diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index ee9e3f4c4..2ac313c58 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -7779,3 +7779,23 @@ Install 1616 17/09/24 12:17:54 bbtools_bbmap True Tests failed iuc 456d8ebb6a28 Install 1616 17/09/24 12:23:56 bbtools_bbmerge True Installed iuc cab19c0452c4 latest 3/3 BB Tools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1616/install_log.txt Install 1616 18/09/24 03:36:38 bbtools_callvariants True Tests failed iuc 7e041c120b96 latest Staging Testing 0/3 BB Tools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1616/install_log.txt Install 1616 18/09/24 10:41:37 bbtools_tadpole True Installed iuc 0ddf147d1897 latest 3/3 BB Tools toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1616/install_log.txt +Update 210 18/09/24 11:50:35 anndata_export False Installed iuc cfaf5a405371 cfaf5a405371 1/1 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 12:10:03 anndata_import False Installed iuc d330b3082107 d330b3082107 8/8 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 12:28:05 anndata_inspect False Installed iuc 0bf7fddf90c7 0bf7fddf90c7 16/16 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 12:47:22 anndata_manipulate False Installed iuc 7e8c677a7b71 7e8c677a7b71 14/14 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 12:50:48 gtdbtk_classify_wf False Installed iuc b907a3c0434f b907a3c0434f 1/1 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 13:05:52 modify_loom False Installed iuc 0f1aaff9b22d 0f1aaff9b22d 6/6 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 13:14:19 recetox_aplcms_align_features False Installed recetox c53a97599181 c53a97599181 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 13:17:15 recetox_aplcms_compute_clusters False Installed recetox 18ec7635bac6 18ec7635bac6 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 13:20:00 recetox_aplcms_compute_template False Installed recetox 134be5abb208 134be5abb208 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 13:23:05 recetox_aplcms_correct_time False Installed recetox 51332c2520c7 51332c2520c7 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 13:40:15 recetox_aplcms_generate_feature_table False Installed recetox b341cfd4baf8 b341cfd4baf8 2/2 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 13:43:07 recetox_aplcms_merge_known_table False Installed recetox cf061712a184 cf061712a184 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 13:45:54 recetox_aplcms_recover_weaker_signals False Installed recetox 24278c6b6d1c 24278c6b6d1c 1/1 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 13:50:41 recetox_aplcms_remove_noise False Installed recetox ea0758b41473 ea0758b41473 2/2 Metabolomics toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 14:21:15 scanpy_cluster_reduce_dimension False Installed iuc 178242b82297 178242b82297 11/11 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 14:49:33 scanpy_filter False Installed iuc 713a0c65b1fe 713a0c65b1fe 12/12 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 15:12:31 scanpy_inspect False Installed iuc 18262103fa61 18262103fa61 14/14 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 15:31:12 scanpy_normalize False Installed iuc 5dada6f76047 5dada6f76047 6/6 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 16:13:12 scanpy_plot False Installed iuc 2dfb2227a16c 2dfb2227a16c 38/38 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt +Update 210 18/09/24 16:37:11 scanpy_remove_confounders False Installed iuc b70219da4a96 b70219da4a96 6/6 Single-cell toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_210/install_log.txt diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index f9db80674..fb373fd16 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,18 +2,18 @@ tools: - name: abricate owner: iuc revisions: - - 4efdca267d51 - - 6e9aea89e388 + - 3f3e247c053d - 78c75f134c16 - c2ef298da409 - - 3f3e247c053d + - 6e9aea89e388 + - 4efdca267d51 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 @@ -26,8 +26,8 @@ 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 @@ -40,56 +40,56 @@ tools: - name: annotatemyids owner: iuc revisions: - - f29602ae449e - - 133f36c29579 - - 1aae04680c4b + - fe3ca740a485 - cd2480f35935 - - 44018dd6b447 + - 3e1f6f6d557e + - 1aae04680c4b - b5d8e5475247 - - a79ee60b6926 + - 44018dd6b447 - 4f2967b27e67 - - 3e1f6f6d557e - - fe3ca740a485 + - a79ee60b6926 + - f29602ae449e + - 133f36c29579 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - e78e25d3b4bd - bc88856eddab + - e78e25d3b4bd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: - - dc027fa56d55 - 7be22100e5e1 - 6519ebe25019 + - dc027fa56d55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - - 09855551d713 - 28433faa6e42 + - 09855551d713 - ca6d970d931c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - d77802fe76f7 - - 92eee5f31117 - - 728dacaf08a9 - da5f1924bb2e + - 728dacaf08a9 + - 92eee5f31117 + - d77802fe76f7 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: - 8fd427007e93 - - fe48aa4ccd5e - 7355bbf5e05f + - fe48aa4ccd5e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -114,17 +114,17 @@ tools: - name: cpat owner: bgruening revisions: - - 1ac12c0cc7a0 - - 7ccc6234b54e - 8e9e228c54c4 + - 7ccc6234b54e + - 1ac12c0cc7a0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: + - 63662ae295d6 - 9d1fbff733cf - d9c3016f7283 - - 63662ae295d6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -148,24 +148,24 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 14f588312c56 - - 756376aeb1ae - 3bbe70fef6df - - 9c15ca7e764e - b6b5cd37f2a2 + - 756376aeb1ae - 9f2455341fac - 582fd74dc2a1 + - 9c15ca7e764e + - 14f588312c56 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: + - 989f7c061f35 - 0ffe5be70caf - - 30fb23d4c31c - 73428a792541 - - a230ea445788 - 8e1ace8f77c6 - - 989f7c061f35 + - a230ea445788 + - 30fb23d4c31c - 1691af4a0d17 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -173,36 +173,36 @@ tools: owner: iuc revisions: - 494f0bb4a993 - - 0418d28136de - 5a5ae61da69c - 30f08d74024f - e94187d661df - 57c6718cbfcc - 563a19373357 + - 0418d28136de tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 4b96ced19f75 + - f31125bb85ea - 1bc5a03faf2e - - f77d7b685bb3 + - 7abc5f6dd595 + - 4b96ced19f75 - d6c7106b7b2e + - f77d7b685bb3 - 2bba2ff070d9 - - f31125bb85ea - - 7abc5f6dd595 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - b3cf4684e9c7 + - 52af33194019 - 54961e026fe4 + - d77fdcca400e + - b3cf4684e9c7 - 520e30695ec3 - d3af38b9c7e1 - - 52af33194019 - fed64e676186 - - d77fdcca400e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -215,8 +215,8 @@ tools: owner: iuc revisions: - 2aea122fbd25 - - 07d7991bf205 - 79261884facd + - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -228,9 +228,9 @@ tools: - name: goseq owner: iuc revisions: - - 602de62d995b - - 43798b4caee0 - ef2ad746b589 + - 43798b4caee0 + - 602de62d995b - 8b3e3657034e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -262,9 +262,9 @@ tools: - name: interproscan owner: bgruening revisions: + - 74810db257cc - c55643c3d813 - 98cafcbd2578 - - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -282,26 +282,26 @@ 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: - - 3c1a01127868 - 370c210d9541 - d46d803ca6cc + - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: + - b815ec682418 + - 033755194fe9 + - c8ac28e8ac44 - e95d52d295d7 - 624606f7c996 - - c8ac28e8ac44 - - 033755194fe9 - - b815ec682418 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -337,11 +337,11 @@ tools: - name: prokka owner: crs4 revisions: - - 8a22554cdde2 - - d643e3b03500 - - eaee459f3d69 - a17498c603ec + - d643e3b03500 + - 8a22554cdde2 - bf68eb663bc3 + - eaee459f3d69 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -379,22 +379,22 @@ tools: - name: snpeff owner: iuc revisions: - - 5c7b70713fb5 - - 268d162b9c49 - - 68693743661e - - 8f92c2b26e6d - cfcf33df7fc0 - 5b80f544c67f - 5a29ab10dba6 + - 8f92c2b26e6d + - 5c7b70713fb5 + - 68693743661e + - 268d162b9c49 - 9473cd297a76 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 5fab4f81391d - - 2b3e65a4252f - 09d6806c609e + - 2b3e65a4252f + - 5fab4f81391d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -406,8 +406,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - eb35257d2e29 - 10b84b577117 + - eb35257d2e29 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -419,16 +419,16 @@ tools: - name: tbprofiler owner: iuc revisions: - - 37213cf56392 - d03af1c7002c - - 037a11682176 - - ac8250086ac3 - - 4839e590cb26 - - e1a9d6fd258d - - ba6f87115e13 - - 809dfc93d593 - 51dd22484644 + - e1a9d6fd258d + - 4839e590cb26 + - ac8250086ac3 - 200c378d85f3 + - 809dfc93d593 + - 37213cf56392 + - 037a11682176 + - ba6f87115e13 - 45083d070fb8 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index d932c5d3d..7fba9c10a 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,71 +2,71 @@ tools: - name: abyss owner: iuc revisions: - - fa5259cc561b - - 8f1b150a2487 - - a929ce596a34 - 7547fcab5d19 - - 890b794c997d - 553bfe8bd0b5 - - 0124fce4654a - 0e93176640ac + - a929ce596a34 + - 0124fce4654a + - fa5259cc561b + - 890b794c997d + - 8f1b150a2487 - 841084c5fc46 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - ddddce450736 - 21e491ad532a - - 94fe43e75ddc + - ddddce450736 - b2860df42e16 - 067592b6b312 + - 94fe43e75ddc - b9e31c5c01c7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 321347bd0494 - 25ca5d73aedf + - 321347bd0494 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - faee8629b460 + - 22286dab5aa1 - 5258e18bbe23 - a7f16f24e9a1 - 3371c5bdc17a - - 22286dab5aa1 + - faee8629b460 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - 53dd00a4ab68 - 8c2167481e72 + - 53dd00a4ab68 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - f18f0b887c31 + - 2babe6d5c561 - e824f5d958d0 - - ea8146ee148f - - cf13a1e03e5b - - 2dd755c1c6ff + - 1e62c28ba91d + - 41030a6c03b7 + - 1440ae06552f - 602fb8e63aa7 + - 2dd755c1c6ff - 4048d82f0c88 + - 94170eee0ad8 + - f18f0b887c31 + - cf13a1e03e5b + - e4bd1e99bacf + - ea8146ee148f - bb935709506a - - 46ae58b1d792 - - 41030a6c03b7 - - 1440ae06552f - 5ecdeca79a0d - - 1e62c28ba91d - - e4bd1e99bacf - - 2babe6d5c561 - - 94170eee0ad8 + - 46ae58b1d792 - 0d243f458b53 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -90,38 +90,38 @@ tools: - 8d4f03b5fe9d - 3ee0ef312022 - 276f5d8712d5 - - e27815e82dd4 - - 3e4f8642c77e - - cb8dfd28c16f - 291923e6f276 + - 3e4f8642c77e + - e27815e82dd4 - 1ce9b1d72ec3 + - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - b2f674562a18 - 01210c4e9144 - 3169a38c2656 + - b2f674562a18 - 460fad600dce tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 7348b69e5109 - 8b330a577046 - - 06bcf65179fb - ba88bc5a6446 + - 06bcf65179fb + - 7348b69e5109 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 5127a713de83 - 3fba9c77550a - - 690c2caa367e + - 5127a713de83 - 3ef480892a9f + - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -133,23 +133,23 @@ tools: - name: hifiasm owner: bgruening revisions: + - 284a1cb82b61 - df25d4fb79b7 - - 60024a528cbd + - 71740308d412 - 5f625c63b8bc - - 2061fb3b81b4 - - 045c7c3d8e59 - - 0ee0c3089254 + - 60024a528cbd - da9d8bf98802 - - 3f7be05a1597 + - 2061fb3b81b4 + - 41cea2aa2dce + - 5bec28269d95 - 9ef6920c3089 + - f3c89da3af16 + - 366a11d316a7 + - 045c7c3d8e59 - 6505bd37670d + - 3f7be05a1597 + - 0ee0c3089254 - ec9e21e9c71b - - 366a11d316a7 - - 5bec28269d95 - - 41cea2aa2dce - - f3c89da3af16 - - 284a1cb82b61 - - 71740308d412 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -167,42 +167,42 @@ tools: - name: megahit owner: iuc revisions: - - a96f3ad4e0d8 - - 7518ee87b53d - - de387b2b2803 - 14ddfc8ffb93 + - de387b2b2803 + - 7518ee87b53d + - a96f3ad4e0d8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: + - 09c589057ee8 + - f8113c25bc6b - eb7b00ec347d - - 39edec572bae - d7edbc9c3a07 - - 09c589057ee8 - 9d79beb19ac3 - - f8113c25bc6b + - 39edec572bae tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 29dabd8db6f2 - - 51c2360aa807 - eadfd71dde37 + - 51c2360aa807 + - 29dabd8db6f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 99ecfdafc64f - - 2ecf5a570907 + - f338e9942b27 + - 3ca2d2a9068c + - 606b09cc9860 - fd128c111ab0 - - eb7a370f6588 - e731ea24e48d - - 606b09cc9860 - - 3ca2d2a9068c - - f338e9942b27 + - 99ecfdafc64f + - eb7a370f6588 + - 2ecf5a570907 - f369ef5f210b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -215,11 +215,11 @@ tools: - name: miniasm owner: iuc revisions: + - b799a615995d - 8b6d0d85252b - 73a3846701e1 - - a7b889b90140 - 8dee0218ac7d - - b799a615995d + - a7b889b90140 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -237,8 +237,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 15200570e926 - 64a1c751d99b + - 15200570e926 - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -251,46 +251,46 @@ tools: - name: pretext_map owner: iuc revisions: - - 79b48f02db49 - - 2b16ba799da9 - - 8fef980d48b5 - - 02831bf9e95f - - bbe19ef04a74 - d256a51a656b + - 02831bf9e95f - dfb8a4497339 + - bbe19ef04a74 + - 8fef980d48b5 + - 79b48f02db49 + - 2b16ba799da9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - a315c25dc813 - e9bd16ba5ebd + - a315c25dc813 - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 72472698a2df - - 3061c8b029e5 - - 675488238c96 - - 342a1d1fed7b - - ebb0dcdb621a - 7594365c546b - - 6fcbee531de6 - 59db8ea8c845 - 875d0f36d66f + - 6fcbee531de6 + - 3061c8b029e5 + - ebb0dcdb621a + - 675488238c96 + - 342a1d1fed7b + - 72472698a2df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - 39bed8de8017 - - 78c533842eeb + - d865b62f501c - aa39b19ca11e + - 39bed8de8017 - cd06929b224b + - 78c533842eeb - a199cd7ac344 - - d865b62f501c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -308,31 +308,31 @@ tools: - name: raven owner: iuc revisions: - - f8564b2d7f63 - - 2b2a352488fa - - 5c55448d0f33 + - 33b7d8481a76 - 3edba9afc9bc - f11b994b7eb2 - - 33b7d8481a76 + - 5c55448d0f33 + - f8564b2d7f63 + - 2b2a352488fa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast owner: iuc revisions: - - 8e66f695d859 - f73ab5187eed + - 8e66f695d859 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - ef69617ecb42 + - e122f9101584 - 28189050e437 - 53c2bc8c2ae3 + - 5fc94b3a4704 - 378e55aeeb25 - 1d06c8b38e77 - - 5fc94b3a4704 - - e122f9101584 + - ef69617ecb42 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -344,12 +344,12 @@ tools: - name: shovill owner: iuc revisions: - - ee17a294d3a3 + - d9f6a00b6db7 + - 196a599ec43d - f698c7604b3b - ad80238462c1 + - ee17a294d3a3 - 865119fcb694 - - 196a599ec43d - - d9f6a00b6db7 - 83ead2be47b2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -364,106 +364,106 @@ tools: - name: spades_biosyntheticspades owner: iuc revisions: - - 904bf932cf78 - - 604782a8a53a - 1fc82fe7ebef - - 7490b213baa9 - 051fd2db8a27 - - 1bb12736175c - c33a476f4001 + - 1bb12736175c + - 7490b213baa9 + - 904bf932cf78 + - 604782a8a53a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 34305b013402 - - ad8b536d1caa - - 655fa188c3cc - 808b3a0a6716 + - fee85957cebe - 9678993ca5bd + - 655fa188c3cc + - 34305b013402 - d6e617c4e338 - - fee85957cebe + - ad8b536d1caa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: + - b8002c3f7141 + - 7e27faaad80e + - 8d4b90bf9caf + - 037f9927c4ff - 6b5a5842531e - 21da31ed41a1 - - 037f9927c4ff - e5a3b75a271f - - 8d4b90bf9caf - - 7e27faaad80e - - b8002c3f7141 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 2a10645aeadd - 86f66ab58e14 - - 5b26685e5d3b - 328aa71f0f3c - - f1532cb33c75 - 9de69775f512 - 7922870efcca + - f1532cb33c75 + - 5b26685e5d3b + - 2a10645aeadd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 85fb02c43042 - 8cc856b935ee - 1708851f8804 - - 6aad515a5270 - e41dcb0e913b - 340bc17f49cf + - 85fb02c43042 + - 6aad515a5270 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - b65a43f70b99 + - 249f6a28c751 - b3490b036c5a - de1260f8a300 + - b65a43f70b99 - d5fb354f745d - d159735a6a9f - - 249f6a28c751 - 6357b127161e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - d5887ace0dd4 - 7897763d14ec + - d5887ace0dd4 + - d2d1df21dfb9 + - b7829778729f + - 9006e5836729 - 33368fec3b70 - dd7ad84f3943 - - b7829778729f - a90db5dbaaf3 - - d2d1df21dfb9 - - 9006e5836729 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: + - 8f631679571f - 6f4c8ad6ea01 - - 505a9833ab5d - - ced385aa976d - 189e837009c9 - - 8f631679571f + - ced385aa976d + - 505a9833ab5d - ed2425b9fd27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e - - 19bdfd1e6fe3 - f31d376ce725 - - 9ded6109434a - 356afed970b4 + - 19bdfd1e6fe3 + - d40ed4eb0c0e + - 9ded6109434a - e59bee4565b3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -472,63 +472,63 @@ tools: revisions: - af40e971a8cc - 6dd935e4984b - - 4688ae3b49b5 - - b23249f81bc4 - - 80a17897564d - ebd801e712bc + - 80a17897564d + - b23249f81bc4 + - 4688ae3b49b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - 59bd28f6265d - - b5e35a2ca4f3 - - bb11fefb23a3 - b64696992ee9 - 937ea677d437 + - 59bd28f6265d + - b5e35a2ca4f3 - cb1e3db43020 + - bb11fefb23a3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - 6bfab4a4a988 - - 2628f6790eda - - 6015aa0303f2 - cb4768eeca3b - 383bb5ad32e2 + - 6015aa0303f2 + - 2628f6790eda - 05bd7504fdb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 8f9f06995f98 - - 3e44ef016b45 - 9e3e80cc4ad4 - - 6e26c9afd301 - - 0a3a602cd1e3 - e022dff952df + - 3e44ef016b45 + - 8f9f06995f98 - e92675014ac9 + - 6e26c9afd301 + - 0a3a602cd1e3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - 08256557922f - - 5da9a0e2fb2d - 8d09f8be269e - 920677cd220f + - 5da9a0e2fb2d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - 4a53b89fa703 - - 37d88f41c810 + - 0e2b4e3f9ca1 - 82398ba86ba7 - d81360ea69d8 - - 0e2b4e3f9ca1 + - 37d88f41c810 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 d508c35e8..bdc278723 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,10 +2,10 @@ tools: - name: integron_finder owner: iuc revisions: - - bfd290fe1588 - - 4768f7f8e93f - 1ae00120dd24 + - bfd290fe1588 - 392f100eebcd + - 4768f7f8e93f tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -17,10 +17,10 @@ tools: - name: mlst owner: iuc revisions: - - ded48b36f3b7 + - 31812e7a1315 - 1f5641a52664 - 8e8dc9a1e3e5 - - 31812e7a1315 + - ded48b36f3b7 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd diff --git a/staging.gvl.org.au/bb_tools.yml b/staging.gvl.org.au/bb_tools.yml index 83a3f4771..a7d9802f0 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -3,12 +3,12 @@ tools: owner: iuc revisions: - 159b04e36791 - - 7beb76ffbc0f - - 204a131e47db - 0840ba83860c - - 1c427e24fb79 + - 204a131e47db + - 7beb76ffbc0f - a9c9d768b751 - d1f62024a08b + - 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 67db033e7..26c8ccdc1 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: + - dde39ba9c031 - 589e7e57fd6d - - ce3c7f062223 + - a1a923cd89e8 + - 07e8b80f278c - 0a5c785ac6db + - ce3c7f062223 - 87ee588b3d45 - - a8eabd2838f6 - - 07e8b80f278c - - e19bebe96cd2 - - a1a923cd89e8 - - dde39ba9c031 - 64e2edfe7a2c - - b28e0cfa7ba1 - a68aa6c1204a + - e19bebe96cd2 + - a8eabd2838f6 + - b28e0cfa7ba1 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 6d462e6ec..0fa814b6a 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -8,9 +8,9 @@ tools: - name: diamond owner: bgruening revisions: - - e8ac2b53f262 - f921014aba5a - 62c9df8382c2 + - e8ac2b53f262 - 54f751e413f4 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu @@ -23,14 +23,14 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - 5edc472ec434 - - cbf3f518b668 - e25d3acf6e68 - 6f386c5dc4fb - - d999e774072a - - 2889433c7ae1 - - a52d2d93e595 - acf4e47b734c + - a52d2d93e595 + - cbf3f518b668 + - 2889433c7ae1 + - d999e774072a + - 5edc472ec434 - 0e3cf9594bb7 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu @@ -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/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index ab104a30a..b60e082ba 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: - - 27ee142314a9 - - f4230f116196 - - 710301bc46fa - 6ca543ec1bf8 - - c8cdde00b105 - da6bd1975a71 - 095ad4d096d1 + - 27ee142314a9 + - 710301bc46fa + - f4230f116196 + - c8cdde00b105 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -105,8 +105,8 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - 67ee76f0e497 - 2a868592ebcb + - 67ee76f0e497 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -124,74 +124,74 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 88076940fa94 - bfb65cb551d8 - 0fac8e2afc13 - - 79cfd9ead848 - 3b8a9d5ced85 + - 79cfd9ead848 + - 88076940fa94 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - 715cd0e87781 - - b46d4b4d995c - - f5d979cb4b54 - - 55918daa5651 - eb6564a60136 + - 55918daa5651 + - b46d4b4d995c - d532b7e5f64b + - 715cd0e87781 + - f5d979cb4b54 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - d2f955aea23a + - 5579659312e6 - 97872d87ba80 - fdf2cc80adb5 - - 5579659312e6 - f26afd1b7104 + - d2f955aea23a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - d1d0efda35c0 - - 319a28774da9 - bc31d02be922 + - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 070e3ecc3fda - - 2c349b027a01 - 4da9ee404eab - - cac1886249a2 - ed736e6eee39 + - 2c349b027a01 + - cac1886249a2 + - 070e3ecc3fda tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - da8753545526 - - 2e219a2d9327 - 807aa4c9293d - - 525ca7c8065f + - f197e34c33a9 - 73008ef1f487 + - 2e219a2d9327 + - da8753545526 - c0c9a5024177 - - f197e34c33a9 - d1f803b5943c + - 525ca7c8065f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 27ea4e1a3f95 + - 7568ae18908a - 2c8ed1b52bf7 - 61094e01eff9 - - c4fbab8e03c5 - 1809414a9454 - - 7568ae18908a + - 27ea4e1a3f95 + - c4fbab8e03c5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -203,18 +203,18 @@ tools: - name: md_converter owner: chemteam revisions: - - ccfbd956a2d3 - d7ec25187599 - - 730ef07b90ae + - ccfbd956a2d3 - ba83f0923369 + - 730ef07b90ae - 79e8ab8f1e81 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 @@ -262,10 +262,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - b59c91adeac1 - - 1400d1977e7b - - 4242b4d68e9c - e6011617c748 + - 4242b4d68e9c + - 1400d1977e7b + - b59c91adeac1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -277,8 +277,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 75ee9c410951 - 7672039a0bb0 + - 75ee9c410951 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -332,9 +332,9 @@ tools: - name: sucos_max_score owner: bgruening revisions: + - 85fad59f8168 - 9b48456a96fe - d4c67ced6abc - - 85fad59f8168 - bf99565cec1f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index f20f38e59..0caa12fbe 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: - - 163688bb8f73 - - fa56d93f7980 - f907216064f6 + - fa56d93f7980 - c97a786e8fb5 + - 163688bb8f73 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -30,9 +30,9 @@ tools: - name: macs2 owner: iuc revisions: - - 495a4173006f - - 640d3af5d833 - f5d67c722d67 + - 640d3af5d833 + - 495a4173006f - 86e2413cf3f8 - 424aefbd7777 tool_panel_section_label: ChiP-seq @@ -46,16 +46,16 @@ tools: - name: rnachipintegrator owner: pjbriggs revisions: - - b695071de766 - 087d9872fb0d + - b695071de766 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer owner: devteam revisions: + - 5c2cc3b58c7d - 74c9214cc8e6 - 4a14714649b4 - - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/staging.gvl.org.au/collection_operations.yml b/staging.gvl.org.au/collection_operations.yml index 374579b7f..37d3af6a7 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -2,17 +2,17 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - 90981f86000f + - 25136a2b0cfe - 830961c48e42 - 33151a38533a - - 25136a2b0cfe tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -31,8 +31,8 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 0046692724f9 - baabc30154cd + - 0046692724f9 - 2dae863c8f42 - 6cbe2f30c2d7 tool_panel_section_label: Collection Operations diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index 2feace8cd..34a9e80fe 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -15,32 +15,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - a3b86937ead6 + - 6ef0b5664c69 - ab9350a8ab4d + - 3b6f97e7094c + - a3b86937ead6 + - e3cbd2287f63 + - 4a6ee918c13a - 5e1240a87bcb + - 367b1ed91207 - 0b3c3ad92827 - f3a19509108a - - 6ef0b5664c69 - - 367b1ed91207 - - e3cbd2287f63 - - 4a6ee918c13a - - 3b6f97e7094c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - 1b5fc03380d4 - 33c99804a32f + - e177a8ea0bf1 - 091bb5922a82 - d4d4e9febf5c + - 54ccb7e1f49a - bd46669113b9 - e525f9ffb9ac - - 54ccb7e1f49a + - 1b5fc03380d4 - 501c21cce614 - 584008e574b2 - 72ed72122deb - - e177a8ea0bf1 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -59,23 +59,23 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - e7ed3c310b74 - 7e801ab2b70e + - e7ed3c310b74 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: + - 8979c288aefb - 77b41c89d856 - 186b8d913e6c - - 8979c288aefb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 614a63f14adf - 4b347702c4aa + - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fml_gff3togtf @@ -87,8 +87,8 @@ tools: - name: gfa_to_fa owner: iuc revisions: - - e33c82b63727 - 8e9d604e92f4 + - e33c82b63727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -100,8 +100,8 @@ tools: - name: gffread owner: devteam revisions: - - 4dea02886337 - 3e436657dcd0 + - 4dea02886337 - 154d00cbbf2d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -134,8 +134,8 @@ tools: - name: tabular_to_fasta owner: devteam revisions: - - 0a7799698fe5 - 0b4e36026794 + - 0a7799698fe5 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq @@ -150,8 +150,8 @@ tools: revisions: - 92ac8e086317 - b9b385097f13 - - 19e45916daf9 - 63769c4217a7 + - 19e45916daf9 - 26c6706bfb07 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index c467842ee..20496f0bb 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -2,106 +2,106 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: + - 29451af70c52 + - a1ca9bccc7f2 - de72ba3ed6f2 - 268e91e540ee - - a1ca9bccc7f2 - - 29451af70c52 - - 5f6d123679f4 - c929a006727f - e821645ef8fc + - 5f6d123679f4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: + - 2d2cf5c1ea8a + - bb1e4f63e0e6 - 7a7fd0f5f15d - 5d11599b8a7d - 0e49b109abc2 - 0e143b4c3987 - 12af64f93288 - - 2d2cf5c1ea8a - - bb1e4f63e0e6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 81b1e3e1fc6c - - dc059492a995 - - c06951d10364 - 1d848bc4585f - - 195e98217334 - 7c1beb6d6eca + - c06951d10364 + - 81b1e3e1fc6c + - 195e98217334 + - dc059492a995 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 26e7304d6737 - - bfff7454b59a + - 3d211717a775 - 71aa86af6762 - 93eb012d9eed - a67ac707496a - - 3d211717a775 - 07418a30ed01 + - bfff7454b59a + - 26e7304d6737 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 29fcfd36e90a - - 2bc10a9ca58b - - b8858746dc1f - 26983857c91a + - 56d5b797ce84 + - 29fcfd36e90a - 5be24eba848d - dd0b7398bb96 - - 56d5b797ce84 + - 2bc10a9ca58b + - b8858746dc1f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: + - ee3a1b0f45f1 + - 72bfafe3330b - 9384cd033f30 + - 7ef978dc1b8a - e6d0bff01239 - 7e6bcd2e5128 - - 7ef978dc1b8a - - ee3a1b0f45f1 - - 72bfafe3330b - c3e012dfe21f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - fd1275e01605 - a60c359ec43c + - 167788df3b46 + - fb9cf9c97ec4 + - b73e213add0c + - 9470f29702f8 + - fd1275e01605 - 514fa53b5efb - d9a637e83828 - - 9470f29702f8 - - b73e213add0c - - fb9cf9c97ec4 - - 167788df3b46 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - ca0616bb2cdf - - 2c37ce318bc3 - e479c7ca5570 - - a02cfa31e9cb - - 86febdcc4283 - c34d11ea4ba6 - 5bffaa8354a1 + - a02cfa31e9cb + - 86febdcc4283 + - 2c37ce318bc3 + - ca0616bb2cdf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 01fb6a7654e6 - 2d466b530754 - - 69a8621ca2f0 - 004aea905d4d + - 69a8621ca2f0 + - 01fb6a7654e6 - 78f405266706 - 1fcb7adc39b8 - 192ef85c0b0b @@ -110,97 +110,97 @@ tools: - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - d9ce4897dbb2 - - d580d6acd1df - - 9ecba5e225a6 + - 459cfa861f0b - db940c262830 + - d9ce4897dbb2 - 3c9f0c486cca - - 2f9e4843f480 + - 9ecba5e225a6 - 137c4beed34b - - 459cfa861f0b + - 2f9e4843f480 + - d580d6acd1df tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: + - fd408d755394 - f264afa9fa6f - - fbe773640707 + - 2c66e43f1c86 - bd7db9e2f2cb - - 32e451def88c - bad3ca889618 - - fd408d755394 - - 2c66e43f1c86 + - 32e451def88c + - fbe773640707 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 231994413f89 - - 56bce3c82278 - - 3b9d990a0a0e - 7fda5607e777 - 9368fbc49c8b + - 3b9d990a0a0e - 7e361d147872 - 4e12ea27f788 + - 231994413f89 + - 56bce3c82278 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - c03c3384cd81 + - e65d16fb2724 + - d9114ef1c8a5 - b1779366c8e9 - 4431f39ede55 - ce4ce3316f74 - - e65d16fb2724 - 94ca68515826 - - d9114ef1c8a5 + - c03c3384cd81 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - f8fc4e5aff9d - d57251071381 - 23f7c5f1fdaf - - 4ed32329e0ed - - b88ebb3672a1 + - f8fc4e5aff9d - 2da482e408b8 + - b88ebb3672a1 + - 4ed32329e0ed - 793665fff0f8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: + - e4c7985d4585 + - 25d830337d31 - ba6efa77fb79 - - a4dfb122e52b + - 512155688d98 - 010e58e9d822 - - 25d830337d31 - - e4c7985d4585 + - a4dfb122e52b - a7849312d328 - c60570fa602f - - 512155688d98 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - c899e0ccff8c - - 4d678170d29b - - aa200e4f3939 - - 38e3f226248b - 00d869ea03a1 - 443d9a9d6d11 - 69264da0ce77 + - aa200e4f3939 + - 38e3f226248b + - 4d678170d29b + - c899e0ccff8c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - c361b12d207a - - a2d70c4fd406 - - 10301d137111 - d806504e96d9 - aac8444d6681 + - c361b12d207a - 6662b1a8d326 + - a2d70c4fd406 + - 10301d137111 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 b08633bbb..e01ac8967 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -16,8 +16,8 @@ tools: - name: obi_convert owner: iuc revisions: - - 4d705e3443a7 - e328ced6cf0a + - 4d705e3443a7 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep @@ -51,15 +51,15 @@ tools: - name: obi_stat owner: iuc revisions: - - 39320fee9d70 - 5f4544915893 + - 39320fee9d70 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab 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 931e5eb7a..42a614fb1 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: - - 832c20329690 - - 63dd26468588 - ce385837c160 - dba489bfcd62 + - 832c20329690 + - 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 91bf6c6a8..8b432fdd3 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -10,9 +10,9 @@ tools: revisions: - 6da3972210ee - cf1322aeb137 - - 62f5fab76dfb - 29bdbc353f20 - d82648ad25a3 + - 62f5fab76dfb 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 d7fa9c205..748602782 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: - - 5eb7e84243f2 - 8665bcc8b847 - - 5915ea1ec9b1 + - 288f97432497 - c053d4cad713 - - 49370cb85f0f - - de6cebe3c043 - - c5e2e5902201 + - b1c926deaa2d + - 5915ea1ec9b1 - 093678460093 - - 135b80fb1ac2 + - 660cffd8d92a + - 44e2cc14f75b - 48f587c13075 + - c5e2e5902201 + - c4b82dce8335 + - 49370cb85f0f - 64172f1c1202 + - 4e5056fefd88 + - 135b80fb1ac2 - fe74900d6dc7 - - b1c926deaa2d - - c4b82dce8335 - - 8c0175e03cee + - 5eb7e84243f2 - e4691e1589d3 - - 44e2cc14f75b - - 660cffd8d92a - - 288f97432497 - - 4e5056fefd88 + - de6cebe3c043 + - 8c0175e03cee tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -40,8 +40,8 @@ tools: owner: devteam revisions: - 8889eb864cef - - f666895cbebd - 9db07fd39f85 + - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -53,8 +53,8 @@ tools: - name: fasta_compute_length owner: devteam revisions: - - de2db1bdfbf8 - 7d37cfda8e00 + - de2db1bdfbf8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -102,8 +102,8 @@ tools: owner: devteam revisions: - f81d4362b6c1 - - ec0b5076173a - f773e98b26cf + - ec0b5076173a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -115,10 +115,10 @@ tools: - name: fasta_stats owner: iuc revisions: - - 56022eb50bbd - - cd0874854f51 - - 0dbb995c7d35 - 9c620a950d3a + - 0dbb995c7d35 + - cd0874854f51 + - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -130,11 +130,11 @@ tools: - name: fastp owner: iuc revisions: - - d60c3f704da0 - - 65b93b623c77 + - dbf9c561ef29 - c59d48774d03 + - 65b93b623c77 + - d60c3f704da0 - 1d8fe9bc4cb0 - - dbf9c561ef29 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -146,15 +146,15 @@ tools: - name: fastq_combiner owner: devteam revisions: - - f1dc2a761c30 - b05e39b9c170 + - f1dc2a761c30 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: - - 10b75444feae - 81a9090d6df3 + - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -167,8 +167,8 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 7861f3b10c68 - 5b87038565bb + - 7861f3b10c68 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality @@ -195,8 +195,8 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: - - c885369b207b - 09a2199cd356 + - c885369b207b tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -216,9 +216,9 @@ tools: - name: fastq_quality_converter owner: devteam revisions: - - 74db4cffab1f - 54053ea6c77e - 045f0e1043f7 + - 74db4cffab1f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -237,8 +237,8 @@ tools: - name: fastq_trimmer owner: devteam revisions: - - b63b2bfb3ea3 - 33794bdb7fe0 + - b63b2bfb3ea3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta @@ -250,8 +250,8 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 529bccd5e4a1 - d5e9e83cd3d8 + - 529bccd5e4a1 - 09070cacefd8 - 567d5b3c52b1 tool_panel_section_label: FASTA/FASTQ @@ -266,8 +266,8 @@ tools: owner: devteam revisions: - 0b7ec11b3c7c - - 4bedca26c133 - 8abdedf55101 + - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -280,9 +280,9 @@ tools: owner: devteam revisions: - cb1e251cac37 + - bdf1ce174e39 - 736b8f6ee456 - 90858c306551 - - bdf1ce174e39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -295,8 +295,8 @@ tools: owner: devteam revisions: - 421f0af4ee95 - - 07497255281e - 7ce1891db6f5 + - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -308,10 +308,10 @@ tools: - name: fastx_renamer owner: devteam revisions: + - 02f8a17a4ebd - f984bb114520 - b29d37ca9e41 - 3599f5451ee2 - - 02f8a17a4ebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -324,8 +324,8 @@ tools: owner: devteam revisions: - 6027ef51ef91 - - e246088b6e34 - 0c2907307ba4 + - e246088b6e34 - 177f0621c266 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -338,10 +338,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: - - 73194cdd4f57 + - 547e8d00f11c - 377ac2829eac - 61b4cedc8934 - - 547e8d00f11c + - 73194cdd4f57 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -365,9 +365,9 @@ tools: - name: pear owner: iuc revisions: + - b4c6f054210a - 037f0acc7830 - f69501361cec - - b4c6f054210a - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -387,22 +387,22 @@ tools: - name: seqkit_sort owner: iuc revisions: - - 61eb4cfc7313 - fdc21382376d + - 61eb4cfc7313 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: - - fe1ae2ebf63d - 812705bcf39c + - fe1ae2ebf63d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - 4b494533146a - 3da72230c066 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -440,10 +440,10 @@ tools: - name: umi_tools_count owner: iuc revisions: - - a535cf1e5da4 + - 24013bf85a6f - b557acca0b56 - 8250ea3a1501 - - 24013bf85a6f + - a535cf1e5da4 - e654095ab143 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -462,12 +462,12 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 6a675c3aa610 - - 9fa7803d1c51 + - 7accf7407811 - 828dba98cdb4 - - f3759eec3018 + - 6a675c3aa610 - 27ac32a22ad2 - - 7accf7407811 + - f3759eec3018 + - 9fa7803d1c51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index 0f1cea47e..367b178fb 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,29 +2,29 @@ tools: - name: fastq_quality_filter owner: devteam revisions: + - ce9cd02d5b88 - e41385662e5e - - 64e9a6afdd0c - 7b4468117008 - - ce9cd02d5b88 + - 64e9a6afdd0c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - 8050e091e99b - c64d534a763c + - 8050e091e99b tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - - e7b2202befea - - 3d0c7bdf12f5 - - f2e8552cf1d0 - 2c64fded1286 - - ff9530579d1f + - e7b2202befea - 2b0c9d9fc6ca + - ff9530579d1f - 9da02be9c6cc + - f2e8552cf1d0 + - 3d0c7bdf12f5 - 5ec9f6bceaee tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu @@ -38,17 +38,17 @@ tools: - name: fastx_nucleotides_distribution owner: devteam revisions: - - 18a51655db17 - - b6b54ba71bd8 - ad116ae3f4d9 + - b6b54ba71bd8 + - 18a51655db17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - 59003d0543cd - - cc0fd298cc17 - 7306ec78632a + - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong @@ -62,23 +62,23 @@ tools: - name: multiqc owner: iuc revisions: - - abfd8a6544d7 + - 3d93dd18d9f8 + - 5e33b465d8d5 + - f7985e0479b9 - 75c93c70d094 + - f7e2f1eb3a16 + - abfd8a6544d7 - b2f1f75d49c4 - - f7985e0479b9 + - bf675f34b056 - 9a913cdee30e - - f7e2f1eb3a16 - - 5e33b465d8d5 - 1c2db0054039 - - bf675f34b056 - - 3d93dd18d9f8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: + - cd7e644cae1d - 949f01671246 - 084bbd8ba7b8 - - cd7e644cae1d tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fetch_alignmentssequences.yml b/staging.gvl.org.au/fetch_alignmentssequences.yml index c01999d90..0dfc5355c 100644 --- a/staging.gvl.org.au/fetch_alignmentssequences.yml +++ b/staging.gvl.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 9e776e7fab4f - 19f42b3ea391 + - 9e776e7fab4f tool_panel_section_label: Fetch Alignments/Sequences tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index 3b6522396..ae96506a7 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - dff7df6fcab5 - 3c623e81be77 + - dff7df6fcab5 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs @@ -15,8 +15,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: - - 141612f8c3e3 - 85ef5f5a0562 + - 141612f8c3e3 - 83a19df00eab tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index 447fa2443..bcced3973 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -2,15 +2,15 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 142d95ab942e - 3630a6e624d4 + - 142d95ab942e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend owner: iuc revisions: - - 4bd4870ecd33 - be828b79bd4d + - 4bd4870ecd33 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate @@ -38,15 +38,15 @@ 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: - - 9db3e299b1c8 - d5b01cc263be + - 9db3e299b1c8 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -59,15 +59,15 @@ tools: - name: gemini_fusions owner: iuc revisions: - - 91d53f89ca54 - 8151a5a0e4f6 + - 91d53f89ca54 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -86,16 +86,16 @@ tools: - name: gemini_load owner: iuc revisions: - - 45296e47d565 - b2c25142267e - cf61daf064fe + - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 2969a1f43b7d - 90021fffff70 + - 2969a1f43b7d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors @@ -123,8 +123,8 @@ tools: owner: iuc revisions: - 666f60a9331a - - 840fb4850be3 - da74170c55c7 + - 840fb4850be3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -151,21 +151,21 @@ tools: - name: gemini_set_somatic owner: iuc revisions: - - ef9991a4a9a7 - e4e2128460e3 + - ef9991a4a9a7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats owner: iuc revisions: - - ee894347fcd6 - 5c9efee9cb1e + - ee894347fcd6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower owner: iuc revisions: - - 0c58ba91d018 - 8f04952b8882 + - 0c58ba91d018 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 6ff1fb2a4..301093442 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -2,35 +2,35 @@ 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 owner: iuc revisions: - - 9744e1124d0f - 39a996d44e16 + - 9744e1124d0f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test owner: iuc revisions: - - 9b4f4533c9ee - 688a8eccea71 + - 9b4f4533c9ee tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index 73c2b821a..5b83f0e5e 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: - - 983bf725dfc2 + - c1b437242fee - e9df53a75f3c + - 983bf725dfc2 - b39347891609 - - c1b437242fee tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,53 +17,53 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - e063168e0a81 - 28587613264f + - e063168e0a81 - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 1790dcf3c32d + - 734abc7ac21d + - 5e6237d58b0c + - c441583adae5 + - 83c7d564b128 + - f5ea3ce9b9b0 + - e407b9da183a - 8848455c0270 - - 653e89d73fc4 + - 9a776b080193 - 516a54ddf218 - - 4317d3cb6cba - ba931a59dd59 - - 6591f049cf7e - - 9a776b080193 - - 6ea73833cf67 - aad3885b3216 - - 7068f48d0ef9 - - c441583adae5 - - e407b9da183a + - 653e89d73fc4 + - 6591f049cf7e + - 1790dcf3c32d + - 1ec814014652 - 69ebb7f46e45 - - f5ea3ce9b9b0 - - 734abc7ac21d - - 83c7d564b128 - - f8054ea1c365 - - 4df8de2d0e48 - - 5e6237d58b0c - e08a7ad4378b - - 1ec814014652 + - 4df8de2d0e48 + - 6ea73833cf67 + - 4317d3cb6cba + - f8054ea1c365 + - 7068f48d0ef9 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 9aaa46d45472 - 75b3b3d0adbf - - 21a560af5913 + - 9aaa46d45472 - 34758ab8aaa4 + - 21a560af5913 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - 054483e27a35 - - af5eccf83605 - 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 07a5cef35..5f1193251 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -2,13 +2,13 @@ tools: - name: circos owner: iuc revisions: - - a64dc31ab7f2 - - 740057a5126d - - 290a11559985 - - fd59d783248a - - ae9994cf526f - c4bde687c846 + - ae9994cf526f + - fd59d783248a - df7356989ac1 + - a64dc31ab7f2 + - 290a11559985 + - 740057a5126d - 4b519282a05b - 7f13dc906cb9 tool_panel_section_label: Graph/Display Data @@ -35,8 +35,8 @@ tools: owner: devteam revisions: - f95284aa2946 - - 7cf5b1d072b5 - 867ab348287d + - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -48,21 +48,21 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 53460afd5115 - - ca7cb0eaad62 - - 3b37b1b1c3a7 - 374e9062d874 + - 3b37b1b1c3a7 - '566197475670' + - ca7cb0eaad62 + - 53460afd5115 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: + - 3d059e9c2fba + - 391a4cc45fea - d3a9e32672ec - da4c086cff5b - - 3d059e9c2fba - 10515715c940 - - 391a4cc45fea tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -80,12 +80,12 @@ tools: - name: ggplot2_point owner: iuc revisions: + - 3b12bf9b4b87 - 1acf88921176 - - 5fe1dc76176e - e3a675da7fd0 - - 299307abd804 - d0fc8b746d57 - - 3b12bf9b4b87 + - 5fe1dc76176e + - 299307abd804 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -103,15 +103,15 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - 97e3b735ed22 + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan owner: iuc revisions: - - 6e8eb0c0d91f - 8f62f666dcb6 + - 6e8eb0c0d91f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -130,17 +130,17 @@ tools: - name: jbrowse owner: iuc revisions: - - a6e57ff585c0 - - 6cd09d7b5f37 - - 17359b808b01 - 667e17248bfe - 2bb2e07a7a21 - - 1cfc579079a6 - - fd5dbf0f732e - - 4542035c1075 - - 112eb40ba6cf + - 17359b808b01 - 836d1aa3e89a - ca2def38369c + - 112eb40ba6cf + - fd5dbf0f732e + - 4542035c1075 + - 1cfc579079a6 + - 6cd09d7b5f37 + - a6e57ff585c0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -158,9 +158,9 @@ tools: - name: pathview owner: iuc revisions: - - fe154a7af404 - f1691de443a7 - 03c13085aecc + - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -174,8 +174,8 @@ tools: revisions: - 62e3a4e8c54c - 85da91bbdbfb - - 1c5dcef5ce0f - f234e2e59d76 + - 1c5dcef5ce0f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -195,8 +195,8 @@ tools: owner: iuc revisions: - 44c66e8d21e6 - - 7c9417381ad5 - 6c571966cfb9 + - 7c9417381ad5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -208,23 +208,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 7dd841a32245 + - 36b848d5f3ec - 4ac4e7083b7e - - 2824d77cd8f8 - - a1abfa420d9d - - 326a3db8d9d1 - 360df4999907 - - 36b848d5f3ec - 14e7c35f3d00 + - 7dd841a32245 + - 2824d77cd8f8 + - 326a3db8d9d1 + - a1abfa420d9d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 73b8cb5bddcd + - 2f557f6abbfb - 83c573f2e73c + - 73b8cb5bddcd - 44608d0193ed - - 2f557f6abbfb tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 @@ -236,7 +236,7 @@ tools: - name: xy_plot owner: devteam revisions: - - 319fa5a9fc1b - ecb437f1d298 + - 319fa5a9fc1b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index f89133be8..82da656cd 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: - - 1a642de6db01 - 14b3f2a4523b + - 1a642de6db01 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -28,15 +28,15 @@ tools: - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 22bd5861706d - 7779b9dcf040 + - 22bd5861706d 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 + - 361608369dda tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_genes @@ -56,8 +56,8 @@ tools: - name: scanpy_find_markers owner: ebi-gxa revisions: - - d8f5224005bb - 0a8e527d1517 + - d8f5224005bb tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes @@ -77,8 +77,8 @@ tools: - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 352cdf3b2f75 - 3c47bc560688 + - 352cdf3b2f75 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony @@ -91,23 +91,23 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: + - 94697510d55f - 9a2f72d7dbd2 - ff6decc0f432 - - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet owner: ebi-gxa revisions: - - 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 - 3027cb62adbd + - 28b1546857b0 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_parameter_iterator @@ -120,15 +120,15 @@ tools: - name: scanpy_plot_embed owner: ebi-gxa revisions: - - 1be0fc4d8654 - 7d5c97823f8b + - 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 @@ -141,8 +141,8 @@ tools: - name: scanpy_read_10x owner: ebi-gxa revisions: - - 287503c35cb4 - 078aa23c9374 + - 287503c35cb4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable @@ -176,29 +176,29 @@ tools: - name: scanpy_run_paga owner: ebi-gxa revisions: - - 6d4f88995e40 - b2768cae00a1 + - 6d4f88995e40 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_pca owner: ebi-gxa revisions: - - 4428dba93375 - 0cf90e01d9f8 + - 4428dba93375 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne owner: ebi-gxa revisions: - - 3fb53f5e46ea - abdb61e4afa3 + - 3fb53f5e46ea tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: - - 0f98603d0116 - ea91cfd0444e + - 0f98603d0116 - 767a675b5254 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 5af371230..e08df84d2 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,51 +2,51 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: + - 921a2da49a0c - ed2cca6b5de4 - a4c13ddcc8ee - - 29f66c353bcb - - 921a2da49a0c - 9edf8894a22d + - 29f66c353bcb tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - ec4b948dc6f0 - 5746d61f0a91 - - 755df866ad0c - 78fb5e286609 - d404277cc87a + - ec4b948dc6f0 + - 755df866ad0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: + - 03dd3c16ae4e + - 977dc15add20 - 11fa44ee0603 - 9e357a8b2ec3 - 4d511437b1e5 - - 03dd3c16ae4e - - 977dc15add20 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - c3e5e2cf12b7 - - 3b5b54ed6392 - 0ba4f56a3613 + - c3e5e2cf12b7 - 41dbf4d162a2 - 77919cc3618e + - 3b5b54ed6392 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - 5308ca68ef3d - - 12d51d7be66f - 7babd8a46fe0 - - 9939786dd9c9 - b63363075c2e + - 12d51d7be66f + - 9939786dd9c9 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 9b1b3184e..6b34afec6 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,124 +2,124 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 0c777d708acc - - 699a5e9146b3 - 7db4fc31dbee - - 8bccb36e055a - 81f0cbca04a7 - 