 @@ 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 @@ -294,9 +300,9 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - d63c1442407f - - c520a52b5174 - 64deddb6a8ec + - c520a52b5174 + - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder @@ -1068,8 +1074,8 @@ tools: - name: rdock_rbdock owner: bgruening revisions: - - e4b7d1507a75 - a22969b08177 + - e4b7d1507a75 - c362398df83b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -1082,10 +1088,10 @@ tools: - name: salsa owner: iuc revisions: - - 9a22227bb6d0 + - ba7b0f11e470 - f77f7a7f3b83 + - 9a22227bb6d0 - 58a870ef434c - - ba7b0f11e470 - ab5b7f6b7198 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index 0b1a23a3e..782923f20 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -39,64 +39,64 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 5a7c56a5cc08 - - 3b8b5bde0bd9 - - 6a457678efcb - 8834daeb9892 - - f73435dc282b - - d7c7ef3353fe - - 81e66674859e + - 3f59ebfbfe3d - a6619171428e + - c78f3d7dd1db - f04a1264e2a2 - - 107d3ba7024a + - 3b8b5bde0bd9 + - 6a457678efcb + - f73435dc282b - '841557158611' - - b89cac5156ec - - 3f59ebfbfe3d - d033ffc1c161 + - d7c7ef3353fe + - 5a7c56a5cc08 - cce7b18495e4 - - c78f3d7dd1db - 26de3a7b1cb9 + - b89cac5156ec + - 81e66674859e + - 107d3ba7024a tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 4755f52427c4 - - 6223845127ea - - 02b8758214b0 + - 659517798cc4 + - a185b079b095 + - aa8cc71438cf + - b0af57c1a968 - 88c4aa435ded - - 5b777002c2de - 5fcd1ece3a6e - - b0af57c1a968 - - 659517798cc4 + - 4755f52427c4 + - 5b777002c2de + - 02b8758214b0 + - 6223845127ea - df47d4845b62 + - e75442c7f4da + - 6283babe736e - 7a2092844346 - 6a726db04d4b - - aa8cc71438cf - - a185b079b095 - 3b96e92e8ec3 - - 6283babe736e - - e75442c7f4da tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - f97743d52b87 - - 70acec670c30 + - b8476e82ac20 + - 111bd54f6bc4 - f87ac61981f0 + - 70acec670c30 + - d1c340a5664b - 24d024316465 - - b8476e82ac20 + - f97743d52b87 - 524d31add34a - - d1c340a5664b - - 111bd54f6bc4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - daddf188c13f - 9e10ba792be2 + - daddf188c13f - feb40665d7cd - 4f6349228462 tool_panel_section_label: Phylogenetics @@ -110,26 +110,26 @@ tools: - name: pangolin owner: iuc revisions: + - ca337cce3888 - ca0d8cf80567 - - 83a69484cb87 - - 5f8727ff21e7 - - 9d61d3fa046c + - 2fa9d4f1b48f + - a2099fb98cdb - 81804a978fc0 + - 9d61d3fa046c - b7e297c2ede6 - 2f1019071464 - - a2099fb98cdb + - 7bb8726be37c + - 03ed9524dcd1 - abf6dbe8c9d7 - - 2fa9d4f1b48f - 437e28791761 - - 36912871ccdc - - 14ae456b8cc5 - b6abccb1f25b - - 42a174224817 - 3a43c3982401 - - ca337cce3888 - - 7bb8726be37c + - 83a69484cb87 + - 36912871ccdc + - 42a174224817 + - 5f8727ff21e7 - 8ad84c5753ea - - 03ed9524dcd1 + - 14ae456b8cc5 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: - - 29ff6a849eac - - 73a469f7dc96 - ea30d3089354 - - a4b71be30c3c - b1e68bbe4cef - ba29b5e2a4be + - 29ff6a849eac + - a4b71be30c3c + - 73a469f7dc96 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - f1ccc8a6eb05 - - 15ac71df11a0 - - 91887494eb97 + - dbe2b2204555 - 809e42326fc2 + - f1ccc8a6eb05 - e88a7de55d6e - - dbe2b2204555 + - 91887494eb97 + - 15ac71df11a0 - 9b2b122d0415 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 9362d244a..838833e9a 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: - - f9242e01365a - - 3f254c5ced1d - - fc288950c3b7 - - 881d7645d1bf - - 7d34178f2812 - 1aac2a13842a - - f6ced08779c4 + - f9242e01365a - a1f0b3f4b781 + - 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 8905b4dcc..c4bd122ea 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: - - 7fbec959cf2b - - ca90d17ff51b - - 5b85006245f3 - - eb085b3dbaf8 - - e7f1b552a695 - - 6ab1a261520a - 2f7702fd0a4c - d00e15139065 - - c0e71cb2bd1b - - 3f188450ca4f - - 3bd420ec162d - e4a053d67e24 + - eb085b3dbaf8 + - 3f188450ca4f + - ca90d17ff51b + - e7f1b552a695 - a58f7eb0df2c + - c0e71cb2bd1b + - 3bd420ec162d + - 7fbec959cf2b + - 5b85006245f3 + - 6ab1a261520a 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 d3760e343..a056eeb68 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,94 +2,94 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - 277dc652246e - - 4c177985028a + - f28ad96b76dc - b18329a8ac14 + - 4c177985028a + - 277dc652246e - 0a18ac48ac53 - - f28ad96b76dc - - ece627528a78 - b574b84afc4d + - ece627528a78 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: + - b41107d8fe89 + - e988563cc6e5 - a9a28e46d54a + - e215f71d7983 - 525f201b86c1 - bf06d196e23d - - b41107d8fe89 - - e215f71d7983 - - e988563cc6e5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - bb6397b94018 - 56da27be956a - 8da3511c9467 + - bb6397b94018 - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - b8c79e70516d - - f23d67e28cc8 - - 528fb09022be - - 890845926d4b - a8157342d9a3 + - 890845926d4b + - 528fb09022be + - f23d67e28cc8 + - b8c79e70516d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 59e85306eae5 - - ae304a72db7b + - a69865da6f80 - a95a82eb4d50 + - ae304a72db7b - 80600735685d + - 59e85306eae5 - 25b83cbd596a - - a69865da6f80 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - ed9ed1e6cca2 + - 611d80c0e29d - f1897eb07081 - - 83aac7741200 + - ed9ed1e6cca2 - e0669b1854b1 - - 611d80c0e29d - 798da6bdff3d + - 83aac7741200 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 5a35e3a8d013 + - 74b61bf5bc4b - a7fb9b395ddf - d426a9107a6c - - 74b61bf5bc4b + - 5a35e3a8d013 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: + - cc430977c8ff - 82f6c2f4332d - 91f0f5922011 - df2187f9013b - - cc430977c8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - ba92b59cd529 - - c5aa9fca18c6 - 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 - - ff8c9e0e8a7b - - ae4dc0c041f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -122,31 +122,31 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - d263296cd73e - d0ea7589e95f + - d263296cd73e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: - - 4081e4faa4ab - - 0fa397f4f40b - 1c5cbf8f79ce + - 0fa397f4f40b + - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib owner: galaxyp revisions: - - fb192dd6658a - 36880dfd9fa7 + - fb192dd6658a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut owner: galaxyp revisions: - - 0d2e93e01e68 - - d6a4dfdad269 - ce1a157a41bd + - d6a4dfdad269 + - 0d2e93e01e68 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -158,8 +158,8 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - 160538a890a6 - d286ff4600dd + - 160538a890a6 - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -173,22 +173,22 @@ tools: - name: maxquant_mqpar owner: galaxyp revisions: - - 3fc2116ac6d9 - 9cb7dcc07dae + - 3fc2116ac6d9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - 9c52362ae7bb + - 837224ad1694 + - f522c08e900c - 7f432d87c82c + - 1f39c833f65f - 4d17fcdeb8ff - - 837224ad1694 - 37d669de2828 + - 9c52362ae7bb - e42225f8a659 - 97a7f34fcb6a - - 1f39c833f65f - - f522c08e900c - 2133b0be850a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -203,53 +203,53 @@ tools: revisions: - 85b8866f06d7 - 0ed07016d668 - - a72ac2c7cc5b - e63db1aa82ee + - a72ac2c7cc5b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - 990b4560ead7 + - 352b37c66d97 - 1974224d63c2 - 767c1d761aaf - - 352b37c66d97 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - deaf035bbe9f - - 99450519d727 - 4f359549383c + - 99450519d727 - 35cc7ca0bdc7 + - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - 06f6826d380c - e79958768a2c - c1343e3389ca + - 06f6826d380c - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - d2eac53666f0 - - d46d64e7964d - b9d453dca8d3 - da986f83631b + - d46d64e7964d + - d2eac53666f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 1199751329b0 - - 8bd7734309f6 - 9bf325045235 + - 8bd7734309f6 - 944b43462104 + - 1199751329b0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -262,17 +262,17 @@ tools: - name: msconvert owner: galaxyp revisions: - - 6153e8ada1ee - ab6c14374bc0 + - 6153e8ada1ee tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstats owner: galaxyp revisions: - 8212e342e482 - - de7593c29499 - - 28434abe6c5c - 593839e1f2c3 + - 28434abe6c5c + - de7593c29499 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -285,10 +285,10 @@ tools: - name: openms_consensusid owner: galaxyp revisions: + - f4be248c3d47 - 4e77b8f12cd3 - 01dbaf6a57e0 - 8960fb791701 - - f4be248c3d47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -304,91 +304,91 @@ tools: revisions: - 6ccbf9a2072c - 518b1730cf2a - - c9eff69a7c62 - 9cdf15d3cfc8 - f7fef900f5b2 + - c9eff69a7c62 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - ca88bd28f116 - - dff6c756eee5 - - 5e948629bc73 - 9876bda3ec53 + - 5e948629bc73 + - dff6c756eee5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 41859bbdc16e - 658494a2cb00 - - 1595601708ec - 890025d6e426 + - 1595601708ec + - 41859bbdc16e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 6634cad7d797 - 5ad0b5bf1deb - 9b7977080f6d + - 6634cad7d797 - 2a93a25f0599 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: - - 52ba9695e752 - - 5ad830edc021 - - febd569ad26f - 4af67edd5aef + - febd569ad26f + - 5ad830edc021 + - 52ba9695e752 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - b2fc8da99bcc + - 39e8fde08881 - 92352a475eed - 27cba4c5fc42 - - 39e8fde08881 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 0efbc235f314 + - 9e26f5c770f8 - d413dc49d650 + - 0efbc235f314 - d3546bb9fd8e - - 9e26f5c770f8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 8a04ed1c1d1b - - ca1740533b59 - 3720e349ba2a + - ca1740533b59 - c28f13cab67a + - 8a04ed1c1d1b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - a5d785af0ad8 + - c427a8628cbe - ca799a7246e7 - - 382cde407f81 + - a5d785af0ad8 - c55dddc5844a - - c427a8628cbe + - 382cde407f81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper @@ -403,11 +403,11 @@ tools: - name: openms_idmerger owner: galaxyp revisions: - - 8d4db262964c - - 18f93351f8b6 - - 34e7afee141d - f817513840a9 + - 34e7afee141d - 1c5f31b8d632 + - 8d4db262964c + - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability @@ -415,32 +415,32 @@ tools: revisions: - 986e03d3201e - 111c3a00136d - - c69f69d7867a - 5d9f175dff81 + - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: + - 0e52c85f3b15 + - 476b5e296979 - 4204882495f2 - be74a8cd7d66 - - 476b5e296979 - - 0e52c85f3b15 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter owner: galaxyp revisions: - - 9866e1170611 - e133b5c8878f + - 9866e1170611 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - a407b6790342 - - f5ec766d80cf - c18d8efa4474 + - f5ec766d80cf - 2b2a7551a857 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -448,33 +448,33 @@ tools: owner: galaxyp revisions: - d0304fb829c0 - - 4e66c4e73909 - 021fdb80f204 + - 4e66c4e73909 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: + - 2735db4dd8d9 - ee860980edc6 - 8098330f6d91 - bf32e0bcf554 - - 2735db4dd8d9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - 08488066d588 - - 0ced5bc9f4dd - a2a6e9551046 + - 0ced5bc9f4dd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: + - de7a553552a6 - 2a9ff56cb279 - 8c01da82292c - - de7a553552a6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring @@ -488,84 +488,84 @@ tools: - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 9f505cd4428f - 496cf619e311 + - 9f505cd4428f - f861ec9fbe59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - d4396637b9f5 - - 0bddef8d144e - c99d5004b74f + - 0bddef8d144e + - d4396637b9f5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 05ec9fb05ed1 - f82b320ceb90 - f9ed7e074900 + - 05ec9fb05ed1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 6e8cc5ed2a9b - d31426ef20f6 - 18826fb8e5db + - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - 2aebe58de46e - - bc63b4d12779 - 4a7b96835140 + - bc63b4d12779 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: + - decc397c3b7e - 3d8d4ada5405 - 6b01678ec2fc - - decc397c3b7e - 5ae104d0da6e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - e039cc5c7aed - - 5182338d5e7c - d6aca689dd48 - - dd173849c3d8 - 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 - - 43b9ed22e8ce - dd71e020e2aa + - 43b9ed22e8ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter @@ -579,25 +579,25 @@ tools: - name: openms_xmlvalidator owner: galaxyp revisions: - - 78c080d36945 - - ad2ba3a95a02 - 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 + - 7f6a1f27553e - fb52e95a370c + - c8b225c69a7f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - 073a2965e3b2 - a6282baa8c6f + - 073a2965e3b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pepquery2 @@ -616,14 +616,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - a72c48001f7c - - 07ff622ec007 - 3ec27b4cee7c - - 3634c90301af - - 7fdd9119cc4f - - 1beff3ddce58 - 943a34df6047 + - 07ff622ec007 + - 1beff3ddce58 - da885ca16cb2 + - 3634c90301af + - 7fdd9119cc4f + - a72c48001f7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -683,10 +683,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 1a5690a5eedc - 12692567c7f9 - - a371252a2cf6 - 265c35540faa + - 1a5690a5eedc + - a371252a2cf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/staging.gvl.org.au/qiime_2.yml b/staging.gvl.org.au/qiime_2.yml index bf015d3f9..52697721b 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: - - 10447a4b0cc3 - 18c6b2b6740f + - 10447a4b0cc3 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 f7de839fc..14c3a2994 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - cd5f98911089 + - e345aadf914f + - 2f1d464ebfd2 - 110a346daf36 - 289b7d6b69a4 + - cd5f98911089 - 42201b90e3f4 - - 2f1d464ebfd2 - - e345aadf914f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -19,11 +19,11 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - 42d9087b4789 - - 8501601a118d - - c207119ba5f6 - 0cd2df8af811 + - 42d9087b4789 - fcce77c09289 + - c207119ba5f6 + - 8501601a118d - 0345dbaaa79b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: + - 89eb29319bf4 - 405a212b32ab - 04db7fd6b238 - - 421c33b8bf17 - - 33486216eec0 - ad5ab22ffe24 - - 89eb29319bf4 + - 33486216eec0 + - 421c33b8bf17 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 - 1d839ead7ad3 - - eb784fa07f80 - 7370bb65bad4 - f6e91108b7b1 + - eb784fa07f80 - 7b72fde3d27e - - fa51dc5e8386 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -73,8 +73,8 @@ tools: - 3d70c2996730 - 1544278c272e - 8a55d29c8fcf - - a3e86cd9cac7 - d30e36c48c93 + - a3e86cd9cac7 - c9b77ced9a78 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -88,11 +88,11 @@ tools: owner: iuc revisions: - e2db212d64ad - - 887cf585cafc - - 564c33e5c3e3 - 7b881f5f5ad5 - - b242deb58952 - a5969aa9347e + - 564c33e5c3e3 + - b242deb58952 + - 887cf585cafc tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -105,10 +105,10 @@ tools: owner: iuc revisions: - e897c74a48bb + - 9a171f9a450b - bd5ff77e2036 - - b4bab607eb05 - 8cff84759bf6 - - 9a171f9a450b + - b4bab607eb05 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad @@ -121,11 +121,11 @@ tools: owner: iuc revisions: - 6dafad990086 - - 33f0793edf93 - - 887e0991eb24 - - adc7a7610d4f - - 5e10f396979e - 4f65e343ecdf + - 5e10f396979e + - adc7a7610d4f + - 887e0991eb24 + - 33f0793edf93 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 - - c5d7050e4ad7 - 97575d01f06b - - 17d39bf0a63a + - c5d7050e4ad7 - 43e3eeb2e0ec + - 17d39bf0a63a + - 4e280b27a831 + - c287418eb288 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -156,9 +156,9 @@ tools: revisions: - a819ec3b362d - 0b8c84a7fdb5 + - 9586f08634c0 - d9bf483266a1 - cd034465d4a4 - - 9586f08634c0 - 09b8edb56d80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -171,12 +171,12 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: + - 69842dd5aa48 + - 95351dd0fd3f - 2645575d1bf2 - - a9c34a289493 - a4b4bd84f69e - bf0e43ab0416 - - 95351dd0fd3f - - 69842dd5aa48 + - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - bb0475c884ff - - 912f904a6e1e + - cfb504394ae1 + - 8a35a3bc6752 - d033e1ccb386 - d1fda11e602f - - 8a35a3bc6752 - - cfb504394ae1 + - bb0475c884ff + - 912f904a6e1e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -236,8 +236,8 @@ tools: owner: iuc revisions: - d504d945a655 - - d1fad35bdb4a - 95286af4139b + - d1fad35bdb4a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index edfd9a1ab..6123428ca 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,8 +2,8 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 7acb00fc980a - cf01dd6c6b1f + - 7acb00fc980a - 31f8063eedea - 2d4e3aff9dc7 tool_panel_section_label: RNA-seq @@ -11,8 +11,8 @@ tools: - name: arriba_get_filters owner: iuc revisions: - - 125d20cb23d7 - 7a5a2d28c539 + - 125d20cb23d7 - 703a2cb3fb38 - 32e542c2a773 tool_panel_section_label: RNA-seq @@ -20,8 +20,8 @@ tools: - name: arriba owner: iuc revisions: - - 01ccd366690d - 45c2ec061cf9 + - 01ccd366690d - 3d61a698e5e1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -77,8 +77,8 @@ tools: - name: cuffcompare owner: devteam revisions: - - f648e5180e40 - e66b9b5b8580 + - f648e5180e40 - ad5d061fbdf2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -91,8 +91,8 @@ tools: - name: cufflinks owner: devteam revisions: - - 6926716bbfb5 - d080005cffe1 + - 6926716bbfb5 - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -105,11 +105,11 @@ tools: - name: cuffmerge owner: devteam revisions: + - 22cf48ad7b16 - 86285ddd4512 - cf747d1bd79a - - 04adc9db1581 - - 22cf48ad7b16 - 6a6717a5f421 + - 04adc9db1581 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -161,9 +161,9 @@ tools: owner: iuc revisions: - 0693ccd171c4 - - e3b16fd7dd08 - - 8f0181aacb7a - 3b36efd62b3e + - 8f0181aacb7a + - e3b16fd7dd08 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: - - d027d1f4984e - - 8fe98f7094de - - 6a3a025714d3 - 0696db066a5b - cd9874cb9019 - 24a09ca67621 - 9a882d108833 + - d027d1f4984e + - 6a3a025714d3 + - 8fe98f7094de tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -193,10 +193,10 @@ tools: - name: dexseq owner: iuc revisions: - - b47c006d90c5 - 2872c633f07e - - 9a7c5b6d8f1e + - b47c006d90c5 - 62adf13b86ea + - 9a7c5b6d8f1e - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -209,18 +209,18 @@ tools: - name: edger owner: iuc revisions: - - 6e53e565fc6a - - 9bdff28ae1b1 - - 555659de7321 - - 334ce9b1bac5 - - 3d89af8a44f0 - 5bf899c13979 + - 6e53e565fc6a - f2843df56434 - - ae2aad0a6d50 - a8305cf0c951 - - 0cb907a2a810 - 070900306913 + - 3d89af8a44f0 + - ae2aad0a6d50 + - 334ce9b1bac5 + - 555659de7321 - df0c8d0a5992 + - 0cb907a2a810 + - 9bdff28ae1b1 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: - - a56fbe2d6ba7 - - 6f66ae7c5f7a - - e6a2a912677a - - 38b6d12edc68 + - f3a5f075498f + - a37612abf7f9 - 7db9d3ea71c9 - af814359d244 - - f3a5f075498f - - 90d16db017d7 + - e6a2a912677a + - a56fbe2d6ba7 - f9d49f5cb597 - ea04b737afa0 - - a37612abf7f9 - 1b851f87fbe0 + - 38b6d12edc68 + - 90d16db017d7 + - 6f66ae7c5f7a 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: - - 3c5e024a18cf - 0f710191a66d - 3c97c841a443 + - 3c5e024a18cf 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: - - 3fb01a8c902d - - 6ab42baa56e9 - 26371a1df031 - d4b55e2beb12 - - 6c19daec423d - a86e80d3c09c + - 3fb01a8c902d - f4af63aaf57a + - 6c19daec423d + - 6ab42baa56e9 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: - - 67b0b160903a - 916cb26bd9d3 - 4418229c501e + - 67b0b160903a 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: - - 5ae5c312d718 - 01247aaf0a10 - 87c11c05d238 - - ce5d418183c5 - 1c75aa5de15e + - ce5d418183c5 + - 5ae5c312d718 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: - - 4f9c4e6566e5 - 10c98fab6c5a - - c971db6f0fe5 + - 4f9c4e6566e5 - 40985510cd98 + - c971db6f0fe5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -387,13 +387,13 @@ tools: - name: limma_voom owner: iuc revisions: + - d6f5fa4ee473 - 32511f586472 - - 97e06a4c7c75 - - 708348a17fa1 - - 58c35179ebf0 - e827f9aae031 - 0921444c832d - - d6f5fa4ee473 + - 97e06a4c7c75 + - 58c35179ebf0 + - 708348a17fa1 - 119b069fc845 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -412,8 +412,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_mapper @@ -443,8 +443,8 @@ 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 @@ -462,21 +462,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - b0f2be869d6d + - b9e04854e2bb + - 4df95e2d7f61 + - c772497b2c32 + - 980d2a2e1180 + - 79de45b5069b + - 0a563fd2f22e - e132e7d02a3e - - 99b17b74a8cd - 5ec75f5dae3c - - 4074fc1940e2 - - b9e04854e2bb - - c7c55b694974 - 3ea5a2a63fa2 - 4014de1b6daf - 7ed2edc1337f - - 0a563fd2f22e - - 980d2a2e1180 - - c772497b2c32 - - 4df95e2d7f61 - - 79de45b5069b + - b0f2be869d6d + - 99b17b74a8cd + - c7c55b694974 + - 4074fc1940e2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -500,14 +500,14 @@ tools: - name: salmon owner: bgruening revisions: - - ebab418107f5 - 2c0ca397d302 - 53e9709776a0 - - f4d5237a84f6 - 15cd64d7c58b - cc05793bb896 - e3d32471da11 + - f4d5237a84f6 - 49121db48873 + - ebab418107f5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -528,14 +528,14 @@ tools: - name: stringtie owner: iuc revisions: - - ae618321f34a - dd4df992d93d + - 1ebd14235b92 + - cef79931dda5 + - 258d696dbd7e + - ae618321f34a - cbf488da3b2c - 914cfcba0ec8 - - 258d696dbd7e - - 1ebd14235b92 - 76d290331481 - - cef79931dda5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -571,10 +571,10 @@ tools: - name: transdecoder owner: iuc revisions: + - 0db979fead3a - c6334cb383ff - ffd1300599a1 - d0d4cef4f967 - - 0db979fead3a 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: - - 74217fbfba4d - - ba3720d7e68b - d6a479fd4281 + - ba3720d7e68b - bcc5f03f1900 + - 74217fbfba4d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -601,10 +601,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 2fb4ee002432 - - c2b82a94493e - - 478f36effca1 - 56162e446004 + - 478f36effca1 + - c2b82a94493e + - 2fb4ee002432 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -616,9 +616,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: - - 3f4094b6a565 - - 9ff3765e7172 - fab23c3b5258 + - 9ff3765e7172 + - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -631,9 +631,9 @@ tools: owner: iuc revisions: - be3f26533209 - - 870ac06dff8e - - 4687ecf0eb2d - 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: - - 5192f657f305 - - c5fbddcac63a - 65e7dea767ea - - 33406f5a445c + - 5192f657f305 - 05ab8d5e04a2 + - 33406f5a445c + - c5fbddcac63a 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: - - a35cba31d904 - 1fdb25a8384d - - 6f0fb35b799c - e406ac71165d + - 6f0fb35b799c + - a35cba31d904 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: - - 7c7fbf13aadd - c2c039e421af - - 964b7efe2639 - 37a1129c89d2 + - 7c7fbf13aadd + - 964b7efe2639 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -691,9 +691,9 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: + - eafea3083352 - 047c22569787 - 1d689e4e1caf - - eafea3083352 - 24e94d84adc9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -706,10 +706,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 3a4ac03d1266 - - 9871104ea630 - - 1812dbc5bb7b - 04bb8bb7c198 + - 1812dbc5bb7b + - 9871104ea630 + - 3a4ac03d1266 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -734,14 +734,14 @@ tools: owner: iuc revisions: - c9cfec002f71 + - 9fa24d5aac68 - 48636f857c4b - - db1f362cca3e - - cee61b3fcf78 - d84caa5a98ad - 8f1c3df4dd49 - - 32b86cd8eb50 - - 9fa24d5aac68 + - cee61b3fcf78 - d2bc35f3d1c5 + - db1f362cca3e + - 32b86cd8eb50 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: - - 4383070d29ed - 2b093007fab9 - - 6fd16fad465d + - 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 636b5a8af..233430f7b 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -4,7 +4,7 @@ tools: revisions: - 27e16a30667a - 080fd5739bb4 - - 1a052c827e88 - 473382134e56 + - 1a052c827e88 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 4173f5b9f..6a80a4428 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: - - 88eedb4abea0 - - 3c661e57a88f - 10184eaa85fc + - 3c661e57a88f + - 88eedb4abea0 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: - - 1dfd95ee241e - cb20f99fd45b - 108db6635177 - 993b19f20c76 + - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -37,8 +37,8 @@ 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 @@ -63,8 +63,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - 9c1c0b947e46 - ef11139d4545 + - 9c1c0b947e46 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -82,10 +82,10 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 30a201c9c310 - - 19ece8afbaab - e7fd6754d093 + - 30a201c9c310 - 5f8e69cc4c6e + - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_bamqc @@ -110,8 +110,8 @@ tools: - name: sam2interval owner: devteam revisions: - - 75557c0908a9 - 8c737b8ddc45 + - 75557c0908a9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_bitwise_flag_filter @@ -123,8 +123,8 @@ tools: - name: sam_pileup owner: devteam revisions: - - a3b4ad6858ff - 890d97772e2a + - a3b4ad6858ff 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: - - 46c6639921f1 - - 9149ad20699a - 12749212f61b + - 46c6639921f1 - 6856f8a01905 + - 9149ad20699a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -178,10 +178,10 @@ tools: - name: samtools_calmd owner: devteam revisions: + - 92ec40abcdcf - 06dc50b7b711 - 33208952b99d - 26b4f9f98aca - - 92ec40abcdcf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -205,11 +205,11 @@ tools: - name: samtools_fastx owner: iuc revisions: + - 720217c23995 + - b906586a6596 - a8d69aee190e - b3d99709fe1a - 66e23b11feae - - 720217c23995 - - b906586a6596 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -221,17 +221,17 @@ tools: - name: samtools_fixmate owner: iuc revisions: - - d2df79922531 - e5ece8fa99de + - d2df79922531 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - fe34990e5ce7 + - 22970df7a40e - db17d5321bad - cc61ade70eb8 - - 22970df7a40e - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -244,11 +244,11 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - fa5d3e61e429 - - 7a6034296ae9 - - 7def34e6cf4d - 811fc2d75ad4 + - 7def34e6cf4d + - 7a6034296ae9 - 88b8c2916784 + - fa5d3e61e429 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -260,28 +260,28 @@ tools: - name: samtools_markdup owner: iuc revisions: - - a389f74c3630 - 40fa6c240105 + - a389f74c3630 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - 65a38e8c8e2a - - 740ce0a18f0d - b40e2d865d52 - cae2794d2deb + - 740ce0a18f0d - 36677f429310 + - 65a38e8c8e2a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 329deb17a9f7 - b61f5d6a7f25 - - 583abf29fc8e - 9da0311ab1dd - fa7ad9b89f4a + - 583abf29fc8e + - 329deb17a9f7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -306,10 +306,10 @@ tools: - name: samtools_reheader owner: devteam revisions: + - 30388d878f81 - bb8cfc6f6e0c - - db000c6007a0 - 85e38b31e8b3 - - 30388d878f81 + - db000c6007a0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -341,10 +341,10 @@ tools: - name: samtools_sort owner: devteam revisions: - - e613c1ad4c4c - - cab3f8d35989 - 6c2c1836728b + - e613c1ad4c4c - d54a4df48867 + - cab3f8d35989 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: - - bcedabb53ddf - - 5d9ae78f34d3 - 135c85f4cfaf - - b7f7826ef1cd - - bd850490c7f1 - 818030fa6bbf + - bd850490c7f1 + - bcedabb53ddf + - b7f7826ef1cd + - 5d9ae78f34d3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -373,12 +373,12 @@ tools: - name: samtools_stats owner: devteam revisions: - - 5a08c09b9311 - 145f6d74ff5e - - 541082d03bef - - 1cc79f49b8d5 - 3a0efe14891f + - 5a08c09b9311 + - 1cc79f49b8d5 - 24c5d43cb545 + - 541082d03bef tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats @@ -390,16 +390,16 @@ tools: - name: samtools_view owner: iuc revisions: - - 6be888be75f9 - - 32dc5f781059 + - bf328cec6a42 + - 5826298f6a73 + - b01db2684fa5 - 350bbc5c2ffd + - b72793637686 + - 6be888be75f9 - 0dbf49c414ae - - b01db2684fa5 - - 5826298f6a73 + - 32dc5f781059 - 2dce91e11ca7 - c370440f901e - - bf328cec6a42 - - b72793637686 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 8788e4f91..82b8fdc71 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: - - 6f6537780379 + - a62c4a11a67d - ea5e944f447d - - d147d6455873 + - 6f6537780379 - 4aab5ae907b6 + - 5cb6146337d8 + - d147d6455873 - 480d9e9d156b - 59bb6d34fca6 - - a62c4a11a67d - - 5cb6146337d8 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 de096f8c1..9da320c0b 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -8,33 +8,32 @@ tools: - name: alevin owner: bgruening revisions: - - b0fe3e482cb7 - - ecb9ea6269ee - - e32b215b7c04 - - c9944a2600f1 - f2000bc73102 + - ecb9ea6269ee + - b0fe3e482cb7 - e4c01dcece8b + - e32b215b7c04 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - 7a6655aa6eb2 - 707023fa62fe - - c0b037b12765 - e1c3c2f2a834 + - 7a6655aa6eb2 + - 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 - - 00712416fdaa - 32e547223c9e - - cfc3f5a57dc6 - - 93dd15e13e6a - - 6f143dfe902a - - 55e35e9203cf + - 00712416fdaa tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -46,13 +45,13 @@ tools: - name: anndata_inspect owner: iuc revisions: - - b9fac48532eb - - 688357ad5e61 - - 14c576ea6148 - - 038e32885fec - - ee98d611afc6 - 39e945f0b2c1 + - ee98d611afc6 + - 038e32885fec + - 688357ad5e61 - 6f0d0c784f09 + - 14c576ea6148 + - b9fac48532eb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -64,13 +63,13 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - b85871dd69f9 - - c4209ea387d4 - 9bd945a03d7b - - ed4996a16f7f - d4af736e7b83 - - 43cb7b5a6fe7 - 3d748954434b + - c4209ea387d4 + - b85871dd69f9 + - 43cb7b5a6fe7 + - ed4996a16f7f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -82,17 +81,19 @@ tools: - name: anndata_ops owner: ebi-gxa revisions: + - 890fb06a2893 + - a4774b7b2e85 - fe75d2414dc0 + - 7ebc22f77d86 - 2e8022f1923c - - a4774b7b2e85 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: + - 769d815e4b0d - 4fff5a293013 - 02b1fe7aed76 - - 769d815e4b0d - 0e70b2dfe4be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -108,19 +109,19 @@ tools: - name: baredsc_combine_1d owner: iuc revisions: - - c32347702e12 + - 050cf43887d3 - b13d3e4c48e1 + - c32347702e12 - 5b7c81b35b89 - - 050cf43887d3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 1d77986f9ddc - 02fc39c8610d - - ae969fdb8442 - 239193b96d72 + - 1d77986f9ddc + - ae969fdb8442 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -157,10 +158,10 @@ tools: owner: iuc revisions: - 8855361fcfc5 - - 2c1200fba922 - - cfe1e6c28d95 - - cdf4443d5625 - a9caad671439 + - cdf4443d5625 + - cfe1e6c28d95 + - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -196,9 +197,9 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 01c37e54e86e - - fb7068d30ec9 - 952abbc4b1de + - fb7068d30ec9 + - 01c37e54e86e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest @@ -221,8 +222,8 @@ tools: owner: bgruening revisions: - f47ac4a0b337 - - 013e53ccc7ac - b9ab56aecd18 + - 013e53ccc7ac tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol @@ -236,72 +237,72 @@ tools: - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - 640e0e45518a - f8320df1866b - 45a386d18509 + - 640e0e45518a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: - 9d02f1819e81 - - f963c251ac77 - c354255ff705 + - f963c251ac77 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint owner: bgruening revisions: + - f881c94fb3b3 - c4ed35f4f77f - 40fee49bc6c3 - - f881c94fb3b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: + - 782bdcb775fb - e06265d204f6 - 2dccb6bb0add - - 782bdcb775fb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - b05f662f9f35 - - 63c8377c58b3 - f0216498a666 + - 63c8377c58b3 + - b05f662f9f35 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions owner: bgruening revisions: - - 8a11d70b6cd8 - c72fa6cb8817 - fe3aa71590d5 + - 8a11d70b6cd8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices owner: bgruening revisions: + - e03780179ee5 - 4f9305d3bb34 - 3ee5332bf57c - - e03780179ee5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - a315574104c6 - - 4401ed529d2c - 3a6a5381db36 + - 4401ed529d2c + - a315574104c6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - 2ba6cee8e4db - c0737631eea1 + - 2ba6cee8e4db - a83732c79949 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -316,17 +317,17 @@ tools: - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - 2786a931cad2 - 2b4d6a8dab36 - cd40ca76865a + - 2786a931cad2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops owner: bgruening revisions: - ffc33339cd3e - - 0410b6aada45 - bf9379529c3e + - 0410b6aada45 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad @@ -348,96 +349,96 @@ tools: - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 7f7c6ead2d0d - - 409396ea5cf0 - bb8849fca57c + - 409396ea5cf0 + - 7f7c6ead2d0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo owner: bgruening revisions: - 51e40e9b6c3c - - b0f33533181d - e4f8fceab96a + - b0f33533181d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad owner: bgruening revisions: - - 55b013e59018 - c261b6b05ee3 + - 55b013e59018 - 32173084d53f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains owner: bgruening revisions: - - b376ef118807 - - 4b194e675916 - b6b8c8672756 + - 4b194e675916 + - b376ef118807 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: + - ed900cd4a0a9 - 910c6a1c3a27 - 1511a8ebe906 - - ed900cd4a0a9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - - f34ab9882252 - 6d042c96aceb - 2aa5b6b65197 + - f34ab9882252 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: - - 9b383d429659 - dd9988943f53 - ea5d67ec94ab + - 9b383d429659 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: + - 6326cd29c1c3 - 06ced663d24f - 11f39d7f6c64 - - 6326cd29c1c3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: + - b4e780e93c91 - beb5b5917d2f - 337705015ee8 - - b4e780e93c91 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: + - 8d203e74869b - 58de3c7c8e89 - e285920f8585 - - 8d203e74869b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicquickqc owner: bgruening revisions: - - ea8fb5e899e8 - 21d859ad4502 + - ea8fb5e899e8 - 5cbd7a902a8d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - f81750434d70 - 1d6af10874d5 + - f81750434d70 - 36dfa2825a59 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -464,19 +465,19 @@ tools: - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 11a3385e03b5 - 1d201e8378b3 - cef9fb4ece1c + - 11a3385e03b5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: - - 4b0adaa31c95 + - e98619de2776 + - db575b4c8b22 - 59be31ac9dc3 - 7784821452ac - - db575b4c8b22 - - e98619de2776 + - 4b0adaa31c95 - eeab712b0b99 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -489,9 +490,9 @@ tools: - name: music_construct_eset owner: bgruening revisions: + - 2cfd0db49bbc - 48f0fb3061b1 - 7ffaa0968da3 - - 2cfd0db49bbc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution @@ -523,11 +524,11 @@ tools: - name: raceid_clustering owner: iuc revisions: - - a4b734cd253b + - f911a64454fb + - 49776718ae90 - c4f39bf4a068 - 7e014059a88d - - 49776718ae90 - - f911a64454fb + - a4b734cd253b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -539,10 +540,10 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: + - 8b917923f7d4 - 43c146e25a43 - d45f092caf24 - 7608d5faee41 - - 8b917923f7d4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf @@ -568,8 +569,8 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - 69018f285aa3 - df8e4e54d367 + - 69018f285aa3 - 6e90c8adf84f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -610,17 +611,17 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: + - f9353ee6a0d4 + - 6f83f8fd381f - 6acb08931836 - - aaa5da8e73a9 - - edec35114f72 + - 8983e7a04ba7 + - 77b91b9bdf52 - cb43c5d3acd3 - b2df381a6004 - - 38db3fef7aad - - f9353ee6a0d4 - - 77b91b9bdf52 - - 8983e7a04ba7 + - aaa5da8e73a9 - 4d8f983cd751 - - 6f83f8fd381f + - edec35114f72 + - 38db3fef7aad tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -632,16 +633,16 @@ tools: - name: scanpy_filter owner: iuc revisions: - - 8cb783c81905 + - 277313130da5 - fc0321c000a3 - - 72a6bebab2a5 + - 64388be6d510 - b409c2486353 - - d636ce5cde16 + - 8cb783c81905 - a03ff8633507 + - d636ce5cde16 - a97abb8cd15b + - 72a6bebab2a5 - 3c86f71498bc - - 277313130da5 - - 64388be6d510 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -653,17 +654,17 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - d86cb2ce311b - - f54f0f0598ad - - 6bd82ed14acd + - 6c145a6868cc - 3081ff5c84a3 - c5d3684f7c4c - - 6c145a6868cc - - 5e9171dc8244 - - cc0deb593fc8 - - c0a80a16560f - 18262103fa61 + - 6bd82ed14acd + - c0a80a16560f + - f54f0f0598ad - 5c3ebe2adc77 + - cc0deb593fc8 + - d86cb2ce311b + - 5e9171dc8244 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -675,17 +676,17 @@ tools: - name: scanpy_normalize owner: iuc revisions: - - 4bda4412b8c2 + - 9f354c7c8c92 + - 7b9fafe32c86 - c9cb76cf8d6c - 94c19fb1281c - - d844935c906c - - 3bcd5445cd7a - - 7b9fafe32c86 - - 56c0d4acef02 - a407e7f8bdc1 - - 146ae5d70b47 + - 4bda4412b8c2 + - 56c0d4acef02 - ab55fe8030b6 - - 9f354c7c8c92 + - 146ae5d70b47 + - 3bcd5445cd7a + - d844935c906c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -697,18 +698,18 @@ tools: - name: scanpy_plot owner: iuc revisions: - - aa0c474463c2 - - 6adf98e782f3 - - 62acdd96d4a0 - - 9b0cdb8cf6be + - 7647e5cd1b8b + - dbbe1ea8ecb1 - 0185bd174ea0 + - 95777145cb92 + - 6adf98e782f3 - 40812a65a78b - - f7446fd8d5e7 - - 7647e5cd1b8b + - 9b0cdb8cf6be - 1072ce66b426 - - dbbe1ea8ecb1 + - f7446fd8d5e7 - 6f5349dd5c49 - - 95777145cb92 + - 62acdd96d4a0 + - aa0c474463c2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -720,31 +721,31 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - d18e7a6e5cd4 - - 73ab2ac53d06 - f2f6c703da06 - - c65fce500915 - - bf2017df9837 - 458e8f43a775 - 215733a383f2 - - a39040ae0a38 - - fe8f16c594ec - 9fb627495ec2 + - 73ab2ac53d06 + - a39040ae0a38 + - d18e7a6e5cd4 + - bf2017df9837 + - c65fce500915 - c5541bfb8feb + - fe8f16c594ec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - 974bb00b2f43 + - c5541bfb8feb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - 8f333f90d8d6 - b834074a9aff - fd808de478b1 + - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -756,9 +757,9 @@ tools: - name: scater_filter owner: iuc revisions: + - 652923ce664f - b7ea9f09c02f - 7a365ec81b52 - - 652923ce664f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -796,9 +797,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: + - 9e5c0bb18d08 - 46fc6751d746 - c99ba278dfa9 - - 9e5c0bb18d08 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca @@ -1027,8 +1028,8 @@ 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 @@ -1061,8 +1062,8 @@ tools: - name: snapatac2_preprocessing owner: iuc revisions: - - cec3e76eaf05 - c5c94e01a1b5 + - cec3e76eaf05 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: squidpy diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index bd5dfc98c..2df93e485 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -34,23 +34,23 @@ tools: revisions: - 562f3c677828 - 4c07ddedc198 - - 419027d822d6 - 2f3c6f2dcf39 + - 419027d822d6 - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - e01e8a9a82f4 - 8564f6927b87 + - e01e8a9a82f4 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all @@ -71,8 +71,8 @@ tools: owner: devteam revisions: - 6c29c7e347e8 - - 7a15159140d1 - cb1c59d69557 + - 7a15159140d1 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - aef56d0e7a61 + - 7442b94d6a1e - 4c4ec859c31a - - 9c3e1d3235c8 - - b1eda492f063 - 840f29aad145 - - 7442b94d6a1e + - b1eda492f063 + - aef56d0e7a61 + - 9c3e1d3235c8 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - 30d21a6041f6 - - d0352e8b4c10 - 375bbd555f4a - 9fda0b82f419 + - d0352e8b4c10 - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: + - cd02bf168d23 + - 8b1b2b91f8d0 - 4cc980df6265 - 2c58b83c9bad - - 8b1b2b91f8d0 - 7ae443e6217d - - cd02bf168d23 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - e10e776f2109 - - bb9fc9d46ea4 - - 1dd433d2c92c + - 7dd3fb35904f - 4bbaf77573ef + - 1dd433d2c92c - ad7e0b4291ee - - 7dd3fb35904f + - e10e776f2109 + - bb9fc9d46ea4 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 9fcbace78..d9ce57e3b 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -14,8 +14,8 @@ tools: - name: add_value owner: devteam revisions: - - 745871c0b055 - 023f0a3760b3 + - 745871c0b055 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -27,21 +27,21 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - 6c6d26ff01ff - f18f67056946 + - 6c6d26ff01ff tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: - - 9cd341095afd - - 02026300aa45 - - 6595517c2dd8 - - 626658afe4cb - aff5135563c6 - - 6e8d94597139 + - 02026300aa45 + - 9cd341095afd - 464b9305180e + - 6e8d94597139 - 13b6f0007d9e + - 6595517c2dd8 + - 626658afe4cb - be25c075ed54 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -79,11 +79,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 37cde8134c6a - - 557ec8d7087d - 90f657745fea + - 37cde8134c6a - 34d29339abab - 9cc411a62277 + - 557ec8d7087d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -115,22 +115,22 @@ tools: - name: query_tabular owner: iuc revisions: - - 83069b38aa85 - - 623f3eb7aa48 + - cf34c344508d - cf4397560712 - - 2e8f945f7285 + - 33d61c89fb8d + - 83069b38aa85 - 1ea4e668bf73 - 3a6b78c39dca - - 33d61c89fb8d - - cf34c344508d + - 623f3eb7aa48 + - 2e8f945f7285 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - ae8c4b2488e7 - - 399da6b5ec21 - 503bcd6ebe4b + - 399da6b5ec21 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -142,10 +142,10 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - b722161a845a - c4d18aa4ec4a - f768f6183386 - bce29ec10b78 + - b722161a845a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -158,15 +158,15 @@ tools: - name: text_processing owner: bgruening revisions: + - ddf54b12c295 + - 86755160afbf - fbf99087e067 - - f46f0e4f75c4 + - a6f147a050a2 - 74a8bef53a00 - 0a8c6b61f0f4 - - 9ff72e942410 - - a6f147a050a2 - - 12615d397df7 - - ddf54b12c295 - d698c222f354 - - 86755160afbf + - 12615d397df7 + - f46f0e4f75c4 + - 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 63d2d7182..c85f74c3c 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -14,9 +14,9 @@ tools: - name: breseq owner: iuc revisions: + - 0d18a3ba2d1c - 82fb5e3bb93e - 85c57cc9b558 - - 0d18a3ba2d1c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -28,67 +28,67 @@ tools: - name: cutesv owner: iuc revisions: - - 23d7e75d850e - c0f8fe52948e + - 23d7e75d850e - cb441f258c37 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: freebayes owner: devteam revisions: - - 57def2d7c093 - - a5937157062f - - ef2c525bd8cd - 156b60c1530f - 04fa42777df9 + - 57def2d7c093 + - ef2c525bd8cd - 3e954e7125bf + - a5937157062f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: + - 435b157bed6d - 09d6e4693887 - e61c9ac190ad - 791f73caa0c8 - - 435b157bed6d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - 65432c3abf6c - - 4805fe3d8fda + - dfadc322b065 - 03627f24605f + - e1461b5c52a0 - b11e8e9c23bf - 