3df9f0a4bf34 + - 699a5e9146b3 + - 0c777d708acc + - 8bccb36e055a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 2436a8807ad1 - - 5bc8cdc17fd0 - 0a53256b48c6 - 5791a7f65275 + - 5bc8cdc17fd0 + - 2436a8807ad1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - e576b73a2e2f - - 9d47aabda459 - 6ad1d3cfdea1 + - 9d47aabda459 + - e576b73a2e2f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: + - b1c2c210813c - 70316d792fc9 - 77f7159d775a - - b1c2c210813c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - f70b215d155c - - d51310ab328a - dba87c4b32d3 + - d51310ab328a + - f70b215d155c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - - f3360fbeda64 - - 85edbb7a436b - 10eed33aa9b2 + - 85edbb7a436b - fcadded98e61 - b07f4839ca77 + - f3360fbeda64 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 - - 664232d2a3f7 - 5bf8eb50b280 + - 664232d2a3f7 + - b58447a2eed2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - 0e4dccaafef5 - e917a2424690 + - 0e4dccaafef5 - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - e8f822eeb9fd - bad171ed1e96 + - e8f822eeb9fd tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - - e7273daa5ae2 - - 670975e92458 - 6070780813d9 + - 670975e92458 + - e7273daa5ae2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: + - ef4aed1d34c4 - cdf8e3c57dae - df3ad3ba5c6f - - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - 2484086dee41 - - 5d28ac336861 - 6a7da2e5f696 + - 5d28ac336861 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - 11f177b1a59e - f2ed92b011a9 + - 11f177b1a59e - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - f8fa0f6718a3 - f24c370e5ea4 + - f8fa0f6718a3 - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -134,73 +134,73 @@ tools: - name: cp_identify_primary_objects owner: bgruening revisions: - - 993faa34333b - - b6eec6087271 - 87d4d92d7487 + - b6eec6087271 + - 993faa34333b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: + - ff1a86a87364 - 6100a22bf4f2 - c09dcda1143f - - ff1a86a87364 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: + - 3a05117669cf - 667a513e67e4 - b178453ea8d1 - - 3a05117669cf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - 2564f461de62 - a1a961c46d4b - ac5bea85a391 + - 2564f461de62 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: + - a32c3f810ade - 20dbb1f7ec7b - 91e03287f285 - - 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 - 6f4715b8540a + - d3890df07463 - 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: - - 79e10d12d90a - - acf3aa487283 - d85f11570109 + - acf3aa487283 + - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture @@ -220,17 +220,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: + - 48102a685037 - 8083a87d2fdf - 3a3033222f61 - - 48102a685037 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 @@ -255,9 +255,9 @@ tools: - name: image_info owner: imgteam revisions: + - 7b6d9412c7f8 - f8b4eada923c - 236ec78b2e53 - - 7b6d9412c7f8 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_segmentation_mask diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index dc42672f6..aee5f52c1 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: + - 78bbd17d0703 - 3e4f434a69c6 + - 3a72fede57ce + - a38934e303b9 - 1069f6db0a0e + - 40737febe339 - d6e72da3ec35 - - f362150bef41 - - 78bbd17d0703 - e319b5b65879 - - a38934e303b9 - - 3a72fede57ce + - f362150bef41 - e4ee04da1c19 - - 40737febe339 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - f91cfb73d369 - - 0135f1d487a0 - c88553ec696e - - 7fe36019c073 - 9537184d421f - - 2b95d5c04908 - - fcbeda41d0ac - - 8f8df367470d + - f91cfb73d369 + - 0135f1d487a0 - 72ddd32392cd + - fcbeda41d0ac - 618297d23022 + - 7fe36019c073 + - 8f8df367470d + - 2b95d5c04908 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - ad0dc9f4c9e2 - - d7e79eb3bcb3 - 2cf4a1cafc16 + - d7e79eb3bcb3 - fafb3d685fa9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: + - a1c2aecd7a0d - ee29337f905c - - 6a1515bb0687 - - 94df24c6bc00 - 43aac8d29685 - - a1c2aecd7a0d - - 28a6f1908fcc + - 7f1cfa4c0e32 + - 3d18f8c3c0f6 - 8d36959b000d + - 28a6f1908fcc + - 94df24c6bc00 - 9eaadf03e0df + - 6a1515bb0687 - ee2beb764a7b - 5dc33613c288 - - 8c05afb547fa - bd2a7d1316b9 - - 7f1cfa4c0e32 - - 3d18f8c3c0f6 + - 8c05afb547fa tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - db536ad45f28 - - 8858fa037a15 - - 86a20ae274fc - - e3bb03cf207a - - bcaa0d571ce2 + - 364f4ffec275 - 5d6ed46cc101 - - 5671e1d3d5ee + - a250929be21b + - e3bb03cf207a + - 8858fa037a15 - cb903c9dc33d - d37ede8589b2 - - 364f4ffec275 - - a250929be21b + - 86a20ae274fc - 9f978da6528a + - bcaa0d571ce2 - c092052ed673 + - 5671e1d3d5ee tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - abbc8041e8ec - - 12d66d0d05ac - - ed28dd32141c - - 38b91a3190cd - - c5c9f02b6167 - - 584beffa972b - - f95f403841ad + - 49236b03e4fd - 230b05597996 + - f95f403841ad + - abbc8041e8ec - e1a015876aa9 - - 49236b03e4fd + - 584beffa972b + - ed28dd32141c - 3b6a16d82c1b - 194e3ceee923 + - 12d66d0d05ac + - c5c9f02b6167 + - 38b91a3190cd tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/join_subtract_and_group.yml b/staging.gvl.org.au/join_subtract_and_group.yml index c221b812b..e6b1e257f 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: - - b8a457820315 - 17e3b698dd52 - f198773344e4 - 0f1724dd59d2 + - b8a457820315 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - ac092723240d - 374cb875d38a - - a513e3fbb4c5 - 22c2a1ac7ae3 + - ac092723240d + - a513e3fbb4c5 - ba0c40780ecf tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/machine_learning.yml b/staging.gvl.org.au/machine_learning.yml index c8bd42820..cde2f80c2 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: + - 66d7efc06000 - 522137aaa9c4 - 772e0e89fc68 - - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: + - f22a9297440f - 8a794e6d3388 - 4d81e3e2fb63 - - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: + - e1317b5502fa + - 2af1346e68c9 - f1b9a42d6809 - 818f9b69d8a0 - b6ef6d0cb6b7 - - 2af1346e68c9 - - e1317b5502fa tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - c80db5d6fd8c - 1588f9076e32 - - 947c2eacccb8 - 05143043ca13 + - 947c2eacccb8 + - c80db5d6fd8c - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 25b46af53232 - 83228baae3c5 - 29e4122c90de - 1552b8cb4a94 + - 25b46af53232 - 9991c4ddde14 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 841a6cc5fc58 + - a07ab242b0b5 - 1a53edc4b438 + - f3dfa4bdf87e - 53616c8b0865 - 060ca94ac049 - - a07ab242b0b5 - - f3dfa4bdf87e + - 841a6cc5fc58 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - 2fc89dcd41c8 + - 91c4e3331208 - 927586a18553 - - 40f4447733b2 - - dc4b5fd604a6 - d4808d5b83da - - 91c4e3331208 + - dc4b5fd604a6 + - 40f4447733b2 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 25ab6b4e376e + - 7626ea9c2e1b - 301e07345c93 - e5a5ad882f1f - c6ae57f774c6 - - 7626ea9c2e1b + - 25ab6b4e376e - 36e8d6d5d01b tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 4ed102b922cb - - 02d2be90dedb - - 0630258dcf35 + - f9639b488779 - b7c3e9a3b954 + - 02d2be90dedb - 80852884053f - - f9639b488779 + - 0630258dcf35 + - 4ed102b922cb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: + - caeb57858702 + - 14180f9c831e - 61634a87efc7 - ec69cbe34b73 - - 14180f9c831e - - caeb57858702 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 c41c2c84b..fd881c447 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 + - 0d4acadabb04 + - 017aba02828d - 03e9b2fbc005 - - a6d65b0c67af - - 749c918495f7 - 3ba8d4563129 - - 0d4acadabb04 + - 937aa69e715f + - cd659e8cc5fa + - f6877ad76b00 + - 749c918495f7 - d5ceb9f3c25b - - 017aba02828d - 17062a0decb7 - - cd659e8cc5fa - - 937aa69e715f + - a6d65b0c67af 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: - - dfd8b7f78c37 - - 3fe632431b68 - 64f11cf59c6e + - 3fe632431b68 - e188dc7a68e6 - - 53646aaaafef - 2477830927ec + - dfd8b7f78c37 + - 53646aaaafef 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: + - 2ff111fac1d7 + - 3e1ea2facca6 - e7f19d6a9af8 - 60afcc2c1d05 - 37b497aa133f - - 2ff111fac1d7 - - 3e1ea2facca6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 8c6cd2650d1f - 09b53c1d4ab1 - - b3eab4b67562 - - be1d967337e4 - - 6b1e195506a3 - - c0c2d0941de8 - - 037c6e54df11 - f54f5baedfdd - - 77b2770508f6 - 3f4d6399997b + - b3eab4b67562 + - be1d967337e4 - 11a0d50a54e6 - 53c0b7a1a0c3 + - 8c6cd2650d1f + - c0c2d0941de8 + - 77b2770508f6 - 5cc34c3f440d + - 037c6e54df11 + - 6b1e195506a3 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 13022c3d3076 + - 42ce70172b72 + - 45795f582ae9 - 5ef7ec16b04f + - 1cd2511a396e - 79b885ce78d7 - - 178bdbdb6d24 + - 13022c3d3076 + - ec9cbd6b9a49 - 00fbfac99d39 + - 178bdbdb6d24 + - 9ee34ba73ebf - b8f5f6e87f5c - - 42ce70172b72 - - ec9cbd6b9a49 - e403d27e8f24 - - 45795f582ae9 - - 9ee34ba73ebf - - 1cd2511a396e 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 7ab814a06..d7a0670f2 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -14,8 +14,8 @@ tools: - name: biotransformer owner: recetox revisions: - - 6cd2a9e6ac49 - 90dc951da294 + - 6cd2a9e6ac49 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_annotate @@ -100,29 +100,29 @@ tools: - name: matchms_filtering owner: recetox revisions: - - a177ac3c752c - 00e66c401366 + - a177ac3c752c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity owner: recetox revisions: - - 84af792d3a78 - d7b517f2c5fe + - 84af792d3a78 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter owner: recetox revisions: - - 9e3c83d2afc3 - 1b09315a3f87 + - 9e3c83d2afc3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export owner: recetox revisions: - - b576ed720711 - f04610d25411 + - b576ed720711 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match @@ -141,8 +141,8 @@ tools: - name: matchms_networking owner: recetox revisions: - - 8147d93d372d - 1d74ae228df3 + - 8147d93d372d tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key @@ -173,8 +173,8 @@ tools: - name: matchms_split owner: recetox revisions: - - 500f473df7e4 - 0cf68b536cd1 + - 500f473df7e4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting @@ -255,20 +255,23 @@ tools: - name: recetox_aplcms_align_features owner: recetox revisions: - - 7b42ee54d757 - 79ad928a0dae + - 7b42ee54d757 + - c53a97599181 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - - f3a18e020cdd + - 18ec7635bac6 - 149b9cc7499b + - f3a18e020cdd tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: + - 134be5abb208 - dfebc82ba1f0 - 481d769e2f7a tool_panel_section_label: Metabolomics @@ -278,18 +281,21 @@ tools: revisions: - 9064aecc78a7 - 02c772a49998 + - 51332c2520c7 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - b3413f335327 - e7305ba0dd38 + - b341cfd4baf8 + - b3413f335327 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: + - cf061712a184 - 17a48d0a80f4 - dd7bbc2b99d1 tool_panel_section_label: Metabolomics @@ -297,14 +303,16 @@ tools: - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - - d7f5878a98c3 - 99d118321d5f + - 24278c6b6d1c + - d7f5878a98c3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - ffbabefbd2e2 + - ea0758b41473 - d90187b0f247 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -317,8 +325,8 @@ 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 diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index 5b1ea4f1d..5d9b60974 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: - - 18676df0cb3a - - 0094893f5001 - 0e63d03c8790 + - 0094893f5001 + - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -41,69 +41,69 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 65db807336bc - - 5b5a7af9fbb4 - - 63f86089423e - 76d3d2b10738 + - 63f86089423e + - 65db807336bc - 7c2100246a2f + - 5b5a7af9fbb4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 18a502a9d287 - - 1c35dadbe76f - - 84fd33a60b35 - 00f5005840fa - 96336c6a2bb7 + - 84fd33a60b35 + - 18a502a9d287 + - 1c35dadbe76f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: + - addaf9d22850 - 34e55239e68b + - e8fba04706d3 - f732237754fc - - addaf9d22850 - a9f4a217dcd6 - - e8fba04706d3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: + - 0776d824d896 - 5fe3edf19b9c - - 75403243703a - 8c202e741d68 + - 75403243703a - 04c15826a0b8 - - 0776d824d896 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: + - 8470de786d47 + - 1c9b3bcd4261 - 43c99742158b - e96bbb9e24ea - 75c8945b0da2 - - 1c9b3bcd4261 - - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - 1d75bd0595e2 - - 5c865a382933 - - 35176674168c - 84743da21318 - 306a40d4bb8f + - 35176674168c + - 5c865a382933 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: + - 555ccac8a4c5 - 78faebd0879c - 32c9ea835770 - - 555ccac8a4c5 - 8daf4564ccda - ac72310b038a tool_panel_section_label: Metagenomic Analysis @@ -111,20 +111,20 @@ tools: - name: dada2_plotqualityprofile owner: iuc revisions: - - f947b4bb5107 - a58e4a43f49c - d60df8727f59 - - cae017b76acb - 7b8cb2b02978 + - f947b4bb5107 + - cae017b76acb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: + - 7f3b59dee073 - 1bc3657cd694 - 04144473e59e - 073608a50ac3 - - 7f3b59dee073 - 7136e9ab70db tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -132,42 +132,43 @@ tools: owner: iuc revisions: - 0a1224c4b781 - - d943081510da - - 9058d8943303 - a7817705348e + - 9058d8943303 + - d943081510da - 19299bb1c6af 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: - - a68b985913ab + - b907a3c0434f + - c4db8c4de66f - 65d52c693b8e - - dbf1798c0dcc - f8f56dd6449f - - c4db8c4de66f + - dbf1798c0dcc + - a68b985913ab tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 15dbb444df71 - 213df31ba341 + - 15dbb444df71 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: + - 6c84982ee6f7 - 654548ae1357 - 6d364c65c946 - - 6c84982ee6f7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -179,9 +180,9 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - bd7a9c6efb10 - - 6aad8ca3918b - e66ab198ec15 + - 6aad8ca3918b + - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table @@ -195,9 +196,9 @@ tools: - name: humann2_unpack_pathways owner: iuc revisions: - - cad93abecac9 - 7f208f1eb64f - 9704f1a3b32d + - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -233,30 +234,30 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - 31c6d107e7a5 - c409a495841f - - e88b731dad59 - 79706f10d680 + - e88b731dad59 + - 31c6d107e7a5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: + - 094ad9c068af - 172920f67a84 - - 714d5a28cc5c - - 71ea608ddfa3 - d24841f5c3d2 - - 094ad9c068af + - 71ea608ddfa3 + - 714d5a28cc5c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - a4d7148ccee4 - - d7e9a3c41657 - - 4137b492233e - 12fb63b5f63f + - d7e9a3c41657 - a293a742194f + - 4137b492233e + - a4d7148ccee4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -268,12 +269,12 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - 75bedfb2078b - - e2c71b852aba - - 64bc7acc22a9 - 6fcb8ac37a3e - cf87759761eb + - 75bedfb2078b + - e2c71b852aba - 97f7bb0851e7 + - 64bc7acc22a9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -292,19 +293,19 @@ tools: owner: iuc revisions: - 5e5a999ffaa9 - - c82508e76ad1 - - 080ea153677c - 2d35528d2141 + - 080ea153677c + - c82508e76ad1 - 4033827c76b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 95bf7479d53c - - 6b7622dda516 - fc6c328c292f - 2cd76b089570 + - 95bf7479d53c + - 6b7622dda516 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -316,8 +317,8 @@ 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 @@ -372,9 +373,9 @@ tools: owner: iuc revisions: - 20e2f64aa1fe + - 328c607150ff - cdee7158adf3 - 4a9da2b6c2e3 - - 328c607150ff tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -407,8 +408,8 @@ tools: - name: kraken_taxonomy_report owner: iuc revisions: - - 27d65c78863c - bfae8da6082c + - 27d65c78863c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -420,8 +421,8 @@ tools: - name: kraken owner: devteam revisions: - - 766d5f63b0f4 - 8ba2174315aa + - 766d5f63b0f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_alpha_diversity @@ -439,8 +440,8 @@ tools: - name: krakentools_combine_kreports owner: iuc revisions: - - 4960abe31b4d - 073c867c5244 + - 4960abe31b4d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -489,22 +490,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 3cc4a60615c0 - - 4fd3b5d8706b - - e073891b2afc + - 327d9f4cc95f - 0270541aaf46 - - 7f5d7b0e9884 + - e073891b2afc - 2cff76cf35c6 - - 327d9f4cc95f - 27250f92a01a + - 3cc4a60615c0 + - 7f5d7b0e9884 + - 4fd3b5d8706b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - eb50e7eca3dc - 76bc4efa1aeb - 708abf08a626 + - eb50e7eca3dc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -577,16 +578,16 @@ tools: - name: metaphlan owner: iuc revisions: + - a16313517e55 + - b89b0765695d + - 1a037928504c - 289b3807e80c - 2131d7dca455 - - a16313517e55 - a92a632c4d9b + - ff8f55893e7d - fd69c607b43f - ef65b083bd0c - 6dee4abadccb - - b89b0765695d - - 1a037928504c - - ff8f55893e7d - 1a6cdf55390f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -633,8 +634,8 @@ tools: - name: picrust2_pathway_pipeline owner: iuc revisions: - - f53beb324696 - 6077821e8ae7 + - f53beb324696 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pipeline @@ -654,8 +655,8 @@ tools: - name: picrust2_shuffle_predictions owner: iuc revisions: - - 677f3c8db525 - 881f2faa5fe7 + - 677f3c8db525 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -667,8 +668,8 @@ 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 @@ -729,13 +730,13 @@ tools: - name: staramr owner: nml revisions: + - 4b9a8031ab74 + - 2fd4d4c9c5c2 - 4d83eccf5f81 - - 3b22de20bd4b - 141afacabcfa - - 4b9a8031ab74 - - be818ae858e4 - aeaa20b96ef2 - - 2fd4d4c9c5c2 + - 3b22de20bd4b + - be818ae858e4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -765,8 +766,8 @@ tools: - name: vsearch owner: iuc revisions: - - 9495df9dd6ef - 576963db5f1b - b3c7199d8786 + - 9495df9dd6ef 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 aeb746c63..e826cebe9 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - ab12df91b47f - 7238968f58f7 + - ab12df91b47f tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - 63b74bfc8052 - f4d7d5755f01 + - 63b74bfc8052 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -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 0b93ff6e2..864e9fad0 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: + - 48c13389050d + - a74dbfee5a86 + - cd07731e4434 - 9eeb13a92d79 + - 9422c5a87ee2 - 098506c54016 + - 80f03df2e2ce + - 2263989660f5 - bdfbaf0c10aa - - cd07731e4434 - - 9422c5a87ee2 + - 6ae5a7b5a0a2 - 9baa871cb1d1 - - a74dbfee5a86 - - 48c13389050d - 8b67dd48fec1 - - 2263989660f5 - - 6ae5a7b5a0a2 - 94b8c6013083 - - 80f03df2e2ce tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - f14193ec1f50 - - 5abf2c2249aa - - aaa0d6a8b808 + - d7ce0ec78e51 - c44f824c051a - - d390fe1567dc - - 3ff17bad4006 - - be78f13134e2 - - fc2e49f91e52 - - 4a60927aaca5 + - 2e093badc689 - f0af8936ed41 + - 4a60927aaca5 - '764845535798' - - 2e093badc689 + - f14193ec1f50 - c18157c68134 - - d7ce0ec78e51 + - fc2e49f91e52 + - 5abf2c2249aa + - d390fe1567dc + - aaa0d6a8b808 + - 3ff17bad4006 - bc3831dd65c1 + - be78f13134e2 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 @@ -67,13 +67,13 @@ tools: owner: rnateam revisions: - f0d493f8f84f - - f1a5908ea2cb - - c5908940967d - - 15974dd17515 - bf28a8cff401 - - a65296ffb4a0 - - 6f28e90db932 + - c5908940967d - 8e649f27aa0d + - f1a5908ea2cb + - 6f28e90db932 + - a65296ffb4a0 + - 15974dd17515 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter @@ -87,40 +87,40 @@ tools: - name: mummer_dnadiff owner: iuc revisions: - - c9685bc0407c - 60698466facd + - c9685bc0407c - 5561a1193611 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - 48823c9635a4 - bcd65de9725b - 57f042937ba7 + - 48823c9635a4 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - ebe3b0f84de9 - fb43e8887350 - 4fc0cb2ac8ae + - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - 636b049e6141 - - e18267f90096 - 7cd7a55a678d + - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - b4124df98b26 - - cf3c9489c088 - 959c1f8dae95 + - cf3c9489c088 + - b4124df98b26 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 b38a79a58..b807c2106 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,8 +8,8 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 18a8d140ec6f - 28928576e1ea + - 18a8d140ec6f - 7c47b3c9e493 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -29,20 +29,20 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: + - 72b5e9dda577 - fc8804320156 - - cb34f00cc10f - a7228a7ea146 - - 79e9a869f40e + - cb34f00cc10f - 0e9e7fcdd543 - - 72b5e9dda577 + - 79e9a869f40e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - 18505fe2bdb1 - - d6cddc06aeae - fa11aa8103b2 + - d6cddc06aeae + - 18505fe2bdb1 - db25ec99c3ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -55,15 +55,15 @@ tools: - name: medaka_variant owner: iuc revisions: - - 43815fa60f3a - - eb746fa6f514 - - 0f5f4a208660 + - 2bf63b38ee9b + - cc36773a3681 + - 222669c4afb6 - edf6d4003fad - ec699520444c - - cc36773a3681 - - 2bf63b38ee9b + - 0f5f4a208660 - 19f3b583a9b3 - - 222669c4afb6 + - eb746fa6f514 + - 43815fa60f3a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -82,60 +82,60 @@ tools: - name: nanoplot owner: iuc revisions: - - a3c4fe6f49ab - - 645159bcee2d - a02b8b3f5a0c - 7b379e98b9a9 + - a3c4fe6f49ab - a38bdcec9e4c - - 0f1c34698076 - edbb6c5028f5 + - 645159bcee2d + - 0f1c34698076 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - d219b6d8158a - - 85a394edc247 - 3b6f94fc7e1d + - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - 90a922f32523 - a8d4be409446 + - 90a922f32523 - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - d376944466bf - - 4857d5bcce52 - 449e9aeded2d + - 4857d5bcce52 + - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - bec636361cfd - de5b3d8f5b90 - a3afc5f0a96c + - bec636361cfd tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: + - 5f76b20953e5 - 93d623d9979c - 543cbeef3949 - - 5f76b20953e5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 28d7819c312f - 1d835c691480 + - 28d7819c312f tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -173,15 +173,15 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 4fe6b96aff72 - 2e22ebec211a + - 4fe6b96aff72 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle owner: iuc revisions: - - 34553d0caa5e - ce8af9373061 + - 34553d0caa5e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index baf73c692..f468fd4f1 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -2,8 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - 592ef3959907 - a5921c09b7b7 + - 592ef3959907 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: annotation_profiler @@ -21,8 +21,8 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: - - 4e85a3a5dbd1 - 71186bb66ca2 + - 4e85a3a5dbd1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_frameshifts @@ -59,19 +59,19 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - baceff842902 - - 97b1b5ad1cda + - d74850cf4e42 - adfd6bf710bd + - baceff842902 - 3e73c97f025d - - d74850cf4e42 + - 97b1b5ad1cda tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - 9dd107db92c2 - - 1586b111d2a3 - 83da94c0e4a6 + - 1586b111d2a3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -83,11 +83,11 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 2f27f3b86827 - - e4b4837f06f5 - - ed1518ce2237 - 1e34d2e3d285 - edacc4bcd3cb + - ed1518ce2237 + - 2f27f3b86827 + - e4b4837f06f5 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -106,8 +106,8 @@ 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 @@ -155,17 +155,17 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 9a40272f56d0 - 6287d0ee459e + - 9a40272f56d0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - b4b2b284230a + - 172815da3d41 - 5bcf0e24f42c - 27a6a256cd23 - - 172815da3d41 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -178,8 +178,8 @@ 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 @@ -191,23 +191,23 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - fea85c467896 - 19bbd19b74b3 + - fea85c467896 - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 0df47f8552f6 - 7776cb18fdf8 + - 0df47f8552f6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 15c2fc266540 - 4c7ebbad42cf + - 15c2fc266540 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -225,12 +225,12 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: + - 5fe20c915fa6 - 9c43baa60906 - - 0cb27ea69dc1 - - d8dc037e3c13 - 2c61c30a57e7 + - 0cb27ea69dc1 - 4ba60cb14cb0 - - 5fe20c915fa6 + - d8dc037e3c13 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -243,18 +243,18 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - aec831b54a5b - 0db22932bc39 - 9d09724f2bf1 + - aec831b54a5b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - df30a2f1db55 + - ed7a967cb11b - 29c738066906 - 6e24e79d3d69 - - ed7a967cb11b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -266,16 +266,16 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: + - ad90c2da4f38 - 3e4d45aca422 - 1865e693d8b2 - - ad90c2da4f38 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_snpeff owner: iuc revisions: - - d107d20dc6bd - def511e8e005 + - d107d20dc6bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -296,8 +296,8 @@ tools: owner: devteam revisions: - 625fd9476402 - - 9946bc39c834 - 94a50db37d1a + - 9946bc39c834 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1047,23 +1047,23 @@ 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: rdock_rbcavity owner: bgruening revisions: - - 7e5c2e4bc227 - 744a777e9f90 + - 7e5c2e4bc227 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rdock_rbdock owner: bgruening revisions: - - c362398df83b - e4b7d1507a75 - a22969b08177 + - c362398df83b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes @@ -1075,11 +1075,11 @@ tools: - name: salsa owner: iuc revisions: + - ab5b7f6b7198 - 9a22227bb6d0 - - f77f7a7f3b83 - ba7b0f11e470 + - f77f7a7f3b83 - 58a870ef434c - - ab5b7f6b7198 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_merge diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index 4de361a35..433b76e83 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -39,57 +39,57 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - f04a1264e2a2 - - cce7b18495e4 - - 26de3a7b1cb9 - - a6619171428e - - 81e66674859e - - d7c7ef3353fe - c78f3d7dd1db - - 6a457678efcb - - 3b8b5bde0bd9 + - b89cac5156ec - '841557158611' - - 107d3ba7024a - - f73435dc282b - - 3f59ebfbfe3d - d033ffc1c161 - - b89cac5156ec - 8834daeb9892 + - 6a457678efcb + - a6619171428e + - 107d3ba7024a + - 3f59ebfbfe3d + - f73435dc282b + - 3b8b5bde0bd9 + - 81e66674859e - 5a7c56a5cc08 + - 26de3a7b1cb9 + - cce7b18495e4 + - f04a1264e2a2 + - d7c7ef3353fe tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 7a2092844346 - - 6a726db04d4b - - 88c4aa435ded - - 5b777002c2de - - a185b079b095 - - e75442c7f4da - - df47d4845b62 - - 6223845127ea - - 6283babe736e - 659517798cc4 - - b0af57c1a968 - - 3b96e92e8ec3 - aa8cc71438cf - - 4755f52427c4 + - 6223845127ea + - df47d4845b62 + - a185b079b095 - 02b8758214b0 + - 88c4aa435ded - 5fcd1ece3a6e + - 3b96e92e8ec3 + - 6283babe736e + - 6a726db04d4b + - 7a2092844346 + - 5b777002c2de + - b0af57c1a968 + - e75442c7f4da + - 4755f52427c4 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - d1c340a5664b - - 111bd54f6bc4 + - f97743d52b87 + - 524d31add34a - b8476e82ac20 + - 111bd54f6bc4 + - 24d024316465 - 70acec670c30 - 0878b7fd5260 - - 524d31add34a - - 24d024316465 - - f97743d52b87 + - d1c340a5664b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade @@ -97,8 +97,8 @@ tools: revisions: - 9e10ba792be2 - 4f6349228462 - - feb40665d7cd - daddf188c13f + - feb40665d7cd tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -110,33 +110,33 @@ tools: - name: pangolin owner: iuc revisions: - - ca0d8cf80567 + - 83a69484cb87 + - 81804a978fc0 + - abf6dbe8c9d7 - 3a43c3982401 - - 03ed9524dcd1 - - 42a174224817 - - 437e28791761 - - 36912871ccdc - - 8ad84c5753ea - 2f1019071464 - - 14ae456b8cc5 - - abf6dbe8c9d7 - - a2099fb98cdb - - 5f8727ff21e7 - - 81804a978fc0 - - b7e297c2ede6 + - 8ad84c5753ea - b6abccb1f25b - - 83a69484cb87 - - ca337cce3888 + - 36912871ccdc + - b7e297c2ede6 + - 437e28791761 + - a2099fb98cdb + - ca0d8cf80567 + - 03ed9524dcd1 + - 42a174224817 + - 9d61d3fa046c - 7bb8726be37c - 2fa9d4f1b48f - - 9d61d3fa046c + - 14ae456b8cc5 + - ca337cce3888 + - 5f8727ff21e7 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 @@ -148,23 +148,23 @@ tools: - name: raxml owner: iuc revisions: - - ea30d3089354 - - 73a469f7dc96 - - 29ff6a849eac - ba29b5e2a4be - a4b71be30c3c + - 29ff6a849eac - b1e68bbe4cef + - 73a469f7dc96 + - ea30d3089354 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - f1ccc8a6eb05 - - 809e42326fc2 - 9b2b122d0415 - - e88a7de55d6e + - 15ac71df11a0 + - 809e42326fc2 - dbe2b2204555 + - e88a7de55d6e - 91887494eb97 - - 15ac71df11a0 + - f1ccc8a6eb05 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 9d65f2365..d6434f063 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: + - 3f254c5ced1d + - 1aac2a13842a - 881d7645d1bf + - 7d34178f2812 - fc288950c3b7 - - 1aac2a13842a - - f9242e01365a + - b502c227b5e6 - a1f0b3f4b781 - f6ced08779c4 - - 3f254c5ced1d - - b502c227b5e6 - - 7d34178f2812 + - f9242e01365a 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 ebd7cb946..c5ed64a34 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -2,16 +2,16 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: + - eb085b3dbaf8 + - e4a053d67e24 + - d00e15139065 - 3bd420ec162d + - 5b85006245f3 - 6ab1a261520a - - a58f7eb0df2c - - 7fbec959cf2b - 2f7702fd0a4c + - a58f7eb0df2c - c0e71cb2bd1b + - 7fbec959cf2b - ca90d17ff51b - - d00e15139065 - - e4a053d67e24 - - eb085b3dbaf8 - - 5b85006245f3 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 505684e97..59b0bc7b9 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,74 +2,74 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - 277dc652246e + - b18329a8ac14 - ece627528a78 - - f28ad96b76dc + - 277dc652246e - 4c177985028a - - 0a18ac48ac53 - b574b84afc4d - - b18329a8ac14 + - f28ad96b76dc + - 0a18ac48ac53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: + - a9a28e46d54a - bf06d196e23d - - e215f71d7983 - e988563cc6e5 - b41107d8fe89 - - a9a28e46d54a + - e215f71d7983 - 525f201b86c1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 4fbffddde8cd - - 56da27be956a - bb6397b94018 + - 4fbffddde8cd - 8da3511c9467 + - 56da27be956a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - 528fb09022be - - f23d67e28cc8 - b8c79e70516d - - 890845926d4b - a8157342d9a3 + - 890845926d4b + - 528fb09022be + - f23d67e28cc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 80600735685d - - a69865da6f80 - - a95a82eb4d50 - 25b83cbd596a - - ae304a72db7b + - a95a82eb4d50 + - a69865da6f80 + - 80600735685d - 59e85306eae5 + - ae304a72db7b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 83aac7741200 - - f1897eb07081 - e0669b1854b1 + - 611d80c0e29d + - f1897eb07081 - ed9ed1e6cca2 - 798da6bdff3d - - 611d80c0e29d + - 83aac7741200 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 5a35e3a8d013 - - d426a9107a6c - 74b61bf5bc4b + - 5a35e3a8d013 - a7fb9b395ddf + - d426a9107a6c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations @@ -85,10 +85,10 @@ tools: owner: galaxyp revisions: - 1693b2126f30 - - c5aa9fca18c6 + - 043f9c91f686 - d2483487e077 - ba92b59cd529 - - 043f9c91f686 + - c5aa9fca18c6 - 10566783d718 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -107,10 +107,10 @@ tools: - name: diann owner: galaxyp revisions: - - ae4dc0c041f9 - - 9fa3dbf06f17 - bf0728e000cd + - ae4dc0c041f9 - ff8c9e0e8a7b + - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -129,9 +129,9 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 1c5cbf8f79ce - - 0fa397f4f40b - 4081e4faa4ab + - 0fa397f4f40b + - 1c5cbf8f79ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib @@ -144,9 +144,9 @@ tools: - 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 @@ -158,16 +158,16 @@ 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 @@ -180,16 +180,16 @@ tools: - name: maxquant owner: galaxyp revisions: - - 7f432d87c82c + - 4d17fcdeb8ff + - 1f39c833f65f - 2133b0be850a - 9c52362ae7bb - - 97a7f34fcb6a - - 1f39c833f65f - - 37d669de2828 - f522c08e900c - e42225f8a659 - - 4d17fcdeb8ff - 837224ad1694 + - 37d669de2828 + - 97a7f34fcb6a + - 7f432d87c82c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -201,62 +201,62 @@ tools: - name: metaquantome_db owner: 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owner: galaxyp revisions: + - 06cca574e337 - 370141bc0da3 - 25529df60a81 - - 06cca574e337 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 9cdf15d3cfc8 - - f7fef900f5b2 - 6ccbf9a2072c + - 9cdf15d3cfc8 - c9eff69a7c62 + - f7fef900f5b2 - 518b1730cf2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - dff6c756eee5 - ca88bd28f116 - 9876bda3ec53 - 5e948629bc73 + - dff6c756eee5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 1595601708ec - - 890025d6e426 - 658494a2cb00 + - 1595601708ec - 41859bbdc16e + - 890025d6e426 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 5ad0b5bf1deb - - 2a93a25f0599 - - 9b7977080f6d - 6634cad7d797 + - 9b7977080f6d + - 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toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: + - ca1740533b59 + - 8a04ed1c1d1b - c28f13cab67a - 3720e349ba2a - - 8a04ed1c1d1b - - ca1740533b59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - a5d785af0ad8 + - c427a8628cbe + - ca799a7246e7 - c55dddc5844a - 382cde407f81 - - ca799a7246e7 - - c427a8628cbe + - a5d785af0ad8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - b5d0905419da - - adca857b4884 - - 8ddb7bab1138 - 39caaa778d2e + - 8ddb7bab1138 + - adca857b4884 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 8d4db262964c - 34e7afee141d - - f817513840a9 - 1c5f31b8d632 + - 8d4db262964c + - f817513840a9 - 18f93351f8b6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: 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tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - 5182338d5e7c - 539a3a4dcc9e - - d6aca689dd48 + - 5182338d5e7c - dd173849c3d8 - e039cc5c7aed + - d6aca689dd48 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 16026cdb1330 - 8a45fd5a608a + - 16026cdb1330 - d426affe977c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - 43b9ed22e8ce - dd71e020e2aa + - 43b9ed22e8ce - 9c70a651a53e 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 - 78c080d36945 + - ad2ba3a95a02 - f036e8cf1a55 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - - c8b225c69a7f - - 7f6a1f27553e - fb52e95a370c + - 7f6a1f27553e + - c8b225c69a7f - 5c2a97a234d6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - a6282baa8c6f - 073a2965e3b2 + - a6282baa8c6f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pepquery2 @@ -609,21 +609,21 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - cb0378d2d487 - 5f49ffce52cb + - cb0378d2d487 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: + - 07ff622ec007 - 7fdd9119cc4f - - 3ec27b4cee7c - - 943a34df6047 - - 3634c90301af - a72c48001f7c + - 943a34df6047 - da885ca16cb2 + - 3634c90301af - 1beff3ddce58 - - 07ff622ec007 + - 3ec27b4cee7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -684,9 +684,9 @@ tools: owner: galaxyp revisions: - 265c35540faa - - 1a5690a5eedc - - a371252a2cf6 - 12692567c7f9 + - a371252a2cf6 + - 1a5690a5eedc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem 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 7a8b04296..c5dd81953 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,11 +2,11 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - e345aadf914f - cd5f98911089 - - 110a346daf36 + - e345aadf914f - 2f1d464ebfd2 - 42201b90e3f4 + - 110a346daf36 - 289b7d6b69a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -19,12 +19,12 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - 8501601a118d - - 42d9087b4789 - - 0cd2df8af811 - fcce77c09289 - - 0345dbaaa79b + - 42d9087b4789 - c207119ba5f6 + - 8501601a118d + - 0345dbaaa79b + - 0cd2df8af811 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: + - 421c33b8bf17 + - ad5ab22ffe24 - 04db7fd6b238 + - 33486216eec0 - 405a212b32ab - - ad5ab22ffe24 - - 421c33b8bf17 - 89eb29319bf4 - - 33486216eec0 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: - - 7b72fde3d27e + - 1d839ead7ad3 - f6e91108b7b1 - - 7370bb65bad4 - - fa51dc5e8386 - eb784fa07f80 - - 1d839ead7ad3 + - fa51dc5e8386 + - 7370bb65bad4 + - 7b72fde3d27e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -70,12 +70,12 @@ tools: - name: stacks2_kmerfilter owner: iuc revisions: - - 3d70c2996730 - - a3e86cd9cac7 + - d30e36c48c93 - c9b77ced9a78 + - a3e86cd9cac7 - 1544278c272e - - d30e36c48c93 - 8a55d29c8fcf + - 3d70c2996730 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -87,12 +87,12 @@ tools: - name: stacks2_populations owner: iuc revisions: - - a5969aa9347e - 564c33e5c3e3 - - b242deb58952 - - 7b881f5f5ad5 - 887cf585cafc + - b242deb58952 - e2db212d64ad + - a5969aa9347e + - 7b881f5f5ad5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,11 +104,11 @@ tools: - name: stacks2_procrad owner: iuc revisions: + - b4bab607eb05 - 9a171f9a450b - bd5ff77e2036 - 8cff84759bf6 - e897c74a48bb - - b4bab607eb05 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - 887e0991eb24 - - adc7a7610d4f - 6dafad990086 - - 33f0793edf93 - - 5e10f396979e - 4f65e343ecdf + - 5e10f396979e + - 887e0991eb24 + - 33f0793edf93 + - adc7a7610d4f 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: - - 97575d01f06b - - 43e3eeb2e0ec - - c5d7050e4ad7 - - c287418eb288 - 17d39bf0a63a + - c5d7050e4ad7 - 4e280b27a831 + - c287418eb288 + - 43e3eeb2e0ec + - 97575d01f06b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -157,8 +157,8 @@ tools: - 0b8c84a7fdb5 - d9bf483266a1 - a819ec3b362d - - 09b8edb56d80 - cd034465d4a4 + - 09b8edb56d80 - 9586f08634c0 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 - bf0e43ab0416 - - 95351dd0fd3f - a4b4bd84f69e - - 69842dd5aa48 - 2645575d1bf2 - a9c34a289493 + - 95351dd0fd3f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -189,11 +189,11 @@ tools: owner: iuc revisions: - d033e1ccb386 - - cfb504394ae1 + - d1fda11e602f - bb0475c884ff - - 8a35a3bc6752 - 912f904a6e1e - - d1fda11e602f + - cfb504394ae1 + - 8a35a3bc6752 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,9 +235,9 @@ tools: - name: stacks_populations owner: iuc revisions: + - 95286af4139b - d504d945a655 - d1fad35bdb4a - - 95286af4139b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -267,8 +267,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 563af4497055 - 96de7538bf0c + - 563af4497055 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index c8e4ee643..46151212a 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,9 +2,9 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - cf01dd6c6b1f - - 31f8063eedea - 2d4e3aff9dc7 + - 31f8063eedea + - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters @@ -18,8 +18,8 @@ tools: - name: arriba owner: iuc revisions: - - 01ccd366690d - 3d61a698e5e1 + - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -68,8 +68,8 @@ tools: - name: cuffcompare owner: devteam revisions: - - f648e5180e40 - e66b9b5b8580 + - f648e5180e40 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks @@ -82,8 +82,8 @@ tools: - name: cuffmerge owner: devteam revisions: - - 6a6717a5f421 - cf747d1bd79a + - 6a6717a5f421 - 86285ddd4512 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -96,8 +96,8 @@ tools: - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - 9a854107dbb2 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -122,8 +122,8 @@ tools: owner: iuc revisions: - 0693ccd171c4 - - e3b16fd7dd08 - 8f0181aacb7a + - e3b16fd7dd08 - 3b36efd62b3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -136,13 +136,13 @@ tools: - name: deseq2 owner: iuc revisions: - - 8fe98f7094de - - 24a09ca67621 - - d027d1f4984e - - 9a882d108833 - 0696db066a5b + - 8fe98f7094de - 6a3a025714d3 - cd9874cb9019 + - 9a882d108833 + - d027d1f4984e + - 24a09ca67621 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -154,11 +154,11 @@ tools: - name: dexseq owner: iuc revisions: + - b47c006d90c5 - df929f257179 + - 62adf13b86ea - 9a7c5b6d8f1e - 2872c633f07e - - 62adf13b86ea - - b47c006d90c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -170,17 +170,17 @@ tools: - name: edger owner: iuc revisions: - - ae2aad0a6d50 - - 555659de7321 - - 070900306913 + - 334ce9b1bac5 - 5bf899c13979 - - f2843df56434 + - 6e53e565fc6a - 9bdff28ae1b1 - - df0c8d0a5992 + - ae2aad0a6d50 + - f2843df56434 + - 555659de7321 - a8305cf0c951 - - 6e53e565fc6a + - df0c8d0a5992 - 0cb907a2a810 - - 334ce9b1bac5 + - 070900306913 - 3d89af8a44f0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -193,8 +193,8 @@ tools: - name: egsea owner: iuc revisions: - - 31ea4992b948 - fba1660fb717 + - 31ea4992b948 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -212,17 +212,17 @@ tools: - name: featurecounts owner: iuc revisions: - - 6f66ae7c5f7a - - 38b6d12edc68 + - e6a2a912677a + - f9d49f5cb597 - 7db9d3ea71c9 - ea04b737afa0 - - af814359d244 - - a56fbe2d6ba7 + - 6f66ae7c5f7a - f3a5f075498f - - f9d49f5cb597 - a37612abf7f9 + - af814359d244 - 90d16db017d7 - - e6a2a912677a + - 38b6d12edc68 + - a56fbe2d6ba7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -252,9 +252,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 0f710191a66d - - f99dd58de04f - 3c97c841a443 + - f99dd58de04f + - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -273,12 +273,12 @@ tools: owner: iuc revisions: - 3fb01a8c902d - - 6c19daec423d - - d4b55e2beb12 - - a86e80d3c09c - f4af63aaf57a - - 6ab42baa56e9 + - d4b55e2beb12 - 26371a1df031 + - 6c19daec423d + - 6ab42baa56e9 + - a86e80d3c09c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -296,9 +296,9 @@ tools: - name: htseq_count owner: lparsons revisions: - - 67b0b160903a - - 4418229c501e - 916cb26bd9d3 + - 4418229c501e + - 67b0b160903a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -316,11 +316,11 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 1c75aa5de15e + - 87c11c05d238 - 01247aaf0a10 + - 1c75aa5de15e - ce5d418183c5 - 5ae5c312d718 - - 87c11c05d238 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -332,10 +332,10 @@ tools: - name: kallisto_quant owner: iuc revisions: - - 40985510cd98 - c971db6f0fe5 - 10c98fab6c5a - 4f9c4e6566e5 + - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -347,14 +347,14 @@ tools: - name: limma_voom owner: iuc revisions: + - 0921444c832d - 708348a17fa1 - - d6f5fa4ee473 - - 32511f586472 + - 58c35179ebf0 - 97e06a4c7c75 - e827f9aae031 - 119b069fc845 - - 0921444c832d - - 58c35179ebf0 + - d6f5fa4ee473 + - 32511f586472 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -403,8 +403,8 @@ 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 @@ -422,21 +422,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - b9e04854e2bb - - e132e7d02a3e - b0f2be869d6d - - 4014de1b6daf - - 99b17b74a8cd - - 7ed2edc1337f - 0a563fd2f22e - - 3ea5a2a63fa2 - - 4df95e2d7f61 + - 4014de1b6daf + - 4074fc1940e2 - 980d2a2e1180 - c772497b2c32 - - 79de45b5069b - - c7c55b694974 - - 4074fc1940e2 + - 3ea5a2a63fa2 - 5ec75f5dae3c + - c7c55b694974 + - 4df95e2d7f61 + - b9e04854e2bb + - e132e7d02a3e + - 99b17b74a8cd + - 7ed2edc1337f + - 79de45b5069b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -460,14 +460,14 @@ tools: - name: salmon owner: bgruening revisions: - - 53e9709776a0 + - 2c0ca397d302 - 49121db48873 - - cc05793bb896 - - 15cd64d7c58b - e3d32471da11 - - ebab418107f5 - - 2c0ca397d302 + - 15cd64d7c58b - f4d5237a84f6 + - ebab418107f5 + - cc05793bb896 + - 53e9709776a0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -479,23 +479,23 @@ tools: - name: seurat owner: iuc revisions: - - fab6ff46e019 - 56242ff81c84 - - c0fd285eb553 - 8c28affc7c48 + - fab6ff46e019 + - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - 258d696dbd7e - - ae618321f34a - - cef79931dda5 - - 914cfcba0ec8 - - cbf488da3b2c - 76d290331481 + - cbf488da3b2c - dd4df992d93d + - 914cfcba0ec8 - 1ebd14235b92 + - ae618321f34a + - 258d696dbd7e + - cef79931dda5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -531,10 +531,10 @@ tools: - name: transdecoder owner: iuc revisions: + - d0d4cef4f967 - 0db979fead3a - - ffd1300599a1 - c6334cb383ff - - d0d4cef4f967 + - ffd1300599a1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -546,10 +546,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - d6a479fd4281 - ba3720d7e68b - - bcc5f03f1900 - 74217fbfba4d + - d6a479fd4281 + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -562,9 +562,9 @@ tools: owner: iuc revisions: - 2fb4ee002432 - - c2b82a94493e - 478f36effca1 - 56162e446004 + - c2b82a94493e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -576,9 +576,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: + - 3f4094b6a565 - 9ff3765e7172 - fab23c3b5258 - - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -590,10 +590,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 34a018cbee9c - 870ac06dff8e - - be3f26533209 - 4687ecf0eb2d + - 34a018cbee9c + - be3f26533209 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -605,11 +605,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 33406f5a445c - 65e7dea767ea - - 05ab8d5e04a2 - - c5fbddcac63a - 5192f657f305 + - c5fbddcac63a + - 33406f5a445c + - 05ab8d5e04a2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -621,10 +621,10 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 6f0fb35b799c - a35cba31d904 - - e406ac71165d - 1fdb25a8384d + - 6f0fb35b799c + - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -651,8 +651,8 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 047c22569787 - eafea3083352 + - 047c22569787 - 1d689e4e1caf - 24e94d84adc9 tool_panel_section_label: RNA-seq @@ -666,10 +666,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 9871104ea630 - - 3a4ac03d1266 - 1812dbc5bb7b + - 3a4ac03d1266 - 04bb8bb7c198 + - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -693,15 +693,15 @@ tools: - name: trinity owner: iuc revisions: - - 48636f857c4b - - 9fa24d5aac68 - - cee61b3fcf78 - - d84caa5a98ad - 8f1c3df4dd49 - - c9cfec002f71 + - db1f362cca3e + - cee61b3fcf78 + - 48636f857c4b - 32b86cd8eb50 - d2bc35f3d1c5 - - db1f362cca3e + - 9fa24d5aac68 + - c9cfec002f71 + - d84caa5a98ad tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -713,9 +713,9 @@ tools: - name: trinotate owner: iuc revisions: + - 6fd16fad465d - 9e61bc67866f - 4383070d29ed - - 6fd16fad465d - 2b093007fab9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index ba833d62f..ee91e8906 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: - - 473382134e56 - 1a052c827e88 + - 473382134e56 - 080fd5739bb4 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 80ab37d88..37a1efdb9 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 - - 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: + - 108db6635177 - cb20f99fd45b - - 993b19f20c76 - 1dfd95ee241e - - 108db6635177 + - 993b19f20c76 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -63,8 +63,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - ef11139d4545 - 9c1c0b947e46 + - ef11139d4545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -82,9 +82,9 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - e7fd6754d093 - - 5f8e69cc4c6e - 19ece8afbaab + - 5f8e69cc4c6e + - e7fd6754d093 - 30a201c9c310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -123,15 +123,15 @@ 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: sam_to_bam @@ -149,9 +149,9 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - dc6ff68ea5e8 - 649a225999a5 - 56c31114ad4a + - dc6ff68ea5e8 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip @@ -163,10 +163,10 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 12749212f61b - - 46c6639921f1 - 9149ad20699a - 6856f8a01905 + - 12749212f61b + - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -179,8 +179,8 @@ tools: owner: devteam revisions: - 26b4f9f98aca - - 06dc50b7b711 - 33208952b99d + - 06dc50b7b711 - 92ec40abcdcf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -205,11 +205,11 @@ tools: - name: samtools_fastx owner: iuc revisions: - - a8d69aee190e - - 66e23b11feae - b906586a6596 - - b3d99709fe1a + - a8d69aee190e - 720217c23995 + - b3d99709fe1a + - 66e23b11feae 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: - - e5ece8fa99de - d2df79922531 + - e5ece8fa99de tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - 22970df7a40e - fefd89ab563c - - fe34990e5ce7 - db17d5321bad + - 22970df7a40e + - fe34990e5ce7 - cc61ade70eb8 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: + - 7a6034296ae9 - 88b8c2916784 - 7def34e6cf4d - - 811fc2d75ad4 - - 7a6034296ae9 - fa5d3e61e429 + - 811fc2d75ad4 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats @@ -267,21 +267,21 @@ tools: - name: samtools_merge owner: iuc revisions: - - cae2794d2deb + - 36677f429310 + - b40e2d865d52 - 65a38e8c8e2a - 740ce0a18f0d - - b40e2d865d52 - - 36677f429310 + - cae2794d2deb tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - 583abf29fc8e - - fa7ad9b89f4a + - 9da0311ab1dd - 329deb17a9f7 + - fa7ad9b89f4a - b61f5d6a7f25 - - 9da0311ab1dd 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: - - 85e38b31e8b3 - - bb8cfc6f6e0c - - 30388d878f81 - db000c6007a0 + - 30388d878f81 + - bb8cfc6f6e0c + - 85e38b31e8b3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -328,8 +328,8 @@ tools: owner: devteam revisions: - a4a10c7924d1 - - b8beef827165 - 344fc91e1bfd + - b8beef827165 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -341,10 +341,10 @@ tools: - name: samtools_sort owner: devteam revisions: - - cab3f8d35989 + - e613c1ad4c4c - d54a4df48867 + - cab3f8d35989 - 6c2c1836728b - - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -356,12 +356,12 @@ tools: - name: samtools_split owner: devteam revisions: - - 135c85f4cfaf - - b7f7826ef1cd - - bd850490c7f1 + - 5d9ae78f34d3 - 818030fa6bbf + - 135c85f4cfaf - bcedabb53ddf - - 5d9ae78f34d3 + - bd850490c7f1 + - b7f7826ef1cd 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: - - 541082d03bef - - 24c5d43cb545 - - 5a08c09b9311 - 3a0efe14891f - 145f6d74ff5e - 1cc79f49b8d5 + - 24c5d43cb545 + - 5a08c09b9311 + - 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: - - 5826298f6a73 - 32dc5f781059 - - b01db2684fa5 - 350bbc5c2ffd - - c370440f901e + - 2dce91e11ca7 + - 5826298f6a73 - b72793637686 + - c370440f901e - 0dbf49c414ae - - 6be888be75f9 + - b01db2684fa5 - bf328cec6a42 - - 2dce91e11ca7 + - 6be888be75f9 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 f912ade43..c5ab9df4c 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -2,13 +2,13 @@ tools: - name: ena_upload owner: iuc revisions: + - 59bb6d34fca6 + - 6f6537780379 + - a62c4a11a67d + - 5cb6146337d8 + - ea5e944f447d - d147d6455873 - 480d9e9d156b - - 59bb6d34fca6 - 4aab5ae907b6 - - ea5e944f447d - - 5cb6146337d8 - - a62c4a11a67d - - 6f6537780379 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 e951b0046..3e9e8451e 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -8,114 +8,118 @@ tools: - name: alevin owner: bgruening revisions: - - e4c01dcece8b + - e32b215b7c04 - f2000bc73102 - - ecb9ea6269ee - c9944a2600f1 - - e32b215b7c04 + - ecb9ea6269ee + - e4c01dcece8b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: + - e1c3c2f2a834 - 707023fa62fe + - cfaf5a405371 - c0b037b12765 - - e1c3c2f2a834 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - fb9e030ffae4 - - cfc3f5a57dc6 - 55e35e9203cf - - 00712416fdaa - 32e547223c9e + - 00712416fdaa + - d330b3082107 + - cfc3f5a57dc6 - 93dd15e13e6a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 93dd15e13e6a + - d330b3082107 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: + - 038e32885fec + - 39e945f0b2c1 - 6f0d0c784f09 + - 688357ad5e61 - ee98d611afc6 - b9fac48532eb - - 688357ad5e61 - - 038e32885fec - - 39e945f0b2c1 + - 0bf7fddf90c7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 6f0d0c784f09 + - 0bf7fddf90c7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: + - 3d748954434b - 43cb7b5a6fe7 - d4af736e7b83 - - 3d748954434b + - ed4996a16f7f + - 7e8c677a7b71 - b85871dd69f9 - 9bd945a03d7b - - ed4996a16f7f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - ed4996a16f7f + - 7e8c677a7b71 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: + - a4774b7b2e85 - fe75d2414dc0 - 2e8022f1923c - - a4774b7b2e85 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - 0e70b2dfe4be + - 769d815e4b0d - 02b1fe7aed76 - 4fff5a293013 - - 769d815e4b0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: + - c29e7bb492bf + - a90f8efe08b4 - aa4a6f0916b4 - 344c2af50552 - - a90f8efe08b4 - - c29e7bb492bf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - 050cf43887d3 - 5b7c81b35b89 - - b13d3e4c48e1 - c32347702e12 + - 050cf43887d3 + - b13d3e4c48e1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 239193b96d72 - - 02fc39c8610d - - 1d77986f9ddc - ae969fdb8442 + - 1d77986f9ddc + - 02fc39c8610d + - 239193b96d72 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -151,11 +155,11 @@ tools: - name: dropletutils owner: iuc revisions: - - cdf4443d5625 - cfe1e6c28d95 - - 2c1200fba922 - - a9caad671439 - 8855361fcfc5 + - a9caad671439 + - 2c1200fba922 + - cdf4443d5625 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -191,8 +195,8 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 01c37e54e86e - fb7068d30ec9 + - 01c37e54e86e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest @@ -205,8 +209,8 @@ tools: - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 163fd744e235 - 23b8d6b8960c + - 163fd744e235 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint @@ -219,8 +223,8 @@ tools: - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - - a63e9713c39d - b892fa1fcaec + - a63e9713c39d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions @@ -240,8 +244,8 @@ tools: - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - 40fee49bc6c3 - f881c94fb3b3 + - 40fee49bc6c3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix @@ -268,15 +272,15 @@ tools: - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 3ee5332bf57c - e03780179ee5 + - 3ee5332bf57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 4401ed529d2c - 3a6a5381db36 + - 4401ed529d2c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat @@ -289,15 +293,15 @@ tools: - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - 62b720dceb56 - ea19190ce5e0 + - 62b720dceb56 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - 2786a931cad2 - 2b4d6a8dab36 + - 2786a931cad2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops @@ -310,29 +314,29 @@ tools: - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: - - 77d8e0fd162a - 5dfba24d7bdd + - 77d8e0fd162a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - 6c5097f6d41e - 972dcccb5bbc + - 6c5097f6d41e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 409396ea5cf0 - 7f7c6ead2d0d + - 409396ea5cf0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo owner: bgruening revisions: - - e4f8fceab96a - 51e40e9b6c3c + - e4f8fceab96a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad @@ -345,22 +349,22 @@ tools: - name: hicexplorer_hicmergedomains owner: bgruening revisions: - - b6b8c8672756 - b376ef118807 + - b6b8c8672756 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - - 1511a8ebe906 - ed900cd4a0a9 + - 1511a8ebe906 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - - 6d042c96aceb - f34ab9882252 + - 6d042c96aceb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions @@ -387,8 +391,8 @@ tools: - name: hicexplorer_hicplotviewpoint owner: bgruening revisions: - - 8d203e74869b - 58de3c7c8e89 + - 8d203e74869b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicquickqc @@ -437,6 +441,7 @@ tools: - e98619de2776 - 59be31ac9dc3 - 4b0adaa31c95 + - 0f1aaff9b22d - eeab712b0b99 - 7784821452ac tool_panel_section_label: Single-cell @@ -450,23 +455,23 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 7ffaa0968da3 - 2cfd0db49bbc - 282819d09a4f + - 7ffaa0968da3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 2ba99a52bd44 - 56371b5a2da9 + - 2ba99a52bd44 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset owner: bgruening revisions: - - 7705cc75ac18 - 8c64a2da3869 + - 7705cc75ac18 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -484,10 +489,10 @@ tools: - name: raceid_clustering owner: iuc revisions: - - a4b734cd253b - 7e014059a88d - - f911a64454fb - 0bff0ee0683a + - f911a64454fb + - a4b734cd253b - c4f39bf4a068 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -500,10 +505,10 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: - - b83fbc90161e - - 7608d5faee41 - d45f092caf24 + - 7608d5faee41 - 43c146e25a43 + - b83fbc90161e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf @@ -529,8 +534,8 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - 69018f285aa3 - df8e4e54d367 + - 69018f285aa3 - a6821f856a1e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -544,10 +549,10 @@ tools: owner: iuc revisions: - 44b935f2271b + - c92d0f9338c5 - e93b008c637a - - 2af7c5086a96 - 72979cac22b2 - - c92d0f9338c5 + - 2af7c5086a96 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -572,68 +577,72 @@ tools: owner: iuc revisions: - 4d8f983cd751 - - 77b91b9bdf52 - b2df381a6004 - - f9353ee6a0d4 + - edec35114f72 + - 178242b82297 + - 6acb08931836 + - 77b91b9bdf52 - 6f83f8fd381f - aaa5da8e73a9 - - 6acb08931836 - - edec35114f72 + - f9353ee6a0d4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - f9353ee6a0d4 + - 178242b82297 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - 277313130da5 + - 72a6bebab2a5 - a03ff8633507 + - d636ce5cde16 - a97abb8cd15b - - b409c2486353 - 3c86f71498bc - - d636ce5cde16 - - 72a6bebab2a5 + - 713a0c65b1fe + - b409c2486353 + - 277313130da5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - 72a6bebab2a5 + - 713a0c65b1fe tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - 5e9171dc8244 - - c5d3684f7c4c - - 6c145a6868cc - 5c3ebe2adc77 - - 3081ff5c84a3 - - f54f0f0598ad - - 6bd82ed14acd - c0a80a16560f - cc0deb593fc8 + - 6bd82ed14acd + - c5d3684f7c4c + - 18262103fa61 + - 3081ff5c84a3 + - f54f0f0598ad + - 6c145a6868cc + - 5e9171dc8244 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - c0a80a16560f + - 18262103fa61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - d844935c906c - - c9cb76cf8d6c - - 94c19fb1281c - a407e7f8bdc1 + - c9cb76cf8d6c + - 5dada6f76047 - 9f354c7c8c92 - ab55fe8030b6 + - 94c19fb1281c - 7b9fafe32c86 - 3bcd5445cd7a tool_panel_section_label: Single-cell @@ -641,54 +650,56 @@ tools: - name: scanpy_normalize owner: iuc revisions: - - 9f354c7c8c92 + - 5dada6f76047 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - 6adf98e782f3 - - f7446fd8d5e7 - - 9b0cdb8cf6be - - 7647e5cd1b8b - 6f5349dd5c49 + - f7446fd8d5e7 + - 2dfb2227a16c + - 6adf98e782f3 - dbbe1ea8ecb1 - 95777145cb92 + - 9b0cdb8cf6be - 1072ce66b426 - aa0c474463c2 + - 7647e5cd1b8b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - 1072ce66b426 + - 2dfb2227a16c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - d18e7a6e5cd4 - a39040ae0a38 - - f2f6c703da06 - - c65fce500915 + - b70219da4a96 - 458e8f43a775 - - bf2017df9837 + - d18e7a6e5cd4 + - f2f6c703da06 - 73ab2ac53d06 - 215733a383f2 + - bf2017df9837 + - c65fce500915 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - a39040ae0a38 + - b70219da4a96 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - 8f333f90d8d6 - - fd808de478b1 - b834074a9aff + - fd808de478b1 + - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -740,9 +751,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - c99ba278dfa9 - 9e5c0bb18d08 - 46fc6751d746 + - c99ba278dfa9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca @@ -982,8 +993,8 @@ tools: - name: snapatac2_clustering owner: iuc revisions: - - 8f8bef61fd0b - afb90d3485df + - 8f8bef61fd0b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_peaks_and_motif @@ -996,15 +1007,15 @@ tools: - name: snapatac2_plotting owner: iuc revisions: - - fecf9664c885 - 370d45e0d1a8 + - fecf9664c885 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing owner: iuc revisions: - - cec3e76eaf05 - fef8f61cb34c + - 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 0521124c7..6c2ccf28c 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -34,23 +34,23 @@ tools: revisions: - 2f3c6f2dcf39 - 746e8e4bf929 - - 419027d822d6 - 562f3c677828 + - 419027d822d6 - 4c07ddedc198 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - 8564f6927b87 - e01e8a9a82f4 + - 8564f6927b87 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: - cb1c59d69557 - - 7a15159140d1 - 6c29c7e347e8 + - 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: - - 7442b94d6a1e - - 840f29aad145 - - 4c4ec859c31a - b1eda492f063 - aef56d0e7a61 + - 840f29aad145 + - 4c4ec859c31a - 9c3e1d3235c8 + - 7442b94d6a1e tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 30d21a6041f6 - - 375bbd555f4a - 07843f917990 - d0352e8b4c10 + - 30d21a6041f6 + - 375bbd555f4a - 9fda0b82f419 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: + - 7ae443e6217d + - 2c58b83c9bad - cd02bf168d23 - 4cc980df6265 - 8b1b2b91f8d0 - - 2c58b83c9bad - - 7ae443e6217d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - e10e776f2109 - - ad7e0b4291ee - - 4bbaf77573ef - - 1dd433d2c92c - - bb9fc9d46ea4 - 7dd3fb35904f + - bb9fc9d46ea4 + - 1dd433d2c92c + - 4bbaf77573ef + - ad7e0b4291ee + - e10e776f2109 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 ef8ce9ab3..27888a441 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -27,22 +27,22 @@ 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: - - aff5135563c6 - - 6e8d94597139 - - 626658afe4cb - 6595517c2dd8 - 9cd341095afd - - 02026300aa45 + - aff5135563c6 + - 464b9305180e - 13b6f0007d9e + - 02026300aa45 + - 6e8d94597139 - be25c075ed54 - - 464b9305180e + - 626658afe4cb tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -54,8 +54,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 3a4694d4354f - 6f54dc6b37da + - 3a4694d4354f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -79,11 +79,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 37cde8134c6a - - 557ec8d7087d + - 9cc411a62277 - 90f657745fea - 34d29339abab - - 9cc411a62277 + - 37cde8134c6a + - 557ec8d7087d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -107,29 +107,29 @@ tools: - name: merge_cols owner: devteam revisions: - - ae7843d06f8f - f2aac0c5c60d - dd40b1e9eebe + - ae7843d06f8f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 33d61c89fb8d - - 1ea4e668bf73 - - 3a6b78c39dca - - 623f3eb7aa48 - 83069b38aa85 + - 623f3eb7aa48 + - cf4397560712 + - 3a6b78c39dca + - 33d61c89fb8d - 2e8f945f7285 - cf34c344508d - - cf4397560712 + - 1ea4e668bf73 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - ae8c4b2488e7 - 503bcd6ebe4b + - ae8c4b2488e7 - 399da6b5ec21 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -142,10 +142,10 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: + - c4d18aa4ec4a + - bce29ec10b78 - b722161a845a - f768f6183386 - - bce29ec10b78 - - c4d18aa4ec4a 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: - - a6f147a050a2 - - 12615d397df7 - ddf54b12c295 - - f46f0e4f75c4 + - 86755160afbf - 74a8bef53a00 + - f46f0e4f75c4 + - 0a8c6b61f0f4 + - fbf99087e067 + - a6f147a050a2 - d698c222f354 + - 12615d397df7 - 9ff72e942410 - - 86755160afbf - - fbf99087e067 - - 0a8c6b61f0f4 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 a4f8e12c8..610c4e1a5 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -8,9 +8,9 @@ tools: - name: breseq owner: iuc revisions: - - 82fb5e3bb93e - 85c57cc9b558 - 0d18a3ba2d1c + - 82fb5e3bb93e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -28,56 +28,56 @@ tools: - name: freebayes owner: devteam revisions: - - 57def2d7c093 - 156b60c1530f - - ef2c525bd8cd - a5937157062f + - ef2c525bd8cd + - 57def2d7c093 - 04fa42777df9 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 09d6e4693887 - - 435b157bed6d - - 791f73caa0c8 - e61c9ac190ad + - 791f73caa0c8 + - 435b157bed6d + - 09d6e4693887 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 074d44697036 - - dfadc322b065 - - 03627f24605f - e1461b5c52a0 - - 65432c3abf6c + - 03627f24605f - 3b4b2121842f + - 65432c3abf6c + - dfadc322b065 - 4805fe3d8fda + - 074d44697036 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 9cb929f21cfa - 7dfca164d2e3 - 701d134358ad + - 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 - - c27549b9aa1f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - cdaab621d454 - aa35ee7f3ab2 + - cdaab621d454 - dbd9f2db9ed8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -96,10 +96,10 @@ tools: - name: snippy owner: iuc revisions: - - 9bccc8404a3c - fa016f1eea1a - - c9a8ef2aa380 - d220115f882b + - 9bccc8404a3c + - c9a8ef2aa380 - 5bbf9eada9c2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -142,21 +142,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - ee4a90760848 + - 3b1e7c170b10 - 32f14a2723ec + - ee4a90760848 - 40f0591deda0 - e7aff4a85df5 - - 3b1e7c170b10 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - 4934c0ac6197 - - 02d81b994ef5 - - 42818629ec4c - adc0645b945c - 9793bc5d741b + - 02d81b994ef5 + - 42818629ec4c 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 41ad3eb85..8be38296e 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: - - 95815a0bb307 - e075b1be5abb - 265fe0f9ea64 + - b7ea370b8f5d - 2c372041ed8c - 6a88248893c4 - - 8a2e296c07ef - - b7ea370b8f5d - ebe5fc018e72 + - 95815a0bb307 + - 8a2e296c07ef 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: - - 21687e35f066 - - 1001172b5089 - - 544cb432072b - - 0fba2c15b40d - - b03984136ce4 - c37b684e7f4e + - b03984136ce4 + - 1001172b5089 - 22637b1a55bf + - 0fba2c15b40d + - 544cb432072b + - 21687e35f066 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -40,14 +40,14 @@ tools: owner: iuc revisions: - 0238f68ad641 - - ccb83bf54de0 - 8ca3647c90fd + - bf1f4994f104 - 143796b504eb - - 8408bffd5616 - - 8627b2b383b4 - 01d6b7d6365e + - 8627b2b383b4 + - ccb83bf54de0 - 3a7084316a6e - - bf1f4994f104 + - 8408bffd5616 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -59,13 +59,13 @@ tools: - name: bcftools_concat owner: iuc revisions: + - abd489215f73 + - 9b5abbf50d23 + - d144af39073a + - f430a1ec7ee4 - 81426b3cf18b - 03e0645395d2 - - 9b5abbf50d23 - 62ca6da715bf - - f430a1ec7ee4 - - d144af39073a - - abd489215f73 - 6b6c992d3a14 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -78,14 +78,14 @@ tools: - name: bcftools_consensus owner: iuc revisions: + - d3081540d175 - 1829900b5dcd + - 2363ef414c9b + - e522022137f6 + - 1171446da5db - 95c6f3f4c77f - 8aa352093d73 - d37e313a41be - - d3081540d175 - - 1171446da5db - - e522022137f6 - - 2363ef414c9b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -98,13 +98,13 @@ tools: owner: iuc revisions: - b14ff40958cb - - 9b29129fb491 - 1137ce8efc1e - 012656fd329f - - 348cd212dbad - - 09f37afb3621 - - 92c0aff8b53e + - 9b29129fb491 - d58d2e8c7a57 + - 92c0aff8b53e + - 09f37afb3621 + - 348cd212dbad 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: - - 7291189e98b4 - de68c11034f6 - ecc9192912b8 - - 367ba501b6eb - 55c0e906c14c - - 1f2183a23823 + - 367ba501b6eb - cfd81f17580b + - 7291189e98b4 + - 1f2183a23823 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -135,11 +135,11 @@ tools: owner: iuc revisions: - ae68ceb4cca3 - - 6c790a091c7c - - 039ea3f1dea9 - - 64a8f7dae3ad - 7cbf3c66d4ad + - 039ea3f1dea9 - e6f4badbe6f3 + - 6c790a091c7c + - 64a8f7dae3ad - d237eaef451f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -152,14 +152,14 @@ tools: - name: bcftools_filter owner: iuc revisions: - - 46fcafba49ec - - 277719af4dd7 - - cdb7b4927742 - e7452697afd9 - - 33bd9301568c - - 6ea7170a016d - - 963a3635b2e1 - 5d6653c989cb + - cdb7b4927742 + - 963a3635b2e1 + - 277719af4dd7 + - 6ea7170a016d + - 33bd9301568c + - 46fcafba49ec tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -171,14 +171,14 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: - - 5a321fab1fe4 - - b7f0f59baa7e + - a1213a0b7b66 - a29a2f40b665 - - 7b4454382d39 - 26d97cdd5410 - - a1213a0b7b66 - 91c1e57d5c7f - 501bfb078342 + - 7b4454382d39 + - b7f0f59baa7e + - 5a321fab1fe4 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: + - 81e4014fa809 - 97d19c008d15 - 15da1ddcfeff - - d7d1663559e9 - - 768d04526638 - - c803c34361e0 - 5f27e814a119 - - 39bca000353d - - 81e4014fa809 + - c803c34361e0 + - 768d04526638 - 709dd8291b83 + - d7d1663559e9 + - 39bca000353d 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: + - 2215287d5cc9 + - 5b006286a458 + - 7ba36babba2d - 85ee7e6c4204 - b1eba148b35b - - 2215287d5cc9 - b931e65638b8 - - b84fda8ebef0 - - 5b006286a458 - 86296490704e - - 7ba36babba2d + - b84fda8ebef0 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: - - 9c711df3258d + - cf06b44624c7 + - 4e1d23e5c691 - 5660b21a0dbd - - 37757ffb4c5f - 31ea13dfe5e6 - 0a5dcc9a8ec2 - - 4e1d23e5c691 + - 37757ffb4c5f - ce9396ddcb2b - - 56556e1267de - f506df85c652 - - cf06b44624c7 + - 56556e1267de + - 9c711df3258d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -251,11 +251,11 @@ tools: owner: iuc revisions: - 1ca7418e46ee + - 48291658fdf6 + - a404f786a94c - 021693fdadaa - 271965b55437 - - 48291658fdf6 - 6deb4d549bc9 - - a404f786a94c - 19905c025d2a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -268,14 +268,14 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - 69d8b7567281 + - c450406f722b - 3f6fadf8b8ff + - f7879f1e77f9 + - 69d8b7567281 + - dadbd61dc4cf - 5ad5d4243987 - 97e8145d7e30 - - c450406f722b - - f7879f1e77f9 - 71c78e0eea52 - - dadbd61dc4cf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -287,14 +287,14 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: + - d31a2e310a52 + - 0fe007201caf - 52f9e4a660e3 + - 6cf13a657cf6 - 283911fe7e1a - 2514e684f8a3 - - cc7f9a4e186b - - d31a2e310a52 - 79f7a1acc2cd - - 6cf13a657cf6 - - 0fe007201caf + - cc7f9a4e186b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -306,14 +306,14 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 80e6e399ccd0 + - a12844ca467a - 1411bef27a75 + - 80e6e399ccd0 - 026a989b7cee + - 75ddd081f608 - 0a62420cb9cd - - 230e424bde67 - - a12844ca467a - 6963a6841d22 - - 75ddd081f608 + - 230e424bde67 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -325,14 +325,14 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - 450a265f92e8 - ba20340426fe - - 5808f77b2bb6 - - bca7ce81688f - - 444e6a756c35 - b10d1510fa84 - e493702b19eb + - 450a265f92e8 - 5acfca5a76af + - 5808f77b2bb6 + - bca7ce81688f + - 444e6a756c35 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: - - 68fec03a63b7 - - 4d236c696844 - - c43399f161f4 - - 157ffcdd3fa7 - - f2482aa4862e - - 12152af85697 - d52b8947b269 - dd72ff87cfd0 + - 12152af85697 + - c43399f161f4 + - 4d236c696844 + - f2482aa4862e + - 68fec03a63b7 + - 157ffcdd3fa7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -364,12 +364,12 @@ tools: owner: iuc revisions: - 0e5d11004815 - - 8dbce095986c - - 75becf493cd3 - 8f2fc0ab30fb + - cbe39e530cbf + - 75becf493cd3 - 29ba253e2e05 + - 8dbce095986c - 6f8e223f78f3 - - cbe39e530cbf 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 - a8630d4fbaf8 - - 88bb477f45f7 - - 9708e3086f32 - 8f5962c43868 - - a367a15c6de5 - f544f71adb73 + - 9708e3086f32 + - e0a856def0b0 - 3ff5654b4e7d + - 88bb477f45f7 + - a367a15c6de5 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 + - 96d0145c041a - 34dc0bbc7e93 + - 4ed46189d6c6 - 6ce175385dd9 - 31c096c6b156 - - 96d0145c041a - - 03e30f06f15f - - 5c9729d54721 - 8b260d252ff4 + - 5c9729d54721 + - 03e30f06f15f 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: - - 681bdf1e22ff - - 2c4941386820 - - a1aad8b559c6 - - 09f5e45a8212 - - a730269af659 - 46eb13bc2c73 - 11af7fce71cf + - 09f5e45a8212 - 40daf124be88 + - 681bdf1e22ff + - a1aad8b559c6 + - a730269af659 + - 2c4941386820 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -438,15 +438,15 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - 3897eaadfbff - - 8cb121b6a1d2 - - f272b8ba0983 - - 882b2e649602 - 12038f59c0f4 + - b74b8cbfc1f1 + - 882b2e649602 - 743cd1472aeb + - f272b8ba0983 + - 8cb121b6a1d2 - 6cbb9c47795c - - b74b8cbfc1f1 - 0594ea1417c8 + - 3897eaadfbff tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -458,12 +458,12 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: - - a9826db86d9a - - 18cf9de1cf73 - - cced6715f926 + - eccb508bb678 - adee7e8b746f - dba06328556a - - eccb508bb678 + - cced6715f926 + - 18cf9de1cf73 + - a9826db86d9a - 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: + - 9f36041495a3 + - fdec14f69010 - 3ce32adc55b2 - e0ad88dec40d - 31a1b89eab9b - - f64e7ca2efd2 - c9935c9e8a24 - - 9f36041495a3 - - fdec14f69010 - e53501abf992 + - f64e7ca2efd2 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: - - 3b7b1fe7b937 - - 79489d5685dd - - d68c43202172 - - d43eb39b989e - b7be725976b6 - - 4db0695a6fc7 + - d43eb39b989e - fd3539749127 + - d68c43202172 + - 4db0695a6fc7 + - 3b7b1fe7b937 - 2331ddcbd5aa + - 79489d5685dd 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 + - 1a989b4110da - 6a636d58dfc2 - - b0d39ef600a7 + - 1ccf0e7fb4f6 - 5296d26b0373 - - 58091e1be01b - - 1a989b4110da + - b0d39ef600a7 - 78cd8b69da4c + - 58091e1be01b 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: + - baa8823f8073 + - 4d3ce9dc1525 + - '388983871932' + - e8af591435d1 - 591cc8518033 - - b17394940c7a - b641062a2587 - - e8af591435d1 - bf8325a07ce7 - - 4d3ce9dc1525 - - '388983871932' - - baa8823f8073 + - b17394940c7a 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: - - 3a233c8eb814 - - 38d75661c235 - - 3ca3de4e5291 - - e6b5cbbf449b - - c2ab91a0d506 - 59fa8742285e - 1a2ef636f48e + - c2ab91a0d506 + - 3a233c8eb814 - d1f8f55f564d + - 3ca3de4e5291 + - e6b5cbbf449b + - 38d75661c235 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -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 @@ -612,8 +612,8 @@ tools: - name: vcfbreakcreatemulti owner: devteam revisions: - - 690b1d846263 - 9fd5d91eb91b + - 690b1d846263 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcheck @@ -626,8 +626,8 @@ tools: - name: vcfcombine owner: devteam revisions: - - 53edb91ed051 - 1f0ba67cc85a + - 53edb91ed051 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcommonsamples @@ -647,9 +647,9 @@ tools: - name: vcffilter owner: devteam revisions: + - 6b935ab36d7b - fa24bf0598f4 - eae7c08ebb6f - - 6b935ab36d7b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup @@ -676,8 +676,8 @@ tools: - name: vcfgenotypes owner: devteam revisions: - - f5653ed90dfd - a60ae8af21a1 + - f5653ed90dfd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom @@ -690,15 +690,15 @@ 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 owner: devteam revisions: - - 17096387c0e6 - d226a7327946 + - 17096387c0e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample @@ -711,8 +711,8 @@ 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 diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index 802c90379..70d35e61e 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,18 +2,18 @@ tools: - name: abricate owner: iuc revisions: - - 3f3e247c053d - - c2ef298da409 + - 78c75f134c16 - 6e9aea89e388 - 4efdca267d51 - - 78c75f134c16 + - 3f3e247c053d + - 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 @@ -26,8 +26,8 @@ tools: - name: aegean_locuspocus owner: iuc revisions: - - c4ac24510b55 - 1fdc517743e6 + - c4ac24510b55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_parseval @@ -40,23 +40,23 @@ tools: - name: annotatemyids owner: iuc revisions: + - a79ee60b6926 + - b5d8e5475247 - 4f2967b27e67 - - cd2480f35935 - 3e1f6f6d557e - - a79ee60b6926 - - 1aae04680c4b - 133f36c29579 - f29602ae449e - - fe3ca740a485 - 44018dd6b447 - - b5d8e5475247 + - cd2480f35935 + - 1aae04680c4b + - fe3ca740a485 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - bc88856eddab - e78e25d3b4bd + - bc88856eddab tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training @@ -71,15 +71,15 @@ tools: owner: bgruening revisions: - 28433faa6e42 - - 09855551d713 - ca6d970d931c + - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - d77802fe76f7 - 92eee5f31117 + - d77802fe76f7 - da5f1924bb2e - 728dacaf08a9 tool_panel_section_label: Annotation @@ -87,9 +87,9 @@ tools: - name: barrnap owner: iuc revisions: - - 8fd427007e93 - 7355bbf5e05f - fe48aa4ccd5e + - 8fd427007e93 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -114,17 +114,17 @@ tools: - name: cpat owner: bgruening revisions: - - 7ccc6234b54e - - 1ac12c0cc7a0 - 8e9e228c54c4 + - 1ac12c0cc7a0 + - 7ccc6234b54e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - - d9c3016f7283 - - 9d1fbff733cf - 63662ae295d6 + - 9d1fbff733cf + - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -148,61 +148,61 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - b6b5cd37f2a2 - - 756376aeb1ae + - 3bbe70fef6df - 14f588312c56 - - 9c15ca7e764e + - 756376aeb1ae - 9f2455341fac - - 3bbe70fef6df + - b6b5cd37f2a2 - 582fd74dc2a1 + - 9c15ca7e764e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - 0ffe5be70caf - - 73428a792541 - - 989f7c061f35 - a230ea445788 - - 30fb23d4c31c - - 8e1ace8f77c6 + - 989f7c061f35 - 1691af4a0d17 + - 8e1ace8f77c6 + - 73428a792541 + - 30fb23d4c31c + - 0ffe5be70caf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 30f08d74024f - 0418d28136de - - 57c6718cbfcc - - 563a19373357 + - 494f0bb4a993 - 5a5ae61da69c + - 57c6718cbfcc - e94187d661df - - 494f0bb4a993 + - 30f08d74024f + - 563a19373357 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - d6c7106b7b2e - - f77d7b685bb3 - 2bba2ff070d9 + - 7abc5f6dd595 + - f77d7b685bb3 - 4b96ced19f75 - 1bc5a03faf2e - f31125bb85ea - - 7abc5f6dd595 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - d3af38b9c7e1 - 54961e026fe4 - - 52af33194019 + - 520e30695ec3 - fed64e676186 - d77fdcca400e - b3cf4684e9c7 - - 520e30695ec3 + - 52af33194019 + - d3af38b9c7e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -214,9 +214,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 07d7991bf205 - 2aea122fbd25 - 79261884facd + - 07d7991bf205 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -230,8 +230,8 @@ tools: revisions: - ef2ad746b589 - 8b3e3657034e - - 43798b4caee0 - 602de62d995b + - 43798b4caee0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -255,16 +255,16 @@ tools: - name: infernal owner: bgruening revisions: - - c9e29ac5d099 - 477d829d3250 + - c9e29ac5d099 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: - 98cafcbd2578 - - 74810db257cc - c55643c3d813 + - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -282,26 +282,26 @@ 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 + - d46d803ca6cc - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - b815ec682418 - - e95d52d295d7 - - 033755194fe9 - 624606f7c996 + - e95d52d295d7 + - b815ec682418 - c8ac28e8ac44 + - 033755194fe9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -343,10 +343,10 @@ tools: - name: prokka owner: crs4 revisions: + - bf68eb663bc3 - d643e3b03500 - a17498c603ec - 8a22554cdde2 - - bf68eb663bc3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -384,29 +384,29 @@ tools: - name: snpeff owner: iuc revisions: - - 268d162b9c49 - - 5b80f544c67f + - cfcf33df7fc0 - 5c7b70713fb5 + - 9473cd297a76 - 8f92c2b26e6d - - 68693743661e - - cfcf33df7fc0 + - 268d162b9c49 + - 5b80f544c67f - 5a29ab10dba6 - - 9473cd297a76 + - 68693743661e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 2b3e65a4252f - 5fab4f81391d + - 2b3e65a4252f - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna owner: rnateam revisions: - - eb35257d2e29 - 10b84b577117 + - eb35257d2e29 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -418,16 +418,16 @@ tools: - name: tbprofiler owner: iuc revisions: - - 4839e590cb26 - - 809dfc93d