3b4b2121842f + - 4805fe3d8fda - 074d44697036 - - dfadc322b065 - - e1461b5c52a0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: + - 9cb929f21cfa - 701d134358ad - 7dfca164d2e3 - - 9cb929f21cfa tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - c27549b9aa1f - f4473557ffc7 - - 971e07ca4456 - 426d707dfc47 + - 971e07ca4456 + - c27549b9aa1f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - dbd9f2db9ed8 - aa35ee7f3ab2 - cdaab621d454 + - dbd9f2db9ed8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -108,11 +108,11 @@ tools: - name: snippy owner: iuc revisions: + - fa016f1eea1a - 5bbf9eada9c2 - - 9bccc8404a3c - 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: - - 32f14a2723ec - ee4a90760848 - - e7aff4a85df5 - 3b1e7c170b10 + - 32f14a2723ec + - e7aff4a85df5 - 40f0591deda0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: + - 42818629ec4c - 9793bc5d741b - adc0645b945c - - 42818629ec4c - - 02d81b994ef5 - 4934c0ac6197 + - 02d81b994ef5 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 34fcb9424..9560b002d 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -2,14 +2,14 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - 2c372041ed8c - - ebe5fc018e72 - - e075b1be5abb - - 95815a0bb307 - - 265fe0f9ea64 + - 8a2e296c07ef - b7ea370b8f5d - 6a88248893c4 - - 8a2e296c07ef + - 95815a0bb307 + - 265fe0f9ea64 + - e075b1be5abb + - ebe5fc018e72 + - 2c372041ed8c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -21,13 +21,13 @@ tools: - name: bcftools_call owner: iuc revisions: - - 22637b1a55bf - - 544cb432072b - - b03984136ce4 - - 21687e35f066 - c37b684e7f4e - - 1001172b5089 - 0fba2c15b40d + - 21687e35f066 + - 544cb432072b + - 1001172b5089 + - 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: - - 8627b2b383b4 - 8ca3647c90fd - - 0238f68ad641 - - 01d6b7d6365e + - 8408bffd5616 + - 8627b2b383b4 - 143796b504eb - - ccb83bf54de0 - 3a7084316a6e - - 8408bffd5616 + - ccb83bf54de0 + - 01d6b7d6365e - bf1f4994f104 + - 0238f68ad641 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: - - 62ca6da715bf - - f430a1ec7ee4 - - 03e0645395d2 - - 9b5abbf50d23 - - d144af39073a - abd489215f73 - 6b6c992d3a14 + - 03e0645395d2 + - 9b5abbf50d23 - 81426b3cf18b + - 62ca6da715bf + - f430a1ec7ee4 + - d144af39073a 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 - 1829900b5dcd - - 1171446da5db - - d3081540d175 - - 8aa352093d73 - d37e313a41be - - e522022137f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -97,14 +97,14 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - b14ff40958cb + - 1137ce8efc1e + - 9b29129fb491 - 348cd212dbad + - b14ff40958cb + - 92c0aff8b53e - 09f37afb3621 - 012656fd329f - - 92c0aff8b53e - - 9b29129fb491 - d58d2e8c7a57 - - 1137ce8efc1e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -116,13 +116,13 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: + - 1f2183a23823 - 55c0e906c14c + - 367ba501b6eb - 7291189e98b4 - - 1f2183a23823 - de68c11034f6 - - ecc9192912b8 - cfd81f17580b - - 367ba501b6eb + - ecc9192912b8 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: - - e6f4badbe6f3 - ae68ceb4cca3 + - e6f4badbe6f3 - 6c790a091c7c - - d237eaef451f - - 7cbf3c66d4ad - 039ea3f1dea9 - 64a8f7dae3ad + - 7cbf3c66d4ad + - d237eaef451f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -152,13 +152,13 @@ tools: - name: bcftools_filter owner: iuc revisions: + - 277719af4dd7 + - cdb7b4927742 + - 33bd9301568c - 5d6653c989cb + - 6ea7170a016d - 963a3635b2e1 - - 33bd9301568c - 46fcafba49ec - - 6ea7170a016d - - 277719af4dd7 - - cdb7b4927742 - e7452697afd9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -171,14 +171,14 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - a1213a0b7b66 - - 5a321fab1fe4 - - 26d97cdd5410 - 501bfb078342 + - a1213a0b7b66 - a29a2f40b665 - - 7b4454382d39 - 91c1e57d5c7f + - 26d97cdd5410 - b7f0f59baa7e + - 5a321fab1fe4 + - 7b4454382d39 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: - - 97d19c008d15 - - 709dd8291b83 - - 768d04526638 - - 15da1ddcfeff - - 39bca000353d - - 81e4014fa809 - 5f27e814a119 + - 81e4014fa809 - d7d1663559e9 + - 768d04526638 + - 39bca000353d + - 97d19c008d15 + - 709dd8291b83 - c803c34361e0 + - 15da1ddcfeff 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: - - 5b006286a458 - - b931e65638b8 - 7ba36babba2d + - 5b006286a458 + - b1eba148b35b - 2215287d5cc9 - 86296490704e - - b1eba148b35b - 85ee7e6c4204 - b84fda8ebef0 + - b931e65638b8 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: - - ce9396ddcb2b - f506df85c652 + - 4e1d23e5c691 - 0a5dcc9a8ec2 - cf06b44624c7 - - 4e1d23e5c691 - - 5660b21a0dbd + - 37757ffb4c5f - 9c711df3258d - 56556e1267de + - ce9396ddcb2b + - 5660b21a0dbd - 31ea13dfe5e6 - - 37757ffb4c5f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -250,13 +250,13 @@ tools: - name: bcftools_norm owner: iuc revisions: - - 1ca7418e46ee - - 271965b55437 + - 19905c025d2a - 6deb4d549bc9 - 48291658fdf6 - 021693fdadaa + - 1ca7418e46ee + - 271965b55437 - a404f786a94c - - 19905c025d2a 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: - - f7879f1e77f9 - - 69d8b7567281 + - 71c78e0eea52 - 3f6fadf8b8ff + - dadbd61dc4cf - 5ad5d4243987 - - 97e8145d7e30 + - 69d8b7567281 + - f7879f1e77f9 - c450406f722b - - 71c78e0eea52 - - dadbd61dc4cf + - 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 - - 52f9e4a660e3 - - 79f7a1acc2cd - cc7f9a4e186b - 6cf13a657cf6 - - 0fe007201caf + - 79f7a1acc2cd - 283911fe7e1a + - 52f9e4a660e3 - 2514e684f8a3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -306,12 +306,12 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 0a62420cb9cd - 026a989b7cee - - a12844ca467a - 75ddd081f608 - 1411bef27a75 - 6963a6841d22 + - 0a62420cb9cd + - a12844ca467a - 230e424bde67 - 80e6e399ccd0 tool_panel_section_label: VCF/BCF @@ -325,14 +325,14 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - 444e6a756c35 + - e493702b19eb + - 5acfca5a76af - ba20340426fe - - bca7ce81688f + - 444e6a756c35 - 450a265f92e8 - - 5acfca5a76af - - e493702b19eb - - 5808f77b2bb6 - b10d1510fa84 + - 5808f77b2bb6 + - bca7ce81688f 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: - - 12152af85697 + - dd72ff87cfd0 + - c43399f161f4 - 4d236c696844 - - d52b8947b269 - 68fec03a63b7 - - 157ffcdd3fa7 - - c43399f161f4 + - d52b8947b269 + - 12152af85697 - f2482aa4862e - - dd72ff87cfd0 + - 157ffcdd3fa7 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: - - 8f2fc0ab30fb - - 29ba253e2e05 - - 8dbce095986c - - cbe39e530cbf - - 0e5d11004815 - 6f8e223f78f3 - 75becf493cd3 + - cbe39e530cbf + - 8f2fc0ab30fb + - 0e5d11004815 + - 8dbce095986c + - 29ba253e2e05 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 - - a8630d4fbaf8 - 88bb477f45f7 - - 9708e3086f32 - - e0a856def0b0 - - 8f5962c43868 + - a8630d4fbaf8 - f544f71adb73 + - 8f5962c43868 + - 9708e3086f32 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: - - 4ed46189d6c6 - 34dc0bbc7e93 - - 8b260d252ff4 - - 31c096c6b156 - - 03e30f06f15f + - 96d0145c041a - 6ce175385dd9 + - 03e30f06f15f + - 8b260d252ff4 - 5c9729d54721 - - 96d0145c041a + - 31c096c6b156 + - 4ed46189d6c6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -419,14 +419,14 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: + - 11af7fce71cf + - 40daf124be88 + - 46eb13bc2c73 - a730269af659 + - 2c4941386820 - 681bdf1e22ff - - 40daf124be88 - 09f5e45a8212 - - 2c4941386820 - - 46eb13bc2c73 - a1aad8b559c6 - - 11af7fce71cf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -438,14 +438,14 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - 0594ea1417c8 - - 6cbb9c47795c - - b74b8cbfc1f1 - f272b8ba0983 - - 12038f59c0f4 - - 743cd1472aeb - - 8cb121b6a1d2 - 3897eaadfbff + - b74b8cbfc1f1 + - 0594ea1417c8 + - 8cb121b6a1d2 + - 743cd1472aeb + - 12038f59c0f4 + - 6cbb9c47795c - 882b2e649602 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -458,12 +458,12 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: - - 18cf9de1cf73 - - adee7e8b746f - - dba06328556a - a9826db86d9a - eccb508bb678 + - adee7e8b746f + - 18cf9de1cf73 - cced6715f926 + - dba06328556a - 238f78e38a8b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -476,14 +476,14 @@ tools: - name: bcftools_query owner: iuc revisions: - - f64e7ca2efd2 - - fdec14f69010 - e0ad88dec40d - - 31a1b89eab9b - - c9935c9e8a24 - - 3ce32adc55b2 - e53501abf992 + - fdec14f69010 + - 31a1b89eab9b - 9f36041495a3 + - 3ce32adc55b2 + - f64e7ca2efd2 + - c9935c9e8a24 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -495,14 +495,14 @@ tools: - name: bcftools_reheader owner: iuc revisions: + - fd3539749127 + - d43eb39b989e - d68c43202172 + - b7be725976b6 - 4db0695a6fc7 + - 79489d5685dd - 2331ddcbd5aa - 3b7b1fe7b937 - - fd3539749127 - - 79489d5685dd - - d43eb39b989e - - b7be725976b6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -514,13 +514,13 @@ tools: - name: bcftools_roh owner: iuc revisions: - - 1ccf0e7fb4f6 + - 5296d26b0373 - 6a636d58dfc2 - - 78cd8b69da4c - 58091e1be01b - - b0d39ef600a7 - - 5296d26b0373 - 1a989b4110da + - b0d39ef600a7 + - 78cd8b69da4c + - 1ccf0e7fb4f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -532,14 +532,14 @@ tools: - name: bcftools_stats owner: iuc revisions: - - 591cc8518033 - bf8325a07ce7 - e8af591435d1 + - b641062a2587 - baa8823f8073 + - 591cc8518033 - '388983871932' - - 4d3ce9dc1525 - - b641062a2587 - b17394940c7a + - 4d3ce9dc1525 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: - - c2ab91a0d506 - - d1f8f55f564d - - 38d75661c235 - 1a2ef636f48e - - 59fa8742285e + - 3ca3de4e5291 + - 38d75661c235 - e6b5cbbf449b + - d1f8f55f564d - 3a233c8eb814 - - 3ca3de4e5291 + - c2ab91a0d506 + - 59fa8742285e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -577,8 +577,8 @@ tools: - name: vcfaddinfo owner: devteam revisions: - - afc0ba768690 - 6ea73d6151ec + - afc0ba768690 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: - - 6faa2c4c71d2 - 01e0321aca98 + - 6faa2c4c71d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes @@ -633,30 +633,30 @@ tools: - name: vcfcommonsamples owner: devteam revisions: - - f1852ecef841 - 254f285dbaaa + - f1852ecef841 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance owner: devteam revisions: - - 48e458c721b3 - 5822b40f3037 + - 48e458c721b3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter owner: devteam revisions: - - 4bdc111b2470 - - eae7c08ebb6f - 6b935ab36d7b + - eae7c08ebb6f + - 4bdc111b2470 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - 11f62f071125 - fc5a64fdd5b2 + - 11f62f071125 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten @@ -690,36 +690,36 @@ tools: - name: vcfleftalign owner: devteam revisions: - - 29f9b782727e - d2406f98a782 + - 29f9b782727e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfprimers owner: devteam revisions: - - 17096387c0e6 - d226a7327946 + - 17096387c0e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample owner: devteam revisions: - - 12b570dd0bc5 - 6257ee3b50d3 + - 12b570dd0bc5 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfselectsamples owner: devteam revisions: - - 958b6484a7f1 - 2ba3b87f904f + - 958b6484a7f1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfsort owner: devteam revisions: - - 5b7120c66efc - ee60203e68d9 + - 5b7120c66efc tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 35d3c8d7a..3fef97aef 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,18 +2,18 @@ tools: - name: abricate owner: iuc revisions: - - 4efdca267d51 - c2ef298da409 - 6e9aea89e388 - 3f3e247c053d - 78c75f134c16 + - 4efdca267d51 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 @@ -26,30 +26,30 @@ tools: - name: aegean_locuspocus owner: iuc revisions: - - 1fdc517743e6 - c4ac24510b55 + - 1fdc517743e6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_parseval owner: iuc revisions: - - d6c074a93c51 - 1b52f0c8ad7f + - d6c074a93c51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - 3e1f6f6d557e + - 44018dd6b447 - a79ee60b6926 + - cd2480f35935 + - b5d8e5475247 + - 3e1f6f6d557e + - 1aae04680c4b + - fe3ca740a485 - 133f36c29579 - - 44018dd6b447 - f29602ae449e - - fe3ca740a485 - - b5d8e5475247 - - cd2480f35935 - 4f2967b27e67 - - 1aae04680c4b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -62,9 +62,9 @@ tools: - name: augustus_training owner: bgruening revisions: + - 6519ebe25019 - 7be22100e5e1 - dc027fa56d55 - - 6519ebe25019 - f1e653756174 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -80,10 +80,10 @@ tools: - name: bakta owner: iuc revisions: - - d77802fe76f7 - - 92eee5f31117 - da5f1924bb2e + - d77802fe76f7 - 728dacaf08a9 + - 92eee5f31117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap @@ -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 @@ -156,60 +156,60 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 3bbe70fef6df - - 756376aeb1ae + - b6b5cd37f2a2 - 9f2455341fac + - 756376aeb1ae + - 9c15ca7e764e - 14f588312c56 + - 3bbe70fef6df - 582fd74dc2a1 - - 9c15ca7e764e - - b6b5cd37f2a2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 989f7c061f35 - 8e1ace8f77c6 - - 0ffe5be70caf - 30fb23d4c31c - - a230ea445788 + - 989f7c061f35 + - 0ffe5be70caf - 1691af4a0d17 + - a230ea445788 - 73428a792541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 5a5ae61da69c + - 494f0bb4a993 - 0418d28136de - - 57c6718cbfcc - 563a19373357 + - 57c6718cbfcc - e94187d661df - - 494f0bb4a993 - 30f08d74024f + - 5a5ae61da69c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - 4b96ced19f75 - - f77d7b685bb3 - d6c7106b7b2e - - 7abc5f6dd595 - - f31125bb85ea - 1bc5a03faf2e - 2bba2ff070d9 + - 7abc5f6dd595 + - f77d7b685bb3 + - f31125bb85ea tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - d77fdcca400e - - b3cf4684e9c7 - 520e30695ec3 - - fed64e676186 - d3af38b9c7e1 + - d77fdcca400e + - b3cf4684e9c7 - 52af33194019 + - fed64e676186 - 54961e026fe4 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -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 @@ -236,9 +236,9 @@ tools: - name: goseq owner: iuc revisions: + - 8b3e3657034e - 43798b4caee0 - 602de62d995b - - 8b3e3657034e - ef2ad746b589 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -271,8 +271,8 @@ tools: owner: bgruening revisions: - 74810db257cc - - c55643c3d813 - 98cafcbd2578 + - c55643c3d813 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -290,26 +290,26 @@ tools: - name: maker_map_ids owner: iuc revisions: - - e906fa778440 - 326f9c294b09 + - e906fa778440 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: - - d46d803ca6cc - - 3c1a01127868 - 370c210d9541 + - 3c1a01127868 + - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - c8ac28e8ac44 - - e95d52d295d7 - - 624606f7c996 - b815ec682418 + - 624606f7c996 - 033755194fe9 + - e95d52d295d7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -357,10 +357,10 @@ tools: - name: prokka owner: crs4 revisions: + - a17498c603ec - 8a22554cdde2 - - d643e3b03500 - bf68eb663bc3 - - a17498c603ec + - d643e3b03500 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -404,15 +404,15 @@ tools: - name: snpeff owner: iuc revisions: - - c7275bd8b4d6 - - 68693743661e - - 268d162b9c49 - - cfcf33df7fc0 - 5a29ab10dba6 - 5b80f544c67f + - 6322be79bd8e + - c7275bd8b4d6 + - cfcf33df7fc0 + - 68693743661e - 5c7b70713fb5 + - 268d162b9c49 - 8f92c2b26e6d - - 6322be79bd8e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift @@ -426,8 +426,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -440,16 +440,16 @@ tools: owner: iuc revisions: - 51dd22484644 - - ba6f87115e13 - - 4839e590cb26 - - ac8250086ac3 - - 200c378d85f3 + - 45083d070fb8 - 8cb134b8c1a5 + - ac8250086ac3 + - 4839e590cb26 - 37213cf56392 + - 200c378d85f3 + - ba6f87115e13 - 037a11682176 - - 45083d070fb8 - - e1a9d6fd258d - d03af1c7002c + - e1a9d6fd258d - 809dfc93d593 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 030b740a0..f46772600 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,45 +2,45 @@ tools: - name: abyss owner: iuc revisions: - - a929ce596a34 - - fa5259cc561b - - d6d5ccc2c581 - - 8f1b150a2487 - - 890b794c997d - - 7547fcab5d19 - - 0124fce4654a - db9b10824c61 + - 7547fcab5d19 - 0e93176640ac - - 553bfe8bd0b5 + - 8f1b150a2487 + - 0124fce4654a + - 890b794c997d - 841084c5fc46 + - d6d5ccc2c581 + - fa5259cc561b + - a929ce596a34 + - 553bfe8bd0b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - 21e491ad532a - - ddddce450736 - - 067592b6b312 - b9e31c5c01c7 - b2860df42e16 + - ddddce450736 + - 067592b6b312 - 94fe43e75ddc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 25ca5d73aedf - 321347bd0494 + - 25ca5d73aedf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: + - 22286dab5aa1 + - 3371c5bdc17a - a7f16f24e9a1 - faee8629b460 - 5258e18bbe23 - - 3371c5bdc17a - - 22286dab5aa1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -54,22 +54,22 @@ tools: owner: iuc revisions: - 5ecdeca79a0d - - e4bd1e99bacf - - 2babe6d5c561 - - 46ae58b1d792 + - e5c372c91e46 + - 0d243f458b53 - 2dd755c1c6ff + - cf13a1e03e5b + - 602fb8e63aa7 + - 4048d82f0c88 - 94170eee0ad8 + - 46ae58b1d792 - bb935709506a - - 4048d82f0c88 - - cf13a1e03e5b + - 2babe6d5c561 - 41030a6c03b7 - - 602fb8e63aa7 - - ea8146ee148f + - 1e62c28ba91d - 1440ae06552f - e824f5d958d0 - - e5c372c91e46 - - 0d243f458b53 - - 1e62c28ba91d + - e4bd1e99bacf + - ea8146ee148f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu @@ -89,24 +89,24 @@ tools: - name: flye owner: bgruening revisions: - - 3ee0ef312022 - - 291923e6f276 + - 276f5d8712d5 + - e27815e82dd4 - 3e4f8642c77e - 1f0769f0b56b - - 8d4f03b5fe9d - - e27815e82dd4 - - cb8dfd28c16f - - 276f5d8712d5 - 1ce9b1d72ec3 + - 3ee0ef312022 + - cb8dfd28c16f + - 8d4f03b5fe9d + - 291923e6f276 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 460fad600dce - - 3169a38c2656 - b2f674562a18 - 01210c4e9144 + - 460fad600dce + - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle @@ -121,12 +121,12 @@ tools: - name: gfastats owner: bgruening revisions: - - f4a3eff8ab85 - - 6ec1b853c8fd - - 3fba9c77550a - - 690c2caa367e - 3ef480892a9f + - 690c2caa367e - 5127a713de83 + - 3fba9c77550a + - 6ec1b853c8fd + - f4a3eff8ab85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -138,24 +138,24 @@ tools: - name: hifiasm owner: bgruening revisions: - - ec9e21e9c71b - - 2061fb3b81b4 - - 5bec28269d95 - - 5161f204ba63 - - df25d4fb79b7 - - 41cea2aa2dce - 3f7be05a1597 - - 366a11d316a7 - - f3c89da3af16 - 6505bd37670d - - 9ef6920c3089 - - 0ee0c3089254 + - ec9e21e9c71b + - f3c89da3af16 - 60024a528cbd - - da9d8bf98802 - - 71740308d412 + - 2061fb3b81b4 + - 5f625c63b8bc - 045c7c3d8e59 + - 71740308d412 + - da9d8bf98802 + - df25d4fb79b7 + - 0ee0c3089254 - 284a1cb82b61 - - 5f625c63b8bc + - 366a11d316a7 + - 9ef6920c3089 + - 41cea2aa2dce + - 5161f204ba63 + - 5bec28269d95 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -179,43 +179,43 @@ tools: - name: megahit owner: iuc revisions: - - 14ddfc8ffb93 - a96f3ad4e0d8 - de387b2b2803 - 7518ee87b53d + - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - d7edbc9c3a07 - - f8113c25bc6b + - eb7b00ec347d - 9d79beb19ac3 + - d7edbc9c3a07 - 39edec572bae - 09c589057ee8 - - eb7b00ec347d + - f8113c25bc6b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - eadfd71dde37 - 29dabd8db6f2 - 51c2360aa807 + - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 2ecf5a570907 - - fd128c111ab0 - e731ea24e48d - - eb7a370f6588 + - fd128c111ab0 + - f369ef5f210b + - 606b09cc9860 + - 2ecf5a570907 - 3ca2d2a9068c - - 99ecfdafc64f - f338e9942b27 - - 606b09cc9860 - - f369ef5f210b + - eb7a370f6588 + - 99ecfdafc64f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -227,10 +227,10 @@ tools: - name: miniasm owner: iuc revisions: - - a7b889b90140 - - b799a615995d - 8dee0218ac7d - 73a3846701e1 + - a7b889b90140 + - b799a615995d - 8b6d0d85252b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -249,9 +249,9 @@ 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 @@ -263,46 +263,46 @@ tools: - name: pretext_map owner: iuc revisions: - - 02831bf9e95f - - c6cec5ab35c1 - - 2b16ba799da9 - 8fef980d48b5 - - d256a51a656b - - bbe19ef04a74 - dfb8a4497339 + - bbe19ef04a74 + - 2b16ba799da9 + - 02831bf9e95f + - d256a51a656b + - c6cec5ab35c1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - 76d4cbefff85 - a315c25dc813 + - 76d4cbefff85 - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 675488238c96 - - 875d0f36d66f + - 59db8ea8c845 - 6fcbee531de6 + - ebb0dcdb621a + - 875d0f36d66f - 7594365c546b - - 3061c8b029e5 - - 72472698a2df - 342a1d1fed7b - - ebb0dcdb621a - - 59db8ea8c845 + - 675488238c96 + - 72472698a2df + - 3061c8b029e5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - cd06929b224b - - d865b62f501c - - 78c533842eeb - aa39b19ca11e + - cd06929b224b - 39bed8de8017 + - d865b62f501c - a199cd7ac344 + - 78c533842eeb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragtag @@ -314,12 +314,12 @@ tools: - name: raven owner: iuc revisions: + - 2b2a352488fa + - f11b994b7eb2 - f8564b2d7f63 + - 5c55448d0f33 - 3edba9afc9bc - 33b7d8481a76 - - 2b2a352488fa - - 5c55448d0f33 - - f11b994b7eb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast @@ -333,12 +333,12 @@ tools: owner: iuc revisions: - 28189050e437 - - 5fc94b3a4704 - 53c2bc8c2ae3 - - e122f9101584 - ef69617ecb42 - - 378e55aeeb25 - 1d06c8b38e77 + - e122f9101584 + - 5fc94b3a4704 + - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -350,92 +350,92 @@ tools: - name: shovill owner: iuc revisions: - - d9f6a00b6db7 - - ee17a294d3a3 - - 83ead2be47b2 - ad80238462c1 - - f698c7604b3b - - 196a599ec43d + - 83ead2be47b2 - 865119fcb694 + - d9f6a00b6db7 + - 196a599ec43d + - f698c7604b3b + - ee17a294d3a3 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 owner: iuc revisions: - - 1bb12736175c + - 604782a8a53a - 1fc82fe7ebef - - 051fd2db8a27 - 7490b213baa9 - - 604782a8a53a - 904bf932cf78 + - 1bb12736175c - c33a476f4001 + - 051fd2db8a27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - d6e617c4e338 - - 9678993ca5bd - 655fa188c3cc - - 808b3a0a6716 + - ad8b536d1caa + - d6e617c4e338 - fee85957cebe + - 808b3a0a6716 + - 9678993ca5bd - 34305b013402 - - ad8b536d1caa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - b8002c3f7141 - - 6b5a5842531e - - 8d4b90bf9caf - e5a3b75a271f - - 7e27faaad80e - 037f9927c4ff - 21da31ed41a1 + - 8d4b90bf9caf + - 6b5a5842531e + - 7e27faaad80e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 7922870efcca + - 328aa71f0f3c - 5b26685e5d3b - 2a10645aeadd + - 86f66ab58e14 + - 7922870efcca - f1532cb33c75 - 9de69775f512 - - 86f66ab58e14 - - 328aa71f0f3c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: + - 85fb02c43042 - 6aad515a5270 - e41dcb0e913b - - 340bc17f49cf - 8cc856b935ee - - 85fb02c43042 - 1708851f8804 + - 340bc17f49cf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - 6357b127161e - - d159735a6a9f - - d5fb354f745d - 249f6a28c751 - de1260f8a300 + - d5fb354f745d + - d159735a6a9f - b65a43f70b99 - b3490b036c5a + - 6357b127161e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades @@ -443,12 +443,12 @@ tools: revisions: - dd7ad84f3943 - 33368fec3b70 - - 7897763d14ec + - d5887ace0dd4 - 9006e5836729 - - b7829778729f - a90db5dbaaf3 - - d5887ace0dd4 + - b7829778729f - d2d1df21dfb9 + - 7897763d14ec tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster @@ -456,53 +456,53 @@ tools: revisions: - 189e837009c9 - ced385aa976d - - 505a9833ab5d - 6f4c8ad6ea01 - - 0368ac680e70 - 8f631679571f + - 0368ac680e70 + - 505a9833ab5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 19bdfd1e6fe3 - - d40ed4eb0c0e - - e59bee4565b3 - 9ded6109434a - - 356afed970b4 - a7ed21de23fe + - d40ed4eb0c0e + - 356afed970b4 + - e59bee4565b3 + - 19bdfd1e6fe3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: + - 4688ae3b49b5 - ebd801e712bc + - 6dd935e4984b - 7673a6c920b2 - - b23249f81bc4 - 80a17897564d - - 4688ae3b49b5 - - 6dd935e4984b + - b23249f81bc4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: + - 937ea677d437 + - 59bd28f6265d - b5e35a2ca4f3 - - ed312479d9eb - cb1e3db43020 - b64696992ee9 - - 59bd28f6265d - - 937ea677d437 + - ed312479d9eb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 2628f6790eda - cb4768eeca3b - - 05bd7504fdb2 - - 383bb5ad32e2 - b9b0246a2be3 + - 383bb5ad32e2 + - 05bd7504fdb2 + - 2628f6790eda - 6015aa0303f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -510,29 +510,29 @@ tools: owner: iuc revisions: - 8f9f06995f98 + - 3e44ef016b45 - 6e26c9afd301 - - e022dff952df - - e92675014ac9 - 0a3a602cd1e3 - 9e3e80cc4ad4 - - 3e44ef016b45 + - e92675014ac9 + - e022dff952df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: + - 08256557922f - 8d09f8be269e - 5da9a0e2fb2d - - 08256557922f - 920677cd220f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 37d88f41c810 - - 82398ba86ba7 - 4a53b89fa703 + - 82398ba86ba7 + - 37d88f41c810 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko @@ -544,8 +544,8 @@ tools: - name: yahs owner: iuc revisions: + - 39495e107274 - 425e63adcc5d - ff4031bfaa22 - - 39495e107274 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index 7d98e94db..9328b582b 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -11,17 +11,17 @@ tools: - name: mlst owner: iuc revisions: - - 1f5641a52664 - - 31812e7a1315 - ded48b36f3b7 - 8e8dc9a1e3e5 + - 31812e7a1315 + - 1f5641a52664 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/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index a765a2481..7c0bc3986 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,27 +2,27 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 159b04e36791 - - 0840ba83860c - - 7beb76ffbc0f - - a9c9d768b751 - - d1f62024a08b - 1c427e24fb79 - d58c27d2c5a7 + - d1f62024a08b + - 7beb76ffbc0f + - a9c9d768b751 - 204a131e47db + - 0840ba83860c + - 159b04e36791 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge owner: iuc revisions: - - cab19c0452c4 - 1bb2b5b52030 + - cab19c0452c4 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_tadpole owner: iuc revisions: - - ce13b4678f18 - 0ddf147d1897 + - ce13b4678f18 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 52bd79064..03f53c7d3 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - 0a5c785ac6db - - 589e7e57fd6d - 64e2edfe7a2c - - a1a923cd89e8 - - dde39ba9c031 - - b28e0cfa7ba1 - - e19bebe96cd2 - - 87ee588b3d45 - ce3c7f062223 + - e19bebe96cd2 + - 0a5c785ac6db - 07e8b80f278c - - a8eabd2838f6 - a68aa6c1204a + - dde39ba9c031 + - 87ee588b3d45 + - b28e0cfa7ba1 + - 589e7e57fd6d + - a8eabd2838f6 + - a1a923cd89e8 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 604ff9d67..58b0749a3 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,8 +8,8 @@ tools: - name: diamond owner: bgruening revisions: - - 62c9df8382c2 - 54f751e413f4 + - 62c9df8382c2 - e8ac2b53f262 - f921014aba5a tool_panel_section_label: Blast + @@ -17,21 +17,21 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - d999e774072a - - 6f386c5dc4fb - - e25d3acf6e68 - acf4e47b734c - a52d2d93e595 - - cbf3f518b668 - - 5edc472ec434 - - 0e3cf9594bb7 + - d999e774072a + - e25d3acf6e68 - 2889433c7ae1 + - 6f386c5dc4fb + - 0e3cf9594bb7 + - 5edc472ec434 + - cbf3f518b668 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart owner: crs4 revisions: - - e9005d1f3cfd - 1334cb4c6b68 + - e9005d1f3cfd 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 168ba9496..ba9f81fc6 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 - - f4230f116196 - 27ee142314a9 - - 710301bc46fa - - c8cdde00b105 + - f4230f116196 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -130,40 +130,40 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 3b8a9d5ced85 - - 79cfd9ead848 - 88076940fa94 - - bfb65cb551d8 + - 79cfd9ead848 - 0fac8e2afc13 + - bfb65cb551d8 + - 3b8a9d5ced85 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - 55918daa5651 - eb6564a60136 - - f5d979cb4b54 - - 715cd0e87781 - - b46d4b4d995c - d532b7e5f64b + - b46d4b4d995c + - 55918daa5651 + - 715cd0e87781 + - f5d979cb4b54 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - 5579659312e6 - - fdf2cc80adb5 - - dae135dfd519 - d2f955aea23a - f26afd1b7104 + - fdf2cc80adb5 + - 5579659312e6 + - dae135dfd519 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: + - bc31d02be922 - d1d0efda35c0 - 319a28774da9 - - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup @@ -172,32 +172,32 @@ tools: - ed736e6eee39 - 2c349b027a01 - cac1886249a2 - - 4da9ee404eab - 070e3ecc3fda + - 4da9ee404eab tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: + - f197e34c33a9 - 2e219a2d9327 + - da8753545526 - 525ca7c8065f - 807aa4c9293d - - f197e34c33a9 - 73008ef1f487 - - c0c9a5024177 - - da8753545526 - d1f803b5943c + - c0c9a5024177 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - c4fbab8e03c5 + - 27ea4e1a3f95 - 2c8ed1b52bf7 + - c4fbab8e03c5 - 61094e01eff9 - - 27ea4e1a3f95 - - 1809414a9454 - 7568ae18908a + - 1809414a9454 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 - 79e8ab8f1e81 - - 730ef07b90ae - d7ec25187599 + - 730ef07b90ae - ccfbd956a2d3 - - 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 @@ -268,9 +268,9 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - e6011617c748 - - e2c36f62e22f - b59c91adeac1 + - e2c36f62e22f + - e6011617c748 - 4242b4d68e9c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -351,10 +351,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 9b48456a96fe - - d4c67ced6abc - - 85fad59f8168 - bf99565cec1f + - 85fad59f8168 + - d4c67ced6abc + - 9b48456a96fe tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 90f5c987f..065091000 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: - - 163688bb8f73 - - fa56d93f7980 - 2605cbdaa7d8 - - c97a786e8fb5 + - fa56d93f7980 - f907216064f6 + - 163688bb8f73 + - c97a786e8fb5 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -25,18 +25,18 @@ tools: - name: macs2 owner: iuc revisions: + - f5d67c722d67 - 495a4173006f - 640d3af5d833 - 86e2413cf3f8 - 424aefbd7777 - - f5d67c722d67 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator owner: pjbriggs revisions: - - 087d9872fb0d - b695071de766 + - 087d9872fb0d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index 582b71716..db98c6b38 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -9,17 +9,17 @@ tools: - name: collapse_collections owner: nml revisions: - - 33151a38533a - - 830961c48e42 - 90981f86000f + - 830961c48e42 + - 33151a38533a - 25136a2b0cfe tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - dfde09461b1e - 3ddd99c7efee + - dfde09461b1e tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,9 +31,9 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 6cbe2f30c2d7 - - 0046692724f9 - 2dae863c8f42 + - 0046692724f9 + - 6cbe2f30c2d7 - baabc30154cd tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index a046d6127..e0784a3ee 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -2,9 +2,9 @@ tools: - name: agat owner: bgruening revisions: + - d6ede73082da - abba05ead5d7 - e7449b2c14bf - - d6ede73082da tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -16,32 +16,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - ab9350a8ab4d - - 3b6f97e7094c - - 6ef0b5664c69 - 5e1240a87bcb - - f3a19509108a - 0b3c3ad92827 - a3b86937ead6 - 4a6ee918c13a + - 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: - - d4d4e9febf5c - - e177a8ea0bf1 - - e525f9ffb9ac - - 501c21cce614 - - 091bb5922a82 - - 1b5fc03380d4 - - 72ed72122deb - bd46669113b9 - - 33c99804a32f - 54ccb7e1f49a + - 1b5fc03380d4 + - 72ed72122deb - 584008e574b2 + - 501c21cce614 + - 33c99804a32f + - e177a8ea0bf1 + - 091bb5922a82 + - d4d4e9febf5c + - e525f9ffb9ac tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -59,8 +59,8 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - e7ed3c310b74 - 7e801ab2b70e + - e7ed3c310b74 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta @@ -74,16 +74,16 @@ tools: - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - 4b347702c4aa + - 614a63f14adf - 43807a65369f tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa owner: iuc revisions: - - 8e9d604e92f4 - e33c82b63727 + - 8e9d604e92f4 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -96,8 +96,8 @@ tools: owner: devteam revisions: - 154d00cbbf2d - - 4dea02886337 - 3e436657dcd0 + - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -115,8 +115,8 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - f5c632894818 - 705821bf30d2 + - f5c632894818 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bam_to_cram @@ -135,19 +135,19 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 2dcfbbf9071a - 78fb18899c99 + - 2dcfbbf9071a - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: + - 63769c4217a7 - 26c6706bfb07 + - b9b385097f13 - 92ac8e086317 - - 63769c4217a7 - 19e45916daf9 - - b9b385097f13 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf @@ -168,9 +168,9 @@ tools: - name: ucsc_wigtobigwig owner: iuc revisions: + - fa49730d1d4b - a2f83a375bf2 - 98704d357ede - - fa49730d1d4b 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 08e1b0cd2..4c95fbd4a 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,93 +2,93 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 268e91e540ee - 5f6d123679f4 - - de72ba3ed6f2 - - e821645ef8fc - 29451af70c52 - a1ca9bccc7f2 + - de72ba3ed6f2 + - e821645ef8fc - c929a006727f + - 268e91e540ee tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 0e143b4c3987 + - 5d11599b8a7d + - 12af64f93288 - bb1e4f63e0e6 - 7a7fd0f5f15d - - 5d11599b8a7d - - 2d2cf5c1ea8a - 0e49b109abc2 - - 12af64f93288 + - 2d2cf5c1ea8a + - 0e143b4c3987 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - c06951d10364 - - 1d848bc4585f + - 81b1e3e1fc6c + - 195e98217334 - 7c1beb6d6eca - dc059492a995 - - 195e98217334 - - 81b1e3e1fc6c + - c06951d10364 + - 1d848bc4585f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 93eb012d9eed + - 71aa86af6762 - 3d211717a775 + - 93eb012d9eed - a67ac707496a - 07418a30ed01 - 26e7304d6737 - - 71aa86af6762 - bfff7454b59a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: + - 56d5b797ce84 - 26983857c91a - - dd0b7398bb96 - - 5be24eba848d - 29fcfd36e90a - - 2bc10a9ca58b - b8858746dc1f - - 56d5b797ce84 + - 2bc10a9ca58b + - dd0b7398bb96 + - 5be24eba848d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - 7e6bcd2e5128 - - c3e012dfe21f - - 7ef978dc1b8a - - e6d0bff01239 - 72bfafe3330b + - c3e012dfe21f - ee3a1b0f45f1 - 9384cd033f30 + - e6d0bff01239 + - 7ef978dc1b8a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - d9a637e83828 - 9470f29702f8 - - fd1275e01605 - fb9cf9c97ec4 - - a60c359ec43c + - d9a637e83828 - b73e213add0c - - 167788df3b46 - 514fa53b5efb + - 167788df3b46 + - fd1275e01605 + - a60c359ec43c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - 5bffaa8354a1 - - 2c37ce318bc3 - 86febdcc4283 + - 2c37ce318bc3 - a02cfa31e9cb - ca0616bb2cdf - e479c7ca5570 @@ -98,109 +98,109 @@ tools: - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 192ef85c0b0b - - 004aea905d4d - - 1fcb7adc39b8 - 78f405266706 - 01fb6a7654e6 - - 69a8621ca2f0 - 2d466b530754 + - 192ef85c0b0b + - 1fcb7adc39b8 + - 69a8621ca2f0 + - 004aea905d4d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: + - 9ecba5e225a6 - d9ce4897dbb2 - - 459cfa861f0b - - 3c9f0c486cca - 2f9e4843f480 - - db940c262830 + - 3c9f0c486cca + - 459cfa861f0b - d580d6acd1df + - db940c262830 - 137c4beed34b - - 9ecba5e225a6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - fbe773640707 - bad3ca889618 - - bd7db9e2f2cb - - fd408d755394 - 2c66e43f1c86 - - f264afa9fa6f - 32e451def88c + - fd408d755394 + - fbe773640707 + - f264afa9fa6f + - bd7db9e2f2cb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: + - 7fda5607e777 - 3b9d990a0a0e - 4e12ea27f788 - - 7e361d147872 - 56bce3c82278 + - 7e361d147872 - 231994413f89 - - 7fda5607e777 - 9368fbc49c8b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - d9114ef1c8a5 - - c03c3384cd81 - - 94ca68515826 - e65d16fb2724 - - b1779366c8e9 + - c03c3384cd81 - ce4ce3316f74 + - d9114ef1c8a5 - 4431f39ede55 + - 94ca68515826 + - b1779366c8e9 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 793665fff0f8 + - 2da482e408b8 + - 4ed32329e0ed - f8fc4e5aff9d + - b88ebb3672a1 + - 793665fff0f8 - 23f7c5f1fdaf - - 4ed32329e0ed - - 2da482e408b8 - d57251071381 - - b88ebb3672a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - a7849312d328 - - 25d830337d31 - - e4c7985d4585 + - 010e58e9d822 - ba6efa77fb79 + - e4c7985d4585 - a4dfb122e52b - - 010e58e9d822 - 512155688d98 + - 25d830337d31 - c60570fa602f + - a7849312d328 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - aa200e4f3939 - - c899e0ccff8c - - 00d869ea03a1 - 69264da0ce77 - - 4d678170d29b - 443d9a9d6d11 + - 00d869ea03a1 + - 4d678170d29b + - c899e0ccff8c + - aa200e4f3939 - 38e3f226248b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - 10301d137111 - - a2d70c4fd406 - c361b12d207a + - a2d70c4fd406 + - 10301d137111 + - aac8444d6681 - d806504e96d9 - 6662b1a8d326 - - aac8444d6681 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 8525c44bf..b4957b080 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -9,8 +9,8 @@ tools: - name: obi_clean owner: iuc revisions: - - 08d873cdd5f6 - 7d16de45c021 + - 08d873cdd5f6 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -23,22 +23,22 @@ tools: - name: obi_grep owner: iuc revisions: - - 02bab5ff7c37 - e9e49cf06b42 + - 02bab5ff7c37 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend owner: iuc revisions: - - 8cb6bd511879 - 94f412098ac8 + - 8cb6bd511879 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -58,14 +58,14 @@ tools: - name: obi_tab owner: iuc revisions: - - 3299c7d5268f - 4cf47c504672 + - 3299c7d5268f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq owner: iuc revisions: - - c0f7b58b4ce4 - d4bea99366f9 + - c0f7b58b4ce4 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index 68ea85a08..caecd371d 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - 832c20329690 + - dba489bfcd62 - ce385837c160 + - 832c20329690 - 63dd26468588 - - dba489bfcd62 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 9c6188c78..9ba532992 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -8,10 +8,10 @@ tools: - name: bwameth owner: iuc revisions: - - 6da3972210ee - - 62f5fab76dfb - 29bdbc353f20 + - 62f5fab76dfb - d82648ad25a3 + - 6da3972210ee - cf1322aeb137 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index 8abdcf54a..8cd49ab4a 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,42 +8,42 @@ tools: - name: cutadapt owner: lparsons revisions: - - de6cebe3c043 - - 660cffd8d92a - - 8c0175e03cee - - 135b80fb1ac2 - - b1c926deaa2d - - c053d4cad713 + - c4b82dce8335 + - 8665bcc8b847 + - fe74900d6dc7 + - 093678460093 + - 5915ea1ec9b1 - 48f587c13075 - - e4691e1589d3 - - 5eb7e84243f2 - 288f97432497 + - 5eb7e84243f2 + - 135b80fb1ac2 - 4e5056fefd88 - - 093678460093 + - 8c0175e03cee + - c5e2e5902201 + - e4691e1589d3 - 44e2cc14f75b - - 5915ea1ec9b1 - - 49370cb85f0f - - 8665bcc8b847 - - fe74900d6dc7 + - b1c926deaa2d + - 660cffd8d92a - 64172f1c1202 - - c4b82dce8335 - - c5e2e5902201 + - de6cebe3c043 + - c053d4cad713 + - 49370cb85f0f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: - - 9db07fd39f85 - f666895cbebd - 8889eb864cef + - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length owner: devteam revisions: - 7d37cfda8e00 - - 5cbde03c1103 - de2db1bdfbf8 + - 5cbde03c1103 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -61,8 +61,8 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 516b97a23d7e - 9457a20156db + - 516b97a23d7e - 859422bcb689 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -76,196 +76,196 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - f773e98b26cf - - ec0b5076173a - f81d4362b6c1 + - ec0b5076173a + - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: - - 56022eb50bbd - - 0dbb995c7d35 - cd0874854f51 + - 0dbb995c7d35 + - 56022eb50bbd - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - 65b93b623c77 - - ecb9f4854617 + - d60c3f704da0 - dbf9c561ef29 + - a626e8c0e1ba + - ecb9f4854617 - 1d8fe9bc4cb0 + - 65b93b623c77 - dbfc505896e9 - - d60c3f704da0 - - a626e8c0e1ba - c59d48774d03 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - 9115b978ce10 - b05e39b9c170 + - 9115b978ce10 - f1dc2a761c30 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: - - 10b75444feae - - 81a9090d6df3 - '144275714590' + - 81a9090d6df3 + - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer owner: devteam revisions: - 47e5dbc3e790 - - 8611b80a14d6 - e9f8633db0a2 + - 8611b80a14d6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation owner: devteam revisions: - 5b87038565bb - - e30352e889fe - 7861f3b10c68 + - e30352e889fe tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality owner: devteam revisions: - - 4e1d64e6385f - 9dfda4e310ed + - 4e1d64e6385f - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - 523c2aff0376 - - 03d57fea6482 - f3936d0632cb + - 03d57fea6482 + - 523c2aff0376 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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_joiner owner: devteam revisions: - - c885369b207b - - 09a2199cd356 - 8d958759cf2a + - 09a2199cd356 + - c885369b207b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - - e39cc71d3ed6 - - 397dc333436b - 249c8393f2d4 - 35e38452bb3f + - e39cc71d3ed6 + - 397dc333436b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter owner: devteam revisions: - - 54053ea6c77e - 74db4cffab1f + - 54053ea6c77e - 045f0e1043f7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats owner: devteam revisions: - - f0e7deab6518 - - f86c27295151 - b1cea1b2fcd0 + - f86c27295151 + - f0e7deab6518 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer owner: devteam revisions: - - 33794bdb7fe0 - - f0b18efb97f1 - b63b2bfb3ea3 + - f0b18efb97f1 + - 33794bdb7fe0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta owner: devteam revisions: - - ac3fed111eb6 - 297962e79f39 + - ac3fed111eb6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter owner: devteam revisions: - - 09070cacefd8 - - 567d5b3c52b1 - - 529bccd5e4a1 - d5e9e83cd3d8 + - 529bccd5e4a1 + - 567d5b3c52b1 + - 09070cacefd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - 8abdedf55101 - - 4bedca26c133 - 0b7ec11b3c7c + - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - 90858c306551 - - 736b8f6ee456 - bdf1ce174e39 - cb1e251cac37 + - 736b8f6ee456 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: - - 7ce1891db6f5 - - 07497255281e - 421f0af4ee95 + - 07497255281e + - 7ce1891db6f5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - - 02f8a17a4ebd - - b29d37ca9e41 - 3599f5451ee2 + - b29d37ca9e41 + - 02f8a17a4ebd - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - 6027ef51ef91 - 177f0621c266 - e246088b6e34 + - 6027ef51ef91 - 0c2907307ba4 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 @@ -278,40 +278,40 @@ tools: owner: iuc revisions: - 037f0acc7830 - - b4c6f054210a - f69501361cec - 2f804526f5fd + - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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 - - 29ef2c5ec205 - 61eb4cfc7313 + - 29ef2c5ec205 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: + - 812705bcf39c - 795cd16de38f - fe1ae2ebf63d - - 812705bcf39c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - 4b494533146a - 3da72230c066 - a019807f4e67 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic @@ -324,40 +324,40 @@ tools: - name: ucsc_fasplit owner: iuc revisions: - - bf04bd405d5b - 71f649c23021 - d3f58a0dc09d + - bf04bd405d5b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - 24013bf85a6f - - e654095ab143 - 71ad4a56c40c - - a535cf1e5da4 - 8250ea3a1501 - b557acca0b56 + - a535cf1e5da4 + - e654095ab143 + - 24013bf85a6f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup owner: iuc revisions: - - f1d33e4c7bd8 - c5a2ee07c4e1 + - f1d33e4c7bd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract owner: iuc revisions: + - 9fa7803d1c51 + - 015cf18f4a15 - 6a675c3aa610 - 27ac32a22ad2 - - 9fa7803d1c51 + - 7accf7407811 - 7a7e33d28f62 - f3759eec3018 - - 7accf7407811 - 828dba98cdb4 - - 015cf18f4a15 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: - - e4e12f0b3af1 - 4c8a1c7d3608 - 953b4821b183 + - e4e12f0b3af1 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 67b483ffa..e04b128de 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,8 +2,8 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - 64e9a6afdd0c - 7b4468117008 + - 64e9a6afdd0c - e41385662e5e - ce9cd02d5b88 tool_panel_section_label: FASTQ Quality Control @@ -18,68 +18,68 @@ tools: - name: fastqc owner: devteam revisions: + - 5ec9f6bceaee + - e7b2202befea - 9da02be9c6cc - - ff9530579d1f - 3d0c7bdf12f5 - - 5ec9f6bceaee - - 2b0c9d9fc6ca - 2c64fded1286 - - e7b2202befea - f2e8552cf1d0 + - 2b0c9d9fc6ca + - ff9530579d1f tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: + - a252d8415583 - c1a33f603da2 - 89d299153577 - - a252d8415583 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - 18a51655db17 - - b6b54ba71bd8 - ad116ae3f4d9 + - b6b54ba71bd8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - 59003d0543cd - - 7306ec78632a - cc0fd298cc17 + - 7306ec78632a + - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - 1f296803dfa3 - 8880fb74ef56 + - 1f296803dfa3 - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 75c93c70d094 - - b2f1f75d49c4 - - c1a4b5f3b432 - abfd8a6544d7 + - f7e2f1eb3a16 + - 75c93c70d094 - 1c2db0054039 - - bf675f34b056 + - 9a913cdee30e + - b2f1f75d49c4 - 3d93dd18d9f8 + - bf675f34b056 + - c1a4b5f3b432 - 5e33b465d8d5 - - 9a913cdee30e - - f7e2f1eb3a16 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 949f01671246 - cd7e644cae1d + - 949f01671246 - 084bbd8ba7b8 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 c01999d90..0dfc5355c 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: - - 9e776e7fab4f - 19f42b3ea391 + - 9e776e7fab4f 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 b747339b5..b329fac45 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -9,15 +9,15 @@ tools: - name: sample_seqs owner: peterjc revisions: - - bdaefd241921 - 7c40a1fbc82e + - bdaefd241921 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_filter_by_id owner: peterjc revisions: - - 83a19df00eab - - 141612f8c3e3 - 85ef5f5a0562 + - 141612f8c3e3 + - 83a19df00eab 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 6585da8c3..8a5dad66d 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -2,8 +2,8 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 3630a6e624d4 - 142d95ab942e + - 3630a6e624d4 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend @@ -16,9 +16,9 @@ tools: - name: gemini_annotate owner: iuc revisions: + - f2f3bc622a16 - 0c8f7322f8fc - 8f53b238a360 - - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -38,8 +38,8 @@ tools: - name: gemini_db_info owner: iuc revisions: - - 4c5f4e9b1931 - 7d75673f4d6f + - 4c5f4e9b1931 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -87,15 +87,15 @@ tools: owner: iuc revisions: - cf61daf064fe - - b2c25142267e - 45296e47d565 + - b2c25142267e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 90021fffff70 - 2969a1f43b7d + - 90021fffff70 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors @@ -122,9 +122,9 @@ tools: - name: gemini_query owner: iuc revisions: + - 666f60a9331a - 840fb4850be3 - da74170c55c7 - - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -137,15 +137,15 @@ tools: - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh owner: iuc revisions: - - 345d41f3f574 - 93967598e18e + - 345d41f3f574 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic @@ -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: - - 8f04952b8882 - 0c58ba91d018 + - 8f04952b8882 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 301093442..62d2c91e4 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -9,8 +9,8 @@ tools: - 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 @@ -23,14 +23,14 @@ tools: - name: mageck_pathway owner: iuc revisions: - - 39a996d44e16 - 9744e1124d0f + - 39a996d44e16 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test owner: iuc revisions: - - 688a8eccea71 - 9b4f4533c9ee + - 688a8eccea71 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index 72075d30f..c3525cc69 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,8 +2,8 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - c1b437242fee - e9df53a75f3c + - c1b437242fee - 983bf725dfc2 - b39347891609 tool_panel_section_label: Get Data @@ -17,54 +17,54 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - 28587613264f - - e063168e0a81 - 1c58de56d587 + - e063168e0a81 + - 28587613264f tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - e407b9da183a + - e08a7ad4378b - 516a54ddf218 - - c441583adae5 - - ba931a59dd59 - 6591f049cf7e - - 6ea73833cf67 - - e08a7ad4378b - - 69ebb7f46e45 + - 9a776b080193 + - f5ea3ce9b9b0 + - 1790dcf3c32d + - ba931a59dd59 + - f8054ea1c365 + - c441583adae5 + - 4317d3cb6cba + - 734abc7ac21d - 653e89d73fc4 - 83c7d564b128 + - 1ec814014652 - 4df8de2d0e48 - - 734abc7ac21d - - 4317d3cb6cba - - 8848455c0270 - - f8054ea1c365 - 7068f48d0ef9 - - f5ea3ce9b9b0 - - 1ec814014652 - - 1790dcf3c32d - - 5e6237d58b0c + - 8848455c0270 + - e407b9da183a + - 69ebb7f46e45 + - 6ea73833cf67 - aad3885b3216 - - 9a776b080193 + - 5e6237d58b0c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: + - 75b3b3d0adbf - 21a560af5913 - 9aaa46d45472 - 34758ab8aaa4 - - 75b3b3d0adbf tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: + - 468c71dac78a + - bfdc6a7ffd3a + - 95fb5712344f - af5eccf83605 - 054483e27a35 - - 95fb5712344f - - bfdc6a7ffd3a - - 468c71dac78a 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 ce0237132..2fa627162 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: - - 740057a5126d + - fd59d783248a + - 7f13dc906cb9 - 290a11559985 - - a64dc31ab7f2 - c4bde687c846 - - 7f13dc906cb9 - - fd59d783248a - - ae9994cf526f + - a64dc31ab7f2 - 4b519282a05b - df7356989ac1 + - ae9994cf526f + - 740057a5126d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,8 +28,8 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - f95284aa2946 - 867ab348287d + - f95284aa2946 - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -42,24 +42,24 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: + - 3b37b1b1c3a7 - 51c6ccaace7e - - 374e9062d874 + - 48b42ee61bc5 - '566197475670' - - 3b37b1b1c3a7 + - 374e9062d874 - 53460afd5115 - - 48b42ee61bc5 - ca7cb0eaad62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - da4c086cff5b - 391a4cc45fea - - 3d059e9c2fba - 10515715c940 - d3a9e32672ec + - 3d059e9c2fba - 1a72f938213e + - da4c086cff5b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -72,26 +72,26 @@ tools: - name: ggplot2_pca owner: iuc revisions: - - ae344ccf9d62 - b1268b7544d3 + - ae344ccf9d62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - e3a675da7fd0 - - 5298e06f14f9 - d0fc8b746d57 - 5fe1dc76176e - - 299307abd804 + - e3a675da7fd0 + - 5298e06f14f9 - 1acf88921176 + - 299307abd804 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 @@ -110,8 +110,8 @@ tools: - name: graphlan owner: iuc revisions: - - 8f62f666dcb6 - 6e8eb0c0d91f + - 8f62f666dcb6 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: - - 17359b808b01 - 6cd09d7b5f37 - fd5dbf0f732e - - 4542035c1075 - - 667e17248bfe - - ca2def38369c - 1cfc579079a6 - - 2bb2e07a7a21 - - 112eb40ba6cf - a6e57ff585c0 + - 17359b808b01 - 836d1aa3e89a + - 112eb40ba6cf + - ca2def38369c + - 2bb2e07a7a21 + - 667e17248bfe + - 4542035c1075 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -158,38 +158,38 @@ tools: owner: iuc revisions: - f1691de443a7 - - 03c13085aecc - fe154a7af404 + - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram owner: iuc revisions: - - bd1416eea1f0 - 594b85e4237a + - bd1416eea1f0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plot_ragtag_paf owner: galaxy-australia revisions: - - 501dcf66c0ce - c1bed78b9ed5 + - 501dcf66c0ce 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 + - 62e3a4e8c54c - 1c5dcef5ce0f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 7b21a9b5922f - 9958188c6195 + - 7b21a9b5922f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -201,10 +201,10 @@ tools: - name: pretext_snapshot owner: iuc revisions: + - 6c571966cfb9 + - 44c66e8d21e6 - 26f2fe7e53a1 - 7c9417381ad5 - - 44c66e8d21e6 - - 6c571966cfb9 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -216,23 +216,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 7dd841a32245 - - 4ac4e7083b7e - - 360df4999907 - a1abfa420d9d - - 2824d77cd8f8 - - 14e7c35f3d00 - 36b848d5f3ec + - 2824d77cd8f8 + - 360df4999907 - 326a3db8d9d1 + - 4ac4e7083b7e + - 7dd841a32245 + - 14e7c35f3d00 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 73b8cb5bddcd + - 44608d0193ed - 83c573f2e73c + - 73b8cb5bddcd - 2f557f6abbfb - - 44608d0193ed 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 bee7d4c4c..3c6815952 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -21,20 +21,24 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph owner: ebi-gxa revisions: + - 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 tool_panel_section_label: HCA Single-cell @@ -44,34 +48,42 @@ tools: revisions: - 23d838d1569d - cc64914b0cf4 + - da611a744112 + - 474a69c47184 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster owner: ebi-gxa revisions: - - fc4b3b46dc9d - 36735850e461 + - 2ccd9f9e2cd0 + - fc4b3b46dc9d + - ad6995afd2e6 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers owner: ebi-gxa revisions: - d8f5224005bb + - 81c34e67f262 + - 49653e680ea4 - 0a8e527d1517 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 79da59a0b180 - 64dd8bb151e1 + - 79da59a0b180 + - 4667fe07bd68 + - 2861ca3bfe4d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn owner: ebi-gxa revisions: - - c9da9192eee5 - 9d76c3d6dff6 + - c9da9192eee5 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_combat @@ -84,8 +96,8 @@ tools: - 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 @@ -99,15 +111,17 @@ tools: - 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 + - 8d9c22419c56 - 3027cb62adbd + - 6b97ffba31da + - 28b1546857b0 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator @@ -120,8 +134,10 @@ tools: - name: scanpy_plot_embed owner: ebi-gxa revisions: - - 1be0fc4d8654 + - 35f6611fb8c3 - 7d5c97823f8b + - 56d22aa6cb3b + - 1be0fc4d8654 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet @@ -148,8 +164,9 @@ tools: - name: scanpy_regress_variable owner: ebi-gxa revisions: - - 0bab2ae44e7a - d18ed15697bb + - 36daab33aecf + - 0bab2ae44e7a tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_diffmap @@ -169,8 +186,8 @@ tools: - name: scanpy_run_fdg owner: ebi-gxa revisions: - - 65c3ec07502b - be019b069e31 + - 65c3ec07502b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_paga @@ -183,13 +200,17 @@ tools: - name: scanpy_run_pca owner: ebi-gxa revisions: + - 3ee74b58c72d - 4428dba93375 - 0cf90e01d9f8 + - 59028945c857 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 tool_panel_section_label: HCA Single-cell @@ -197,15 +218,19 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: + - 0f98603d0116 - 767a675b5254 + - fe562424a0a6 - ea91cfd0444e - - 0f98603d0116 + - bd4a244faeb8 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - 4cc9362782b4 - e2d0dc8a50ca + - f86b2c3bc459 + - 5605f8452eb3 + - 4cc9362782b4 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 47a721f7b..d0a954c22 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,56 +2,56 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 0f611e7d7858 + - 29f66c353bcb + - a4c13ddcc8ee - 9edf8894a22d - 921a2da49a0c + - 0f611e7d7858 - ed2cca6b5de4 - - a4c13ddcc8ee - - 29f66c353bcb tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - d404277cc87a - - 755df866ad0c + - 5746d61f0a91 + - 78fb5e286609 - ec4b948dc6f0 + - d404277cc87a - 11de0d28ab30 - - 78fb5e286609 - - 5746d61f0a91 + - 755df866ad0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 03dd3c16ae4e - - f72063d9426b - - 9e357a8b2ec3 - 977dc15add20 - 4d511437b1e5 - 11fa44ee0603 + - f72063d9426b + - 9e357a8b2ec3 + - 03dd3c16ae4e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - 0ba4f56a3613 - - c3e5e2cf12b7 - 77919cc3618e - - 1da5f169b491 - 41dbf4d162a2 + - c3e5e2cf12b7 - 3b5b54ed6392 + - 1da5f169b491 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 7babd8a46fe0 + - b63363075c2e - f741330d4a71 - - 5308ca68ef3d - 9939786dd9c9 - - b63363075c2e + - 7babd8a46fe0 - 12d51d7be66f + - 5308ca68ef3d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index 129618979..b929f1429 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: - - 81f0cbca04a7 - 699a5e9146b3 + - 3df9f0a4bf34 - 8bccb36e055a + - 81f0cbca04a7 - 0c777d708acc - 7db4fc31dbee - - 3df9f0a4bf34 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - 5791a7f65275 - - 5bc8cdc17fd0 - - 2436a8807ad1 - 0a53256b48c6 + - 2436a8807ad1 + - 5bc8cdc17fd0 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 @@ -38,8 +38,8 @@ tools: - name: 2d_simple_filter owner: imgteam revisions: - - d51310ab328a - f70b215d155c + - d51310ab328a - dba87c4b32d3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -53,32 +53,32 @@ tools: owner: imgteam revisions: - f3360fbeda64 + - 85edbb7a436b - fcadded98e61 - 10eed33aa9b2 - b07f4839ca77 - - 85edbb7a436b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 984358e43242 - 6e65fd971e13 + - 984358e43242 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - b58447a2eed2 - - 5bf8eb50b280 - 664232d2a3f7 + - 5bf8eb50b280 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - eb6c08714244 - 0e4dccaafef5 + - eb6c08714244 - e917a2424690 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -92,64 +92,64 @@ tools: - name: cp_common owner: bgruening revisions: - - 6070780813d9 - 670975e92458 - e7273daa5ae2 + - 6070780813d9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - - df3ad3ba5c6f - ef4aed1d34c4 - cdf8e3c57dae + - df3ad3ba5c6f 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: - 11f177b1a59e - - bace5a93a97c - f2ed92b011a9 + - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - f8fa0f6718a3 - - f24c370e5ea4 - d0178bdcd00e + - f24c370e5ea4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - 3245681b2f6d - - 31d195bedf6d - ad271f78a87a + - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - 993faa34333b - - 87d4d92d7487 - b6eec6087271 + - 87d4d92d7487 + - 993faa34333b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - 6100a22bf4f2 - ff1a86a87364 + - 6100a22bf4f2 - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -164,16 +164,16 @@ tools: - name: cp_measure_granularity owner: bgruening revisions: - - ac5bea85a391 - 2564f461de62 - a1a961c46d4b + - ac5bea85a391 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 20dbb1f7ec7b - a32c3f810ade + - 20dbb1f7ec7b - 91e03287f285 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -181,8 +181,8 @@ tools: owner: bgruening revisions: - 5499dc6f8ac1 - - b64af54c5c09 - 8536b1ae0254 + - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality @@ -197,24 +197,24 @@ tools: owner: bgruening revisions: - 980aed9e8fd5 - - 407925835dd9 - e52c75a28c4b + - 407925835dd9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: + - d85f11570109 - 79e10d12d90a - acf3aa487283 - - d85f11570109 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - 035a58c7f54a - - b76841ee5560 - 80b200ae516b + - b76841ee5560 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -227,8 +227,8 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 48102a685037 - 8083a87d2fdf + - 48102a685037 - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -236,8 +236,8 @@ tools: owner: bgruening revisions: - 33f4fa1413fb - - 27edbb90ab2b - 4ecf93628f97 + - 27edbb90ab2b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -249,8 +249,8 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 972d2c365739 - 1fd453cd757b + - 972d2c365739 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: idr_download_by_ids @@ -264,8 +264,8 @@ tools: owner: imgteam revisions: - f8b4eada923c - - 236ec78b2e53 - 7b6d9412c7f8 + - 236ec78b2e53 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index 4e8a2470c..c43a6e5ed 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,31 +2,31 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 3e4f434a69c6 - - 40737febe339 - - 3a72fede57ce - - e319b5b65879 - f362150bef41 - - 78bbd17d0703 - a38934e303b9 + - e319b5b65879 - 1069f6db0a0e - - e4ee04da1c19 + - 3a72fede57ce - d6e72da3ec35 + - 78bbd17d0703 + - 40737febe339 + - 3e4f434a69c6 + - e4ee04da1c19 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 2b95d5c04908 + - 618297d23022 + - 7fe36019c073 + - 8f8df367470d - f91cfb73d369 - - c88553ec696e - - 9537184d421f - fcbeda41d0ac - - 8f8df367470d - - 72ddd32392cd + - 2b95d5c04908 - 0135f1d487a0 - - 7fe36019c073 - - 618297d23022 + - 72ddd32392cd + - c88553ec696e + - 9537184d421f tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked @@ -42,53 +42,53 @@ tools: owner: iuc revisions: - 94df24c6bc00 - - ee29337f905c + - 7f1cfa4c0e32 + - 5dc33613c288 + - 8d36959b000d + - 43aac8d29685 + - a1c2aecd7a0d + - 28a6f1908fcc - bd2a7d1316b9 - 8c05afb547fa - - a1c2aecd7a0d - - 43aac8d29685 - - 9eaadf03e0df - - ee2beb764a7b - - 8d36959b000d - - 5dc33613c288 + - ee29337f905c - 6a1515bb0687 + - ee2beb764a7b - 3d18f8c3c0f6 - - 28a6f1908fcc - - 7f1cfa4c0e32 + - 9eaadf03e0df tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - d37ede8589b2 - e3bb03cf207a - - 9f978da6528a - - c092052ed673 - - 86a20ae274fc + - 5d6ed46cc101 + - a250929be21b - cb903c9dc33d - - bcaa0d571ce2 - - 5671e1d3d5ee - 364f4ffec275 - - a250929be21b + - 86a20ae274fc + - bcaa0d571ce2 - db536ad45f28 - - 5d6ed46cc101 + - 5671e1d3d5ee - 8858fa037a15 + - c092052ed673 + - d37ede8589b2 + - 9f978da6528a tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 584beffa972b - - 194e3ceee923 - - e1a015876aa9 - - 12d66d0d05ac + - 230b05597996 - 38b91a3190cd + - 3b6a16d82c1b + - 194e3ceee923 - c5c9f02b6167 + - ed28dd32141c - abbc8041e8ec - - 230b05597996 - 49236b03e4fd - - ed28dd32141c - f95f403841ad - - 3b6a16d82c1b + - 584beffa972b + - e1a015876aa9 + - 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 89d47c9e1..c604c60d1 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -3,18 +3,18 @@ tools: owner: iuc revisions: - 0f1724dd59d2 - - f198773344e4 - - b8a457820315 - 17e3b698dd52 + - b8a457820315 + - f198773344e4 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - 374cb875d38a - - ba0c40780ecf - ac092723240d - - a513e3fbb4c5 + - 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 c018fb0b0..b24e13e9f 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -3,8 +3,8 @@ tools: owner: bgruening revisions: - 66d7efc06000 - - 522137aaa9c4 - 772e0e89fc68 + - 522137aaa9c4 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config @@ -18,83 +18,83 @@ tools: - name: keras_train_and_eval owner: bgruening revisions: + - f1b9a42d6809 + - b6ef6d0cb6b7 - e1317b5502fa - 818f9b69d8a0 - - b6ef6d0cb6b7 - 2af1346e68c9 - - f1b9a42d6809 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - 05143043ca13 - - 8334dc98c48e + - c80db5d6fd8c - 947c2eacccb8 + - 8334dc98c48e - 1588f9076e32 - - c80db5d6fd8c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 9991c4ddde14 - 83228baae3c5 - - 25b46af53232 - - 29e4122c90de - 1552b8cb4a94 + - 29e4122c90de + - 9991c4ddde14 + - 25b46af53232 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - a07ab242b0b5 + - 53616c8b0865 + - 060ca94ac049 - f3dfa4bdf87e - 841a6cc5fc58 + - a07ab242b0b5 - 1a53edc4b438 - - 53616c8b0865 - - 060ca94ac049 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 91c4e3331208 - - 927586a18553 - 2fc89dcd41c8 + - 91c4e3331208 - d4808d5b83da - - 40f4447733b2 + - 927586a18553 - dc4b5fd604a6 + - 40f4447733b2 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 36e8d6d5d01b - - e5a5ad882f1f - c6ae57f774c6 - - 25ab6b4e376e - 301e07345c93 + - 36e8d6d5d01b - 7626ea9c2e1b + - 25ab6b4e376e + - e5a5ad882f1f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: + - 0630258dcf35 + - f9639b488779 - 80852884053f - 4ed102b922cb - 02d2be90dedb - b7c3e9a3b954 - - f9639b488779 - - 0630258dcf35 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 14180f9c831e - - ec69cbe34b73 - caeb57858702 - 61634a87efc7 + - ec69cbe34b73 + - 14180f9c831e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index cebe8d577..40a17e786 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - 17062a0decb7 - - 3ba8d4563129 - - 0d4acadabb04 - - f6877ad76b00 - - 017aba02828d - - 749c918495f7 - 03e9b2fbc005 - cd659e8cc5fa + - a6d65b0c67af + - 749c918495f7 - d5ceb9f3c25b + - 0d4acadabb04 + - 017aba02828d - 937aa69e715f - - a6d65b0c67af + - 3ba8d4563129 + - 17062a0decb7 + - f6877ad76b00 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -31,12 +31,12 @@ tools: - name: bwa owner: devteam revisions: - - 64f11cf59c6e - - 53646aaaafef - 2477830927ec + - 53646aaaafef + - 64f11cf59c6e - dfd8b7f78c37 - - 3fe632431b68 - e188dc7a68e6 + - 3fe632431b68 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: + - 60afcc2c1d05 + - e7f19d6a9af8 - 3e1ea2facca6 - 37b497aa133f - - e7f19d6a9af8 - 2ff111fac1d7 - - 60afcc2c1d05 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - f54f5baedfdd - - b3eab4b67562 - - 11a0d50a54e6 - - 6b1e195506a3 - - 77b2770508f6 - - be1d967337e4 - 09b53c1d4ab1 + - 8c6cd2650d1f + - 53c0b7a1a0c3 - 037c6e54df11 + - be1d967337e4 + - 11a0d50a54e6 + - 6b1e195506a3 + - f54f5baedfdd - c0c2d0941de8 - - 53c0b7a1a0c3 - - 8c6cd2650d1f - 3f4d6399997b + - b3eab4b67562 + - 77b2770508f6 - 5cc34c3f440d tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 178bdbdb6d24 + - 5ef7ec16b04f - b8f5f6e87f5c - - e403d27e8f24 - - 42ce70172b72 - - 1cd2511a396e + - 9ee34ba73ebf + - 178bdbdb6d24 + - ec9cbd6b9a49 - 45795f582ae9 - - 13022c3d3076 - - 5ef7ec16b04f - 79b885ce78d7 + - 42ce70172b72 - 00fbfac99d39 - - 9ee34ba73ebf - - ec9cbd6b9a49 + - 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 db5cef7e9..e4c48b68a 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.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 @@ -76,8 +76,8 @@ tools: - name: matchms_convert owner: recetox revisions: - - 9e83636da9d3 - b9cc12600553 + - 9e83636da9d3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering @@ -90,8 +90,8 @@ tools: - name: matchms_fingerprint_similarity owner: recetox revisions: - - 84af792d3a78 - fd890f162ce6 + - 84af792d3a78 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter @@ -104,8 +104,8 @@ tools: - name: matchms_metadata_export owner: recetox revisions: - - f04610d25411 - 8832425b1ff6 + - f04610d25411 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match @@ -169,8 +169,8 @@ tools: - name: msmetaenhancer owner: recetox revisions: - - b5467dead5b1 - 90745ecc5e9f + - b5467dead5b1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msnbase_readmsdata @@ -218,8 +218,8 @@ tools: - name: ramclustr_define_experiment owner: recetox revisions: - - f2c1d0bbb074 - 5f2b58dadb39 + - f2c1d0bbb074 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr @@ -234,44 +234,44 @@ tools: revisions: - 79ad928a0dae - 7b42ee54d757 - - ec196e27a61a - 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 - - 149b9cc7499b tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: + - dfebc82ba1f0 - 134be5abb208 - 50b9918aeff2 - - dfebc82ba1f0 - 481d769e2f7a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - - 501a232f3cd5 - - 51332c2520c7 + - a82db010c53e - 02c772a49998 + - 501a232f3cd5 - 9064aecc78a7 - - a82db010c53e + - 51332c2520c7 - 30bf4e35da3e tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - b341cfd4baf8 - 89178a72388a + - b341cfd4baf8 - b3413f335327 - e7305ba0dd38 tool_panel_section_label: Metabolomics @@ -279,27 +279,27 @@ tools: - name: recetox_aplcms_merge_known_table owner: recetox revisions: + - 17a48d0a80f4 - dd7bbc2b99d1 - b7c8a44b9cc1 - cf061712a184 - - 17a48d0a80f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - f92b1b64da93 - - 24278c6b6d1c - - d7f5878a98c3 - 99d118321d5f + - d7f5878a98c3 + - 24278c6b6d1c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - ea0758b41473 - ffbabefbd2e2 - d90187b0f247 + - ea0758b41473 - 7acd11ddc061 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -331,8 +331,8 @@ tools: - name: rmassbank owner: recetox revisions: - - 5a6bb93ec656 - 0b28816c1c2c + - 5a6bb93ec656 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: spec2vec_similarity diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index 95c419fb5..4440ad3b2 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -2,23 +2,23 @@ tools: - name: bracken owner: iuc revisions: - - 1d4bd12f01cf - 0c7b6eb7e752 + - 1d4bd12f01cf tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_bins owner: iuc revisions: - - 0e63d03c8790 - 18676df0cb3a - 0094893f5001 + - 0e63d03c8790 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise owner: iuc revisions: - - 7f1aaa1932d8 - a8216def322b + - 7f1aaa1932d8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -90,100 +90,100 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 65db807336bc - - 7c2100246a2f - - 76d3d2b10738 - 63f86089423e - 5b5a7af9fbb4 + - 65db807336bc + - 76d3d2b10738 + - 7c2100246a2f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 96336c6a2bb7 - 00f5005840fa - 84fd33a60b35 - - 18a502a9d287 - 1c35dadbe76f + - 18a502a9d287 + - 96336c6a2bb7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: + - e8fba04706d3 + - a9f4a217dcd6 - addaf9d22850 - f732237754fc - 34e55239e68b - - e8fba04706d3 - - a9f4a217dcd6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 75403243703a - 0776d824d896 + - 8c202e741d68 - 5fe3edf19b9c + - 75403243703a - 04c15826a0b8 - - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 8470de786d47 - 1c9b3bcd4261 - 75c8945b0da2 - - e96bbb9e24ea - 43c99742158b + - e96bbb9e24ea + - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: + - 1d75bd0595e2 + - 35176674168c - 306a40d4bb8f - 84743da21318 - - 35176674168c - 5c865a382933 - - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: + - ac72310b038a - 32c9ea835770 - - 8daf4564ccda - 555ccac8a4c5 - - ac72310b038a + - 8daf4564ccda - 78faebd0879c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - d60df8727f59 - a58e4a43f49c - 7b8cb2b02978 - - cae017b76acb - f947b4bb5107 + - d60df8727f59 + - cae017b76acb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 073608a50ac3 - - 1bc3657cd694 - - 7136e9ab70db - 04144473e59e + - 7136e9ab70db + - 073608a50ac3 - 7f3b59dee073 + - 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 @@ -197,14 +197,14 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - 4d9445dff47b - 5c7ba3d85a01 - - dbf1798c0dcc + - 4d9445dff47b - c4db8c4de66f - - a68b985913ab + - b907a3c0434f - 65d52c693b8e + - dbf1798c0dcc - f8f56dd6449f - - b907a3c0434f + - a68b985913ab tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -217,9 +217,9 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 654548ae1357 - - 6d364c65c946 - 6c84982ee6f7 + - 6d364c65c946 + - 654548ae1357 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -231,17 +231,17 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - e66ab198ec15 - - bd7a9c6efb10 - 6aad8ca3918b + - bd7a9c6efb10 + - e66ab198ec15 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - d77397f09da1 - - b084117133af - c6676a890f50 + - b084117133af + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways @@ -267,53 +267,53 @@ tools: - name: humann_barplot owner: iuc revisions: - - 5fea25ee6275 - 523ae8314ef5 + - 5fea25ee6275 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_join_tables owner: iuc revisions: - - f01ca38fb6c5 - 6bf703133209 + - f01ca38fb6c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 8237a0f225db - e88b731dad59 - - 31c6d107e7a5 - c409a495841f + - 8237a0f225db - 79706f10d680 + - 31c6d107e7a5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: + - 714d5a28cc5c - 71ea608ddfa3 - d24841f5c3d2 - - 714d5a28cc5c - - aabf8cfb8fef - 094ad9c068af + - aabf8cfb8fef - 172920f67a84 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: + - a293a742194f - d7e9a3c41657 - 4137b492233e - - 2bdd84912a2b - - a293a742194f - a4d7148ccee4 + - 2bdd84912a2b - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -326,20 +326,20 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: + - 6fcb8ac37a3e - 64bc7acc22a9 + - e2c71b852aba + - a92c06a3afa7 - 75bedfb2078b - - 97f7bb0851e7 - cf87759761eb - - a92c06a3afa7 - - 6fcb8ac37a3e - - e2c71b852aba + - 97f7bb0851e7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - 81c5dd1c777f - e9d12c223a80 + - 81c5dd1c777f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler @@ -351,22 +351,22 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 2d35528d2141 - - 4e5e73d03f0d - - 4033827c76b8 - c82508e76ad1 - - 5e5a999ffaa9 - 080ea153677c + - 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 - - c2803012bbb3 - - 6b7622dda516 - 95bf7479d53c + - c2803012bbb3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: itsx @@ -378,8 +378,8 @@ 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 @@ -399,8 +399,8 @@ tools: - name: khmer_count_median owner: iuc revisions: - - b3d513c7093e - 570505540a7b + - b3d513c7093e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_extract_partitions @@ -413,22 +413,22 @@ tools: - name: khmer_filter_abundance owner: iuc revisions: - - 29a4d6e2ae9c - b86562b4f3fd + - 29a4d6e2ae9c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_filter_below_abundance_cutoff owner: iuc revisions: - - 00f7064c564b - 19607c740d19 + - 00f7064c564b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_normalize_by_median owner: iuc revisions: - - b1fe2ef3d244 - 4d23ab83ea29 + - b1fe2ef3d244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition @@ -447,10 +447,10 @@ tools: - name: kraken2 owner: iuc revisions: - - 4a9da2b6c2e3 - - cdee7158adf3 - 20e2f64aa1fe - 328c607150ff + - cdee7158adf3 + - 4a9da2b6c2e3 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: - - 5bee9adae474 - 67236d921e83 + - 5bee9adae474 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: - - bfae8da6082c - 27d65c78863c + - bfae8da6082c 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: - - 8ba2174315aa - 766d5f63b0f4 + - 8ba2174315aa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_alpha_diversity @@ -523,23 +523,23 @@ tools: - name: krakentools_extract_kraken_reads owner: iuc revisions: - - 4bf1e2701504 - f329328da134 + - 4bf1e2701504 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2krona owner: iuc revisions: - - 2deaada69b14 - 88d274322340 - 02bbace216f2 + - 2deaada69b14 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa owner: iuc revisions: - - bb96a1e6583d - d33cf727ed94 + - bb96a1e6583d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: lotus2 @@ -569,22 +569,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 7f5d7b0e9884 + - 2cff76cf35c6 - 0270541aaf46 - - 3cc4a60615c0 - 327d9f4cc95f - e073891b2afc - - 2cff76cf35c6 - - 27250f92a01a + - 3cc4a60615c0 - 4fd3b5d8706b + - 27250f92a01a + - 7f5d7b0e9884 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 @@ -657,19 +657,19 @@ tools: - name: metaphlan owner: iuc revisions: - - fd69c607b43f + - 1a037928504c - ec368db926f4 - - 6dee4abadccb - - a16313517e55 + - b89b0765695d + - 289b3807e80c + - fd69c607b43f + - 1a6cdf55390f + - 2131d7dca455 - ff8f55893e7d - 740fd2d16a28 - - 2131d7dca455 + - a16313517e55 - a92a632c4d9b - ef65b083bd0c - - 1a6cdf55390f - - b89b0765695d - - 1a037928504c - - 289b3807e80c + - 6dee4abadccb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -688,7 +688,6 @@ tools: - name: phyloseq_from_dada2 owner: iuc revisions: - - 87064cb77a52 - 40ebae5bbe51 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -715,15 +714,15 @@ tools: - 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 owner: iuc revisions: - - 6077821e8ae7 - f53beb324696 + - 6077821e8ae7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline @@ -743,8 +742,8 @@ tools: - name: picrust2_shuffle_predictions owner: iuc revisions: - - 881f2faa5fe7 - 677f3c8db525 + - 881f2faa5fe7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -756,8 +755,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 8e2ac1b8f70a - 0ba7dfaa941d + - 8e2ac1b8f70a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -794,26 +793,26 @@ tools: - name: polypolish owner: iuc revisions: - - f355085dd2aa - 915637bd1d1a + - f355085dd2aa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: recentrifuge owner: iuc revisions: - - 591175c0f051 - d4fbfd31696c + - 591175c0f051 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: staramr owner: nml revisions: - - 2fd4d4c9c5c2 - - aeaa20b96ef2 - - be818ae858e4 - 4b9a8031ab74 - - 3b22de20bd4b + - aeaa20b96ef2 - 4d83eccf5f81 + - 3b22de20bd4b + - 2fd4d4c9c5c2 + - be818ae858e4 - 141afacabcfa 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 350bb5efe..bc3ed5768 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - 67cb43432196 - e866e31f6da3 + - 67cb43432196 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 72be09dfd803 - 2344ed181ae6 + - 72be09dfd803 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 72466a344..c90e866be 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: + - 94b8c6013083 - 9eeb13a92d79 + - 9422c5a87ee2 - 2263989660f5 - 098506c54016 - cd07731e4434 - - 48c13389050d - - 8b67dd48fec1 - - bdfbaf0c10aa - - 94b8c6013083 - 80f03df2e2ce - - 9422c5a87ee2 - - a74dbfee5a86 - - 6ae5a7b5a0a2 + - bdfbaf0c10aa - 9baa871cb1d1 + - 6ae5a7b5a0a2 + - a74dbfee5a86 + - 8b67dd48fec1 + - 48c13389050d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - 3ff17bad4006 - - be78f13134e2 + - f14193ec1f50 - f0af8936ed41 - - 5abf2c2249aa - - aaa0d6a8b808 - - d7ce0ec78e51 - - 4a60927aaca5 - - bc3831dd65c1 - c44f824c051a - - c18157c68134 + - 5abf2c2249aa + - be78f13134e2 - '764845535798' - - f14193ec1f50 - - fc2e49f91e52 - d390fe1567dc + - c18157c68134 + - bc3831dd65c1 + - 4a60927aaca5 + - aaa0d6a8b808 + - fc2e49f91e52 - 2e093badc689 + - d7ce0ec78e51 + - 3ff17bad4006 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -68,36 +68,36 @@ tools: owner: rnateam revisions: - f1a5908ea2cb - - 6f28e90db932 - bf28a8cff401 - - c5908940967d - - a65296ffb4a0 - 15974dd17515 + - 6f28e90db932 - 8e649f27aa0d - f0d493f8f84f + - a65296ffb4a0 + - c5908940967d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: + - b3acbb3a6af0 - fbca557a4847 - e8fdceffea4c - - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 5561a1193611 - 60698466facd - c9685bc0407c + - 5561a1193611 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - 48823c9635a4 - 57f042937ba7 + - 48823c9635a4 - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -112,16 +112,16 @@ tools: - name: mummer_nucmer owner: iuc revisions: - - 7cd7a55a678d - 636b049e6141 - e18267f90096 + - 7cd7a55a678d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - cf3c9489c088 - - 959c1f8dae95 - b4124df98b26 + - 959c1f8dae95 + - cf3c9489c088 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 6844fa186..e6c2d5591 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: - - 18a8d140ec6f - - 9aa9d92c3c51 - 7c47b3c9e493 + - 9aa9d92c3c51 - 28928576e1ea + - 18a8d140ec6f 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: - - 99c9427219d3 + - fc5b6491cf78 - 63d8ecfcfab1 + - 99c9427219d3 - 6942f170cc43 - - fc5b6491cf78 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus_pipeline owner: iuc revisions: - - a7228a7ea146 - - 0e9e7fcdd543 - - 72b5e9dda577 - 79e9a869f40e + - 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 - - fa11aa8103b2 - db25ec99c3ea - - d6cddc06aeae + - fa11aa8103b2 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -58,22 +58,22 @@ tools: - name: medaka_variant owner: iuc revisions: - - 2bf63b38ee9b - - 43815fa60f3a - - 19f3b583a9b3 + - 0f5f4a208660 + - eb746fa6f514 + - ec699520444c - edf6d4003fad - cc36773a3681 - - 0f5f4a208660 + - 2bf63b38ee9b - 222669c4afb6 - - ec699520444c - - eb746fa6f514 + - 19f3b583a9b3 + - 43815fa60f3a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - c0fb573c1e8d - b833eff63b10 + - c0fb573c1e8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -85,53 +85,53 @@ tools: - name: nanoplot owner: iuc revisions: + - 645159bcee2d + - 7b379e98b9a9 - a38bdcec9e4c - - a3c4fe6f49ab - - edbb6c5028f5 - a02b8b3f5a0c - - 645159bcee2d + - edbb6c5028f5 + - a3c4fe6f49ab - 0f1c34698076 - - 7b379e98b9a9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 85a394edc247 - 3b6f94fc7e1d - d219b6d8158a + - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - 90a922f32523 - - be95355fef8d - a8d4be409446 + - be95355fef8d + - 90a922f32523 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 4857d5bcce52 - 449e9aeded2d + - 4857d5bcce52 - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - a3afc5f0a96c - - de5b3d8f5b90 - bec636361cfd + - de5b3d8f5b90 + - a3afc5f0a96c tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 93d623d9979c - 5f76b20953e5 - 543cbeef3949 + - 93d623d9979c 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: - - 47936349f3e9 - d1805f9c4c82 + - 47936349f3e9 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: - - 0433aad600e9 - 336791b5665f + - 0433aad600e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist @@ -176,8 +176,8 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 626b6c2be5c2 - 2e22ebec211a + - 626b6c2be5c2 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index dd68353f0..9b71bc881 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -27,11 +27,11 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - baceff842902 - - adfd6bf710bd - 97b1b5ad1cda - - d74850cf4e42 + - adfd6bf710bd - 3e73c97f025d + - baceff842902 + - d74850cf4e42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder @@ -51,13 +51,13 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 1e34d2e3d285 - - ed1518ce2237 + - 19b6a2f0dbe2 - e4b4837f06f5 - e9ee4d074d5d - 2f27f3b86827 - 13851aefa67a - - 19b6a2f0dbe2 + - 1e34d2e3d285 + - ed1518ce2237 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -76,15 +76,15 @@ 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 - 38ccd4589990 + - 48a42ca61006 - 5711fc06a63e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -98,8 +98,8 @@ tools: - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - fcb8bdd124f4 - 81a286e4c5a2 + - fcb8bdd124f4 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco @@ -112,8 +112,8 @@ tools: - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - 4d3eff1bc421 - b1bc53e9bbc5 + - 4d3eff1bc421 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: - - 6287d0ee459e - 9a40272f56d0 + - 6287d0ee459e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 52b6a4d98009 - - b4b2b284230a - 27a6a256cd23 - 172815da3d41 + - 52b6a4d98009 + - b4b2b284230a 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: - - d74c740bdb25 - d210e1f185bd + - d74c740bdb25 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -160,16 +160,16 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 19bbd19b74b3 - fea85c467896 - 87febc68b45b + - 19bbd19b74b3 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 @@ -194,35 +194,35 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 4ba60cb14cb0 - - d8dc037e3c13 - 2c61c30a57e7 - - 9c43baa60906 - - 5fe20c915fa6 + - d8dc037e3c13 - 0cb27ea69dc1 + - 4ba60cb14cb0 + - 5fe20c915fa6 + - 9c43baa60906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos owner: iuc revisions: - - 14785f8a3725 - d9339bb8127e + - 14785f8a3725 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mothur_toolsuite owner: iuc revisions: - - 9d09724f2bf1 - aec831b54a5b + - 9d09724f2bf1 - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: + - 6e24e79d3d69 - 29c738066906 - df30a2f1db55 - - 6e24e79d3d69 - ed7a967cb11b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -241,16 +241,16 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - 3e4d45aca422 - ad90c2da4f38 + - 3e4d45aca422 - 1865e693d8b2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - def511e8e005 - d107d20dc6bd + - def511e8e005 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -262,17 +262,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - d63c1442407f - - c520a52b5174 - 64deddb6a8ec + - c520a52b5174 + - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - 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 +783,8 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - d64562a4ebb3 - 544f6d2329ac + - d64562a4ebb3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes @@ -796,11 +796,11 @@ tools: - name: salsa owner: iuc revisions: - - f77f7a7f3b83 - - ba7b0f11e470 - 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 e9a260da0..0b5a386c4 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -33,66 +33,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - '841557158611' - - 8834daeb9892 + - a6619171428e - 3f59ebfbfe3d - - 6a457678efcb - - 81e66674859e - - 26de3a7b1cb9 - - b89cac5156ec - - c78f3d7dd1db - - 3b8b5bde0bd9 - - f73435dc282b + - '841557158611' - 107d3ba7024a - 5a7c56a5cc08 - f04a1264e2a2 - - d033ffc1c161 + - f73435dc282b + - 3b8b5bde0bd9 + - 81e66674859e - cce7b18495e4 + - 26de3a7b1cb9 + - b89cac5156ec + - 8834daeb9892 + - c78f3d7dd1db - d7c7ef3353fe - - a6619171428e + - d033ffc1c161 + - 6a457678efcb tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 6223845127ea - - 4755f52427c4 - - df47d4845b62 - 3b96e92e8ec3 + - 5b777002c2de + - df47d4845b62 + - 7a2092844346 + - aa8cc71438cf + - 02b8758214b0 + - a185b079b095 + - 4755f52427c4 + - 6223845127ea - 88c4aa435ded + - 659517798cc4 - b0af57c1a968 - - 7a2092844346 - e75442c7f4da - 6283babe736e - - 659517798cc4 - - 6a726db04d4b - 5fcd1ece3a6e - - a185b079b095 - - 02b8758214b0 - - aa8cc71438cf - - 5b777002c2de + - 6a726db04d4b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 70acec670c30 + - d1c340a5664b + - 24d024316465 + - f97743d52b87 - f87ac61981f0 - b8476e82ac20 - c1d53e95327f - - d1c340a5664b + - 70acec670c30 - 111bd54f6bc4 - - f97743d52b87 - - 24d024316465 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - 4f6349228462 - - feb40665d7cd - daddf188c13f - 9e10ba792be2 + - feb40665d7cd + - 4f6349228462 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: - - 2fa9d4f1b48f - - ca0d8cf80567 - - 437e28791761 - - 83a69484cb87 - - 3a43c3982401 - - 8ad84c5753ea - - ca337cce3888 + - 81804a978fc0 - 7bb8726be37c + - 2f1019071464 + - ca337cce3888 + - 42a174224817 + - ca0d8cf80567 - 14ae456b8cc5 + - 9d61d3fa046c + - b7e297c2ede6 + - 2fa9d4f1b48f + - abf6dbe8c9d7 + - 03ed9524dcd1 - b6abccb1f25b - - 42a174224817 - - 2f1019071464 - 5f8727ff21e7 - - b7e297c2ede6 + - 83a69484cb87 - a2099fb98cdb - - 9d61d3fa046c - - 03ed9524dcd1 - - abf6dbe8c9d7 - - 81804a978fc0 + - 3a43c3982401 + - 437e28791761 - 36912871ccdc + - 8ad84c5753ea tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 7157a5b34a68 - 2bf47d57ebb5 + - 7157a5b34a68 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 - - 29ff6a849eac - ba29b5e2a4be - - 73a469f7dc96 - - a4b71be30c3c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - f1ccc8a6eb05 - - dbe2b2204555 - 809e42326fc2 - 9b2b122d0415 - - 15ac71df11a0 - - 91887494eb97 - e88a7de55d6e + - dbe2b2204555 + - 91887494eb97 + - f1ccc8a6eb05 + - 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 beb608e1c..eb13b3b88 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - f9242e01365a - - fc288950c3b7 - 881d7645d1bf - - f6ced08779c4 - a1f0b3f4b781 - - b502c227b5e6 - - 3f254c5ced1d - 7d34178f2812 + - fc288950c3b7 - 1aac2a13842a + - 3f254c5ced1d + - f6ced08779c4 + - b502c227b5e6 + - f9242e01365a tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomic_ai.yml b/usegalaxy.org.au/proteomic_ai.yml index b17531596..60fab0b79 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: - - 2f7702fd0a4c - - 6ab1a261520a - - eb085b3dbaf8 - - a58f7eb0df2c + - c0e71cb2bd1b - ca90d17ff51b - - e7f1b552a695 + - eb085b3dbaf8 + - 6ab1a261520a - d00e15139065 - 3bd420ec162d - - c0e71cb2bd1b - - 7fbec959cf2b + - 2f7702fd0a4c + - e7f1b552a695 + - e4a053d67e24 - 5b85006245f3 + - a58f7eb0df2c - 3f188450ca4f - - e4a053d67e24 + - 7fbec959cf2b 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 74ab74de4..49cc9b524 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -3,92 +3,92 @@ tools: owner: galaxyp revisions: - 277dc652246e - - 4c177985028a - - b18329a8ac14 - 0a18ac48ac53 - - b574b84afc4d + - b18329a8ac14 - f28ad96b76dc - ece627528a78 + - 4c177985028a + - b574b84afc4d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: + - a9a28e46d54a - bf06d196e23d - - 525f201b86c1 - e215f71d7983 - e988563cc6e5 + - 525f201b86c1 - b41107d8fe89 - - a9a28e46d54a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - 56da27be956a - - 8da3511c9467 - 4fbffddde8cd + - 8da3511c9467 - bb6397b94018 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - b8c79e70516d - 528fb09022be + - a8157342d9a3 - 890845926d4b - f23d67e28cc8 - - a8157342d9a3 + - b8c79e70516d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - a95a82eb4d50 - - ae304a72db7b - - 80600735685d - - a69865da6f80 - 59e85306eae5 + - ae304a72db7b - 25b83cbd596a + - a95a82eb4d50 + - a69865da6f80 + - 80600735685d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: + - 83aac7741200 - 798da6bdff3d + - 611d80c0e29d - e0669b1854b1 - f1897eb07081 - - 611d80c0e29d - ed9ed1e6cca2 - - 83aac7741200 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - d426a9107a6c - 5a35e3a8d013 - - a7fb9b395ddf - 74b61bf5bc4b + - d426a9107a6c + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - cc430977c8ff - - 82f6c2f4332d - - df2187f9013b - 91f0f5922011 + - df2187f9013b + - 82f6c2f4332d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - d2483487e077 - - c5aa9fca18c6 - 10566783d718 - 1693b2126f30 - ba92b59cd529 + - c5aa9fca18c6 - 043f9c91f686 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -107,10 +107,10 @@ tools: - name: diann owner: galaxyp revisions: - - ae4dc0c041f9 - bf0728e000cd - - ff8c9e0e8a7b - 9fa3dbf06f17 + - ff8c9e0e8a7b + - ae4dc0c041f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -122,24 +122,24 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: - - d263296cd73e - - d0ea7589e95f - eac99effe86f + - d0ea7589e95f + - d263296cd73e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: - - 0fa397f4f40b - 4081e4faa4ab + - 0fa397f4f40b - 1c5cbf8f79ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib owner: galaxyp revisions: - - 36880dfd9fa7 - fb192dd6658a + - 36880dfd9fa7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut @@ -159,16 +159,16 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - e66f552a3c47 - d286ff4600dd - 160538a890a6 + - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 60ee8c592b13 - 71411ac28268 + - 60ee8c592b13 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar @@ -181,15 +181,15 @@ tools: - name: maxquant owner: galaxyp revisions: + - 7f432d87c82c + - 37d669de2828 + - 4d17fcdeb8ff - 97a7f34fcb6a - - f522c08e900c - 9c52362ae7bb - e42225f8a659 - - 37d669de2828 - - 4d17fcdeb8ff - - 1f39c833f65f - 837224ad1694 - - 7f432d87c82c + - f522c08e900c + - 1f39c833f65f - 2133b0be850a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -202,27 +202,27 @@ tools: - name: metaquantome_db owner: galaxyp revisions: - - e63db1aa82ee - - a72ac2c7cc5b - 85b8866f06d7 + - a72ac2c7cc5b + - e63db1aa82ee - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 1974224d63c2 + - 352b37c66d97 - 767c1d761aaf + - 1974224d63c2 - 990b4560ead7 - - 352b37c66d97 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 4f359549383c - 35cc7ca0bdc7 - deaf035bbe9f + - 4f359549383c - 99450519d727 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -230,16 +230,16 @@ tools: owner: galaxyp revisions: - 06f6826d380c + - c7745841de24 - e79958768a2c - c1343e3389ca - - c7745841de24 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - b9d453dca8d3 - d2eac53666f0 + - b9d453dca8d3 - da986f83631b - d46d64e7964d tool_panel_section_label: Proteomics @@ -248,9 +248,9 @@ tools: owner: galaxyp revisions: - 9bf325045235 - - 8bd7734309f6 - - 944b43462104 - 1199751329b0 + - 944b43462104 + - 8bd7734309f6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -270,8 +270,8 @@ tools: - name: msstats owner: galaxyp revisions: - - 28434abe6c5c - 593839e1f2c3 + - 28434abe6c5c - de7593c29499 - 8212e342e482 tool_panel_section_label: Proteomics @@ -279,178 +279,178 @@ tools: - 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: + - 01dbaf6a57e0 + - 8960fb791701 - f4be248c3d47 - 4e77b8f12cd3 - - 8960fb791701 - - 01dbaf6a57e0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - 370141bc0da3 - - 06cca574e337 - 25529df60a81 + - 06cca574e337 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - - f7fef900f5b2 - - 9cdf15d3cfc8 - - 518b1730cf2a - - 6ccbf9a2072c - c9eff69a7c62 + - 6ccbf9a2072c + - 518b1730cf2a + - 9cdf15d3cfc8 + - f7fef900f5b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - dff6c756eee5 - - ca88bd28f116 - 9876bda3ec53 + - ca88bd28f116 - 5e948629bc73 + - dff6c756eee5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: + - 658494a2cb00 - 1595601708ec - - 41859bbdc16e - 890025d6e426 - - 658494a2cb00 + - 41859bbdc16e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 2a93a25f0599 - 9b7977080f6d - - 5ad0b5bf1deb + - 2a93a25f0599 - 6634cad7d797 + - 5ad0b5bf1deb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - fe4e4587d265 - - 05d5e1ddc985 - - d6878d27f051 - 0bb5056cb775 + - d6878d27f051 + - 05d5e1ddc985 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - 52ba9695e752 - - 4af67edd5aef - 5ad830edc021 - febd569ad26f + - 4af67edd5aef tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - b2fc8da99bcc - 92352a475eed - 27cba4c5fc42 + - b2fc8da99bcc - 39e8fde08881 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 0efbc235f314 - 9e26f5c770f8 - d413dc49d650 - d3546bb9fd8e + - 0efbc235f314 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: + - c28f13cab67a - 8a04ed1c1d1b - 3720e349ba2a - - c28f13cab67a - ca1740533b59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - c427a8628cbe - c55dddc5844a + - c427a8628cbe - ca799a7246e7 - - a5d785af0ad8 - 382cde407f81 + - a5d785af0ad8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - b5d0905419da - - 39caaa778d2e - 8ddb7bab1138 - adca857b4884 + - b5d0905419da + - 39caaa778d2e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 18f93351f8b6 + - 1c5f31b8d632 - 8d4db262964c - - 34e7afee141d + - 18f93351f8b6 - f817513840a9 - - 1c5f31b8d632 + - 34e7afee141d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 111c3a00136d - 5d9f175dff81 - - c69f69d7867a - 986e03d3201e + - c69f69d7867a + - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - 0e52c85f3b15 - - 476b5e296979 - be74a8cd7d66 - 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 - - c18d8efa4474 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver owner: galaxyp revisions: - 021fdb80f204 - - d0304fb829c0 - 4e66c4e73909 + - d0304fb829c0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_mztabexporter owner: galaxyp revisions: - - ee860980edc6 - 8098330f6d91 + - ee860980edc6 - 2735db4dd8d9 - bf32e0bcf554 tool_panel_section_label: Proteomics @@ -458,9 +458,9 @@ tools: - 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 @@ -482,8 +482,8 @@ tools: - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 9f505cd4428f - f861ec9fbe59 + - 9f505cd4428f - 496cf619e311 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -498,8 +498,8 @@ tools: - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 4bb198c0bd3e - 8b814eafce2c + - 4bb198c0bd3e - 89254095cbf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -515,75 +515,75 @@ tools: owner: galaxyp revisions: - d31426ef20f6 - - 18826fb8e5db - 6e8cc5ed2a9b + - 18826fb8e5db tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - - bc63b4d12779 - 2aebe58de46e - 4a7b96835140 + - bc63b4d12779 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - decc397c3b7e - - 6b01678ec2fc - 3d8d4ada5405 + - 6b01678ec2fc - 5ae104d0da6e + - decc397c3b7e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - 539a3a4dcc9e - dd173849c3d8 - - 5182338d5e7c - d6aca689dd48 + - 5182338d5e7c - e039cc5c7aed + - 539a3a4dcc9e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - d426affe977c - - 8a45fd5a608a - 16026cdb1330 + - 8a45fd5a608a 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: - - d063e2fe4ba4 - 9020199dba0a - 1b03536aa3c9 + - d063e2fe4ba4 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - ad2ba3a95a02 - - f036e8cf1a55 - 78c080d36945 + - f036e8cf1a55 + - ad2ba3a95a02 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - fb52e95a370c - c8b225c69a7f - 5c2a97a234d6 + - fb52e95a370c - 7f6a1f27553e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -603,21 +603,21 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - 5f49ffce52cb - cb0378d2d487 + - 5f49ffce52cb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: - - 1beff3ddce58 - - a72c48001f7c - - 7fdd9119cc4f + - 3ec27b4cee7c - 07ff622ec007 - - 943a34df6047 + - a72c48001f7c - 3634c90301af - da885ca16cb2 - - 3ec27b4cee7c + - 7fdd9119cc4f + - 1beff3ddce58 + - 943a34df6047 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -677,10 +677,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 12692567c7f9 - 265c35540faa - a371252a2cf6 - 1a5690a5eedc + - 12692567c7f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/usegalaxy.org.au/qiime_2.yml b/usegalaxy.org.au/qiime_2.yml index bf015d3f9..52697721b 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: - - 10447a4b0cc3 - 18c6b2b6740f + - 10447a4b0cc3 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 35daee129..ba560f6ae 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,10 +2,10 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: + - 110a346daf36 - e345aadf914f - cd5f98911089 - 2f1d464ebfd2 - - 110a346daf36 - 42201b90e3f4 - 289b7d6b69a4 tool_panel_section_label: RAD-seq @@ -13,121 +13,121 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - fcce77c09289 + - 42d9087b4789 + - 0345dbaaa79b - 0cd2df8af811 - 8501601a118d - c207119ba5f6 - - 0345dbaaa79b - - 42d9087b4789 + - fcce77c09289 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - 89eb29319bf4 - - 33486216eec0 - 421c33b8bf17 - - 405a212b32ab + - 33486216eec0 - ad5ab22ffe24 - 04db7fd6b238 + - 405a212b32ab + - 89eb29319bf4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - eb784fa07f80 - - 7b72fde3d27e - f6e91108b7b1 + - 7b72fde3d27e - 7370bb65bad4 - - 1d839ead7ad3 - fa51dc5e8386 + - 1d839ead7ad3 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - - d30e36c48c93 - - 1544278c272e - - c9b77ced9a78 - a3e86cd9cac7 - 8a55d29c8fcf - 3d70c2996730 + - d30e36c48c93 + - c9b77ced9a78 + - 1544278c272e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - a5969aa9347e - - 887cf585cafc - b242deb58952 - - 7b881f5f5ad5 - - 564c33e5c3e3 - e2db212d64ad + - 887cf585cafc + - 564c33e5c3e3 + - 7b881f5f5ad5 + - a5969aa9347e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - b4bab607eb05 - - bd5ff77e2036 - - 8cff84759bf6 - 9a171f9a450b + - 8cff84759bf6 + - bd5ff77e2036 + - b4bab607eb05 - e897c74a48bb tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: + - adc7a7610d4f - 4f65e343ecdf - - 33f0793edf93 - 5e10f396979e - - 887e0991eb24 - - adc7a7610d4f - 6dafad990086 + - 33f0793edf93 + - 887e0991eb24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - c287418eb288 - - 17d39bf0a63a - - 97575d01f06b - - c5d7050e4ad7 - 43e3eeb2e0ec - 4e280b27a831 + - c5d7050e4ad7 + - 97575d01f06b + - c287418eb288 + - 17d39bf0a63a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - cd034465d4a4 - 9586f08634c0 + - cd034465d4a4 - d9bf483266a1 + - 09b8edb56d80 - a819ec3b362d - 0b8c84a7fdb5 - - 09b8edb56d80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: + - a9c34a289493 + - 69842dd5aa48 - a4b4bd84f69e - 95351dd0fd3f - - 69842dd5aa48 - bf0e43ab0416 - 2645575d1bf2 - - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - bb0475c884ff - d033e1ccb386 + - d1fda11e602f - cfb504394ae1 + - bb0475c884ff - 912f904a6e1e - 8a35a3bc6752 - - d1fda11e602f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -164,8 +164,8 @@ tools: owner: iuc revisions: - d1fad35bdb4a - - 95286af4139b - d504d945a655 + - 95286af4139b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -195,8 +195,8 @@ 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/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 2a0c2c69f..6f29d6272 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,27 +2,27 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: + - 7acb00fc980a - 2d4e3aff9dc7 - cf01dd6c6b1f - - 7acb00fc980a - 31f8063eedea 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: - - 01ccd366690d - - 45c2ec061cf9 - 3d61a698e5e1 + - 45c2ec061cf9 + - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -89,9 +89,9 @@ tools: - name: cuffcompare owner: devteam revisions: - - f648e5180e40 - ad5d061fbdf2 - e66b9b5b8580 + - f648e5180e40 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -105,19 +105,19 @@ tools: - name: cuffmerge owner: devteam revisions: - - 04adc9db1581 - - 6a6717a5f421 - - 22cf48ad7b16 - 86285ddd4512 - cf747d1bd79a + - 04adc9db1581 + - 22cf48ad7b16 + - 6a6717a5f421 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: + - 9a854107dbb2 - 28b94cfbfdb9 - 6cbfede05833 - - 9a854107dbb2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -142,49 +142,49 @@ tools: - name: describe_samples owner: iuc revisions: - - 0693ccd171c4 - 3b36efd62b3e - 8f0181aacb7a - e3b16fd7dd08 + - 0693ccd171c4 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: + - 24a09ca67621 - d027d1f4984e - - 0696db066a5b - 6a3a025714d3 - cd9874cb9019 - 8fe98f7094de + - 0696db066a5b - 9a882d108833 - - 24a09ca67621 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - 2872c633f07e - - 62adf13b86ea - - df929f257179 - b47c006d90c5 - 9a7c5b6d8f1e + - df929f257179 + - 2872c633f07e + - 62adf13b86ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 070900306913 + - 5bf899c13979 + - 0cb907a2a810 + - 6e53e565fc6a + - df0c8d0a5992 - 3d89af8a44f0 - 555659de7321 - - ae2aad0a6d50 + - 070900306913 - 334ce9b1bac5 - - df0c8d0a5992 + - f2843df56434 - a8305cf0c951 - 9bdff28ae1b1 - - f2843df56434 - - 5bf899c13979 - - 0cb907a2a810 - - 6e53e565fc6a + - ae2aad0a6d50 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -203,18 +203,18 @@ tools: - name: featurecounts owner: iuc revisions: - - af814359d244 - - a37612abf7f9 - - f3a5f075498f + - a56fbe2d6ba7 - 7db9d3ea71c9 - - e6a2a912677a + - 90d16db017d7 + - a37612abf7f9 + - 38b6d12edc68 + - af814359d244 - f9d49f5cb597 - 6f66ae7c5f7a - 1b851f87fbe0 - - 38b6d12edc68 - - a56fbe2d6ba7 + - f3a5f075498f - ea04b737afa0 - - 90d16db017d7 + - e6a2a912677a 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 - - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -253,20 +253,20 @@ tools: owner: iuc revisions: - 6c19daec423d - - a86e80d3c09c - 26371a1df031 - - 3fb01a8c902d - f4af63aaf57a - - 6ab42baa56e9 + - 3fb01a8c902d + - a86e80d3c09c - d4b55e2beb12 + - 6ab42baa56e9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - 916cb26bd9d3 - - 67b0b160903a - 4418229c501e + - 67b0b160903a 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: - - 87c11c05d238 - 5ae5c312d718 - - 01247aaf0a10 - 1c75aa5de15e - ce5d418183c5 + - 87c11c05d238 + - 01247aaf0a10 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - 10c98fab6c5a - - 4f9c4e6566e5 - - c971db6f0fe5 - 40985510cd98 + - c971db6f0fe5 + - 4f9c4e6566e5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 708348a17fa1 - 0921444c832d - e827f9aae031 - - 32511f586472 + - 119b069fc845 + - 97e06a4c7c75 + - 708348a17fa1 - 58c35179ebf0 + - 32511f586472 - d6f5fa4ee473 - - 97e06a4c7c75 - - 119b069fc845 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -316,8 +316,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - dbbe92348c7a - a8d24f4b6d95 + - dbbe92348c7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_quantifier @@ -360,21 +360,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 99b17b74a8cd - 3ea5a2a63fa2 - - e132e7d02a3e - - 7ed2edc1337f + - 980d2a2e1180 - 4df95e2d7f61 - c7c55b694974 - - c772497b2c32 - 4074fc1940e2 + - c772497b2c32 - b0f2be869d6d - - 79de45b5069b - - 980d2a2e1180 - - b9e04854e2bb - - 4014de1b6daf - 5ec75f5dae3c + - b9e04854e2bb + - 7ed2edc1337f + - 79de45b5069b - 0a563fd2f22e + - 99b17b74a8cd + - 4014de1b6daf + - e132e7d02a3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -386,36 +386,36 @@ tools: - name: salmon owner: bgruening revisions: - - 2c0ca397d302 - - 15cd64d7c58b + - e3d32471da11 - ebab418107f5 - - f4d5237a84f6 + - 2c0ca397d302 - 49121db48873 + - 15cd64d7c58b - 53e9709776a0 + - f4d5237a84f6 - cc05793bb896 - - e3d32471da11 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - - fab6ff46e019 + - c0fd285eb553 - 8c28affc7c48 + - fab6ff46e019 - 56242ff81c84 - - 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 - dd4df992d93d - - cbf488da3b2c - - 914cfcba0ec8 - 1ebd14235b92 - - ae618321f34a - - 76d290331481 - - cef79931dda5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -445,8 +445,8 @@ tools: - name: transdecoder owner: iuc revisions: - - 0db979fead3a - d0d4cef4f967 + - 0db979fead3a - ffd1300599a1 - c6334cb383ff tool_panel_section_label: RNA-seq @@ -454,81 +454,81 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - d6a479fd4281 - ba3720d7e68b - - 74217fbfba4d - bcc5f03f1900 + - d6a479fd4281 + - 74217fbfba4d 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 - - 56162e446004 - - 478f36effca1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: - 3f4094b6a565 - - fab23c3b5258 - 9ff3765e7172 + - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 870ac06dff8e - 4687ecf0eb2d - - be3f26533209 - 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 - - 05ab8d5e04a2 - - 5192f657f305 - c5fbddcac63a + - 05ab8d5e04a2 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 - - e406ac71165d + - 1fdb25a8384d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - - 964b7efe2639 - 37a1129c89d2 - - c2c039e421af - 7c7fbf13aadd + - c2c039e421af + - 964b7efe2639 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - - 1d689e4e1caf - - 047c22569787 - - 24e94d84adc9 - 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 +547,15 @@ tools: - name: trinity owner: iuc revisions: + - 9fa24d5aac68 + - db1f362cca3e - d84caa5a98ad - cee61b3fcf78 - - 9fa24d5aac68 - - 48636f857c4b - 32b86cd8eb50 - c9cfec002f71 - - 8f1c3df4dd49 - d2bc35f3d1c5 - - db1f362cca3e + - 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 53b800e78..44ba177fb 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: - - 473382134e56 - - 27e16a30667a - 1a052c827e88 + - 27e16a30667a + - 473382134e56 - 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 29079f86b..5f73eaa62 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 - - 993b19f20c76 - 108db6635177 + - 993b19f20c76 - 1dfd95ee241e + - cb20f99fd45b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_mapped @@ -32,8 +32,8 @@ tools: - 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: bamtools @@ -75,17 +75,17 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 19ece8afbaab - 5f8e69cc4c6e - e7fd6754d093 - 30a201c9c310 + - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc owner: iuc revisions: - - 17b35d23731f - e38af83df163 + - 17b35d23731f 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: - - a3b4ad6858ff - 890d97772e2a + - a3b4ad6858ff tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam owner: devteam revisions: - - 0e60e2dd20af - cf1ffd88f895 + - 0e60e2dd20af 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: - - 56c31114ad4a - 649a225999a5 + - 56c31114ad4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - 9149ad20699a - - 6856f8a01905 - 46c6639921f1 + - 6856f8a01905 - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - 06dc50b7b711 - 33208952b99d - - 92ec40abcdcf - 26b4f9f98aca + - 06dc50b7b711 + - 92ec40abcdcf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_coverage @@ -160,38 +160,38 @@ tools: - name: samtools_fastx owner: iuc revisions: + - b906586a6596 + - b3d99709fe1a - a8d69aee190e - 66e23b11feae - - b906586a6596 - 720217c23995 - - b3d99709fe1a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fixmate owner: iuc revisions: - - d2df79922531 - e5ece8fa99de + - d2df79922531 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - fe34990e5ce7 - - cc61ade70eb8 - fefd89ab563c - - 22970df7a40e + - cc61ade70eb8 - db17d5321bad + - fe34990e5ce7 + - 22970df7a40e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: + - 7a6034296ae9 - 811fc2d75ad4 - 7def34e6cf4d - - 7a6034296ae9 - - fa5d3e61e429 - 88b8c2916784 + - fa5d3e61e429 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_markdup @@ -205,8 +205,8 @@ tools: owner: iuc revisions: - b40e2d865d52 - - cae2794d2deb - 65a38e8c8e2a + - cae2794d2deb - 36677f429310 - 740ce0a18f0d tool_panel_section_label: SAM/BAM @@ -215,26 +215,26 @@ tools: owner: devteam revisions: - b61f5d6a7f25 + - 9da0311ab1dd - 8da515fbc1bf - 329deb17a9f7 - 583abf29fc8e - - 9da0311ab1dd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - 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_reheader owner: devteam revisions: - - 30388d878f81 - bb8cfc6f6e0c - - db000c6007a0 + - 30388d878f81 - 85e38b31e8b3 + - db000c6007a0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -247,28 +247,28 @@ tools: owner: devteam revisions: - b8beef827165 - - a4a10c7924d1 - 344fc91e1bfd + - a4a10c7924d1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - 6c2c1836728b - - cab3f8d35989 - e613c1ad4c4c - d54a4df48867 + - cab3f8d35989 + - 6c2c1836728b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - 818030fa6bbf - - b7f7826ef1cd - bcedabb53ddf - 5d9ae78f34d3 - - 135c85f4cfaf + - 818030fa6bbf + - b7f7826ef1cd - bd850490c7f1 + - 135c85f4cfaf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats @@ -277,23 +277,23 @@ tools: - 3a0efe14891f - 541082d03bef - 24c5d43cb545 - - 1cc79f49b8d5 - - 5a08c09b9311 - 145f6d74ff5e + - 5a08c09b9311 + - 1cc79f49b8d5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: + - 0dbf49c414ae - b72793637686 + - 6be888be75f9 - 2dce91e11ca7 - bf328cec6a42 - - 0dbf49c414ae - - 6be888be75f9 - c370440f901e - - 5826298f6a73 - 350bbc5c2ffd - - 32dc5f781059 + - 5826298f6a73 - b01db2684fa5 + - 32dc5f781059 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 fbc135542..42a3138a9 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: + - 6f6537780379 - a62c4a11a67d - - d147d6455873 - - 480d9e9d156b + - 4aab5ae907b6 - ea5e944f447d - 5cb6146337d8 - - 4aab5ae907b6 - 59bb6d34fca6 - - 6f6537780379 + - d147d6455873 + - 480d9e9d156b 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 1e9de4518..6d20fb847 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -8,100 +8,102 @@ tools: - name: alevin owner: bgruening revisions: - - ecb9ea6269ee - e4c01dcece8b - e32b215b7c04 - - f2000bc73102 + - ecb9ea6269ee - b0fe3e482cb7 + - f2000bc73102 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: + - 7a6655aa6eb2 - 707023fa62fe - - c0b037b12765 - e1c3c2f2a834 - - 7a6655aa6eb2 + - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: + - 6f143dfe902a - 93dd15e13e6a - 32e547223c9e - - fb9e030ffae4 - cfc3f5a57dc6 - 55e35e9203cf - - 6f143dfe902a - 00712416fdaa + - fb9e030ffae4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 038e32885fec - - 39e945f0b2c1 - - b9fac48532eb + - 14c576ea6148 - 6f0d0c784f09 - ee98d611afc6 - - 14c576ea6148 + - 39e945f0b2c1 + - 038e32885fec + - b9fac48532eb - 688357ad5e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - 9bd945a03d7b + - 3d748954434b + - d4af736e7b83 - 43cb7b5a6fe7 - - ed4996a16f7f - c4209ea387d4 - - d4af736e7b83 - - 3d748954434b + - ed4996a16f7f - b85871dd69f9 + - 9bd945a03d7b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - - a4774b7b2e85 - - 2e8022f1923c + - 890fb06a2893 + - 7ebc22f77d86 - fe75d2414dc0 + - 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 - - 02b1fe7aed76 - 4fff5a293013 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - a90f8efe08b4 - - 344c2af50552 - - aa4a6f0916b4 - c29e7bb492bf + - aa4a6f0916b4 + - 344c2af50552 + - a90f8efe08b4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - 5b7c81b35b89 - - c32347702e12 - 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: + - ae969fdb8442 - 239193b96d72 - 1d77986f9ddc - 02fc39c8610d - - ae969fdb8442 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -138,10 +140,10 @@ tools: owner: iuc revisions: - a9caad671439 + - 8855361fcfc5 - cdf4443d5625 - cfe1e6c28d95 - 2c1200fba922 - - 8855361fcfc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: episcanpy_build_matrix @@ -171,9 +173,9 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 952abbc4b1de - fb7068d30ec9 - 01c37e54e86e + - 952abbc4b1de tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest @@ -187,129 +189,129 @@ tools: - name: hicexplorer_chicexportdata owner: bgruening revisions: + - 23b8d6b8960c - cab616fe7e64 - 163fd744e235 - - 23b8d6b8960c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - 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 - - 9ea228a9afc8 - b892fa1fcaec + - 9ea228a9afc8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - 640e0e45518a - - 45a386d18509 - f8320df1866b + - 45a386d18509 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: - - c354255ff705 - f963c251ac77 + - c354255ff705 - 9d02f1819e81 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - c4ed35f4f77f - 40fee49bc6c3 + - c4ed35f4f77f - f881c94fb3b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: + - e06265d204f6 - 782bdcb775fb - 2dccb6bb0add - - e06265d204f6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - b05f662f9f35 - - f0216498a666 - 63c8377c58b3 + - f0216498a666 + - b05f662f9f35 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions owner: bgruening revisions: - fe3aa71590d5 - - 8a11d70b6cd8 - c72fa6cb8817 + - 8a11d70b6cd8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - 4f9305d3bb34 - - 3ee5332bf57c - e03780179ee5 + - 3ee5332bf57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 4401ed529d2c - a315574104c6 - 3a6a5381db36 + - 4401ed529d2c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - 2ba6cee8e4db - a83732c79949 - c0737631eea1 + - 2ba6cee8e4db tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - 30d7390bc918 - - ea19190ce5e0 - 62b720dceb56 + - ea19190ce5e0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - 2786a931cad2 - cd40ca76865a + - 2786a931cad2 - 2b4d6a8dab36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops owner: bgruening revisions: + - 0410b6aada45 - ffc33339cd3e - bf9379529c3e - - 0410b6aada45 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: + - 07dd436ea686 - 77d8e0fd162a - 5dfba24d7bdd - - 07dd436ea686 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites @@ -323,32 +325,32 @@ tools: - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - bb8849fca57c - 409396ea5cf0 - 7f7c6ead2d0d + - bb8849fca57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo owner: bgruening revisions: - - e4f8fceab96a - 51e40e9b6c3c - b0f33533181d + - e4f8fceab96a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad owner: bgruening revisions: - - 32173084d53f - 55b013e59018 + - 32173084d53f - c261b6b05ee3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains owner: bgruening revisions: - - b376ef118807 - 4b194e675916 + - b376ef118807 - b6b8c8672756 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -356,56 +358,56 @@ tools: owner: bgruening revisions: - 910c6a1c3a27 - - ed900cd4a0a9 - 1511a8ebe906 + - ed900cd4a0a9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - - f34ab9882252 - - 6d042c96aceb - 2aa5b6b65197 + - 6d042c96aceb + - f34ab9882252 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: - - dd9988943f53 - - ea5d67ec94ab - 9b383d429659 + - ea5d67ec94ab + - dd9988943f53 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: + - 11f39d7f6c64 - 6326cd29c1c3 - 06ced663d24f - - 11f39d7f6c64 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - beb5b5917d2f - 337705015ee8 + - beb5b5917d2f - b4e780e93c91 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: - - 58de3c7c8e89 - e285920f8585 - 8d203e74869b + - 58de3c7c8e89 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicquickqc owner: bgruening revisions: + - 21d859ad4502 - ea8fb5e899e8 - 5cbd7a902a8d - - 21d859ad4502 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices @@ -431,28 +433,28 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - 1de2276f633f - 27fe5cd1729c - f36828ebdc54 + - 1de2276f633f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: + - 11a3385e03b5 - 1d201e8378b3 - cef9fb4ece1c - - 11a3385e03b5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: + - e98619de2776 + - eeab712b0b99 + - db575b4c8b22 + - 7784821452ac - 59be31ac9dc3 - 4b0adaa31c95 - - 7784821452ac - - db575b4c8b22 - - eeab712b0b99 - - e98619de2776 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -464,16 +466,16 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 48f0fb3061b1 - - 7ffaa0968da3 - 2cfd0db49bbc + - 7ffaa0968da3 + - 48f0fb3061b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 8cd2ecfa2e61 - 56371b5a2da9 + - 8cd2ecfa2e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset @@ -500,43 +502,43 @@ tools: revisions: - a4b734cd253b - c4f39bf4a068 - - f911a64454fb - 7e014059a88d - 49776718ae90 + - f911a64454fb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: - - 8b917923f7d4 - - d45f092caf24 - 43c146e25a43 - 7608d5faee41 + - 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 - - 2b0d3e2f402a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory owner: iuc revisions: - 6e90c8adf84f - - df8e4e54d367 - 69018f285aa3 + - df8e4e54d367 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: + - 2bfd55b87af3 - 44b935f2271b - - 72979cac22b2 - c92d0f9338c5 - - 2bfd55b87af3 + - 72979cac22b2 - e93b008c637a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -555,95 +557,95 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - 38db3fef7aad - - 6acb08931836 - - 4d8f983cd751 - 8983e7a04ba7 + - f9353ee6a0d4 - 6f83f8fd381f - - aaa5da8e73a9 + - 4d8f983cd751 - 77b91b9bdf52 - - f9353ee6a0d4 - b2df381a6004 - cb43c5d3acd3 + - aaa5da8e73a9 + - 6acb08931836 + - 38db3fef7aad tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - 3c86f71498bc + - d636ce5cde16 + - 64388be6d510 - b409c2486353 - - 72a6bebab2a5 - - 277313130da5 - - fc0321c000a3 - - 8cb783c81905 - a03ff8633507 - a97abb8cd15b - - 64388be6d510 - - d636ce5cde16 + - fc0321c000a3 + - 8cb783c81905 + - 72a6bebab2a5 + - 3c86f71498bc + - 277313130da5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - 18262103fa61 - - c0a80a16560f - - d86cb2ce311b - - 5e9171dc8244 + - 6bd82ed14acd - c5d3684f7c4c - - 3081ff5c84a3 - - 5c3ebe2adc77 + - 18262103fa61 - f54f0f0598ad + - 5c3ebe2adc77 - 6c145a6868cc - - 6bd82ed14acd + - 3081ff5c84a3 + - 5e9171dc8244 + - d86cb2ce311b + - c0a80a16560f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - ab55fe8030b6 - 56c0d4acef02 - - 9f354c7c8c92 + - 146ae5d70b47 - c9cb76cf8d6c - - a407e7f8bdc1 - - 7b9fafe32c86 - 4bda4412b8c2 - 94c19fb1281c - 3bcd5445cd7a + - ab55fe8030b6 + - 9f354c7c8c92 + - 7b9fafe32c86 + - a407e7f8bdc1 - d844935c906c - - 146ae5d70b47 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - 9b0cdb8cf6be - - 7647e5cd1b8b - - aa0c474463c2 - - 40812a65a78b + - 1072ce66b426 - 62acdd96d4a0 - - 6adf98e782f3 - - 95777145cb92 + - 9b0cdb8cf6be - 0185bd174ea0 - - f7446fd8d5e7 - - 1072ce66b426 + - 95777145cb92 + - 7647e5cd1b8b - dbbe1ea8ecb1 - 6f5349dd5c49 + - 6adf98e782f3 + - aa0c474463c2 + - f7446fd8d5e7 + - 40812a65a78b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - fe8f16c594ec - - 215733a383f2 - 458e8f43a775 - - a39040ae0a38 + - fe8f16c594ec - c65fce500915 - - 9fb627495ec2 - - 73ab2ac53d06 - - d18e7a6e5cd4 - - bf2017df9837 - c5541bfb8feb + - bf2017df9837 + - 73ab2ac53d06 + - 215733a383f2 + - 9fb627495ec2 + - a39040ae0a38 - f2f6c703da06 + - d18e7a6e5cd4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -658,8 +660,8 @@ tools: owner: iuc revisions: - 652923ce664f - - b7ea9f09c02f - 7a365ec81b52 + - b7ea9f09c02f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_normalize @@ -685,9 +687,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - c99ba278dfa9 - 46fc6751d746 - 9e5c0bb18d08 + - c99ba278dfa9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_tsne @@ -909,15 +911,15 @@ tools: - name: sinto_barcode owner: iuc revisions: - - fb61eb03e313 - d1b34ac42b8f + - fb61eb03e313 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - 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 diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index cffa3f0e0..f4345b739 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: - - 4c07ddedc198 - 419027d822d6 + - 4c07ddedc198 + - 746e8e4bf929 - 562f3c677828 - 2f3c6f2dcf39 - - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all @@ -56,23 +56,23 @@ tools: - name: dwt_ivc_all owner: devteam revisions: - - 506ae7b0d85d - 0b89b03ad760 + - 506ae7b0d85d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - 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 owner: devteam revisions: - - cb1c59d69557 - - 6c29c7e347e8 - 7a15159140d1 + - 6c29c7e347e8 + - cb1c59d69557 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -114,43 +114,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: + - 7442b94d6a1e + - b1eda492f063 + - 840f29aad145 - 4c4ec859c31a - 9c3e1d3235c8 - - 840f29aad145 - aef56d0e7a61 - - 7442b94d6a1e - - b1eda492f063 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: + - 07843f917990 - d0352e8b4c10 - 375bbd555f4a - 9fda0b82f419 - 30d21a6041f6 - - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 4cc980df6265 - 8b1b2b91f8d0 - - 2c58b83c9bad - 7ae443e6217d + - 4cc980df6265 + - 2c58b83c9bad - cd02bf168d23 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - 4bbaf77573ef - bb9fc9d46ea4 - 1dd433d2c92c - - ad7e0b4291ee - - e10e776f2109 - 7dd3fb35904f + - 4bbaf77573ef + - e10e776f2109 + - ad7e0b4291ee tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index 309154426..d1b6b9104 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -14,8 +14,8 @@ tools: - name: add_value owner: devteam revisions: - - 745871c0b055 - 023f0a3760b3 + - 745871c0b055 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -34,14 +34,14 @@ tools: - name: column_maker owner: devteam revisions: - - 13b6f0007d9e - - aff5135563c6 - 6e8d94597139 - - 464b9305180e - - 6595517c2dd8 - be25c075ed54 + - 464b9305180e - 02026300aa45 - 9cd341095afd + - 6595517c2dd8 + - 13b6f0007d9e + - aff5135563c6 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: - - 3a4694d4354f - 6f54dc6b37da + - 3a4694d4354f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -78,11 +78,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 34d29339abab - - 9cc411a62277 - - 37cde8134c6a - 557ec8d7087d + - 9cc411a62277 + - 34d29339abab - 90f657745fea + - 37cde8134c6a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -106,21 +106,21 @@ tools: - name: merge_cols owner: devteam revisions: - - dd40b1e9eebe - ae7843d06f8f + - dd40b1e9eebe tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - cf34c344508d - - cf4397560712 - - 3a6b78c39dca - - 2e8f945f7285 - 83069b38aa85 - - 33d61c89fb8d - 623f3eb7aa48 - 1ea4e668bf73 + - 2e8f945f7285 + - 33d61c89fb8d + - cf4397560712 + - cf34c344508d + - 3a6b78c39dca tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace @@ -140,9 +140,9 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - bce29ec10b78 - c4d18aa4ec4a - b722161a845a + - bce29ec10b78 - f768f6183386 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -156,14 +156,14 @@ tools: - name: text_processing owner: bgruening revisions: - - 74a8bef53a00 - - fbf99087e067 - - 9ff72e942410 - d698c222f354 - - 86755160afbf + - ddf54b12c295 - 12615d397df7 - - f46f0e4f75c4 - a6f147a050a2 - - ddf54b12c295 + - 86755160afbf + - 74a8bef53a00 + - f46f0e4f75c4 + - 9ff72e942410 + - fbf99087e067 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/variant_calling.yml b/usegalaxy.org.au/variant_calling.yml index 1a2e88a21..70e89d571 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -14,9 +14,9 @@ tools: - name: breseq owner: iuc revisions: - - 0d18a3ba2d1c - 85c57cc9b558 - 82fb5e3bb93e + - 0d18a3ba2d1c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -28,67 +28,67 @@ tools: - name: cutesv owner: iuc revisions: + - cb441f258c37 - c0f8fe52948e - 23d7e75d850e - - cb441f258c37 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: freebayes owner: devteam revisions: + - 57def2d7c093 - 156b60c1530f - 04fa42777df9 - - ef2c525bd8cd - - 57def2d7c093 - 3e954e7125bf + - ef2c525bd8cd - a5937157062f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: + - 791f73caa0c8 - 09d6e4693887 - e61c9ac190ad - 435b157bed6d - - 791f73caa0c8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 074d44697036 - - b11e8e9c23bf - 65432c3abf6c - - 03627f24605f + - 074d44697036 - 4805fe3d8fda - - dfadc322b065 - - e1461b5c52a0 + - 03627f24605f - 3b4b2121842f + - e1461b5c52a0 + - dfadc322b065 + - b11e8e9c23bf tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 7dfca164d2e3 - 701d134358ad + - 7dfca164d2e3 - 9cb929f21cfa tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - 426d707dfc47 - c27549b9aa1f - - 971e07ca4456 - f4473557ffc7 + - 971e07ca4456 + - 426d707dfc47 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - dbd9f2db9ed8 - - cdaab621d454 - aa35ee7f3ab2 + - cdaab621d454 + - dbd9f2db9ed8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -101,16 +101,16 @@ tools: owner: iuc revisions: - 43fffeed243f - - 93c4b04a0769 - ceff2f6a5368 + - 93c4b04a0769 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: + - fa016f1eea1a - d220115f882b - 5bbf9eada9c2 - - fa016f1eea1a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -146,21 +146,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: + - 3b1e7c170b10 - 40f0591deda0 - - 32f14a2723ec - - ee4a90760848 - e7aff4a85df5 - - 3b1e7c170b10 + - ee4a90760848 + - 32f14a2723ec tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - 02d81b994ef5 - - adc0645b945c - 9793bc5d741b + - adc0645b945c - 42818629ec4c - 4934c0ac6197 + - 02d81b994ef5 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_copynumber diff --git a/usegalaxy.org.au/vcfbcf.yml b/usegalaxy.org.au/vcfbcf.yml index 01f676e0b..83eaf500e 100644 --- a/usegalaxy.org.au/vcfbcf.yml +++ b/usegalaxy.org.au/vcfbcf.yml @@ -2,27 +2,27 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - 6a88248893c4 + - e075b1be5abb + - b7ea370b8f5d + - 8a2e296c07ef - 265fe0f9ea64 - ebe5fc018e72 - - 8a2e296c07ef + - 6a88248893c4 - 95815a0bb307 - - b7ea370b8f5d - - e075b1be5abb - 2c372041ed8c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call owner: iuc revisions: - - 1001172b5089 - - 07396b423218 - - 0fba2c15b40d - - b03984136ce4 - c37b684e7f4e - 22637b1a55bf - 21687e35f066 + - 07396b423218 - 544cb432072b + - b03984136ce4 + - 1001172b5089 + - 0fba2c15b40d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -30,76 +30,76 @@ tools: revisions: - 8408bffd5616 - 8ca3647c90fd - - 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name: bcftools_query_list_samples owner: iuc revisions: + - cced6715f926 + - eccb508bb678 - adee7e8b746f - a9826db86d9a - 18cf9de1cf73 - - 2c80b0d6bde0 - dba06328556a + - 2c80b0d6bde0 - 238f78e38a8b - - cced6715f926 - - eccb508bb678 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query owner: iuc revisions: - - 31a1b89eab9b - e0ad88dec40d - - 9f36041495a3 - - e53501abf992 - fdec14f69010 + - e53501abf992 + - 31a1b89eab9b + - f64e7ca2efd2 - 3ce32adc55b2 + - 9f36041495a3 - c9935c9e8a24 - - f64e7ca2efd2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader owner: iuc revisions: + - b7be725976b6 + - 3b7b1fe7b937 + - d68c43202172 + - fd3539749127 - 2331ddcbd5aa - 79489d5685dd - 4db0695a6fc7 - d43eb39b989e - - fd3539749127 - - 3b7b1fe7b937 - - b7be725976b6 - - d68c43202172 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh owner: iuc revisions: + - 1a989b4110da - 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devteam revisions: - - 70bc6ced57f7 - 84959112d9a6 + - 70bc6ced57f7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect @@ -442,15 +442,15 @@ tools: - name: vcfcheck owner: devteam revisions: - - aa8e8c96ca06 - 5e850c85ba32 + - aa8e8c96ca06 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine owner: devteam revisions: - - 53edb91ed051 - 1f0ba67cc85a + - 53edb91ed051 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcommonsamples @@ -463,23 +463,23 @@ tools: - 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: + - eae7c08ebb6f - 6b935ab36d7b - 4bdc111b2470 - - eae7c08ebb6f 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 @@ -499,8 +499,8 @@ tools: - name: vcfgenotypes owner: devteam revisions: - - a60ae8af21a1 - f5653ed90dfd + - a60ae8af21a1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom @@ -513,8 +513,8 @@ tools: - name: vcfleftalign owner: devteam revisions: - - d2406f98a782 - 29f9b782727e + - d2406f98a782 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfprimers @@ -534,8 +534,8 @@ tools: - name: vcfselectsamples owner: devteam revisions: - - 958b6484a7f1 - 2ba3b87f904f + - 958b6484a7f1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfsort @@ -554,7 +554,7 @@ tools: - name: vcfvcfintersect owner: devteam revisions: - - 6f6bf10618d7 - 166c4f50525f + - 6f6bf10618d7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/viral_tools.yml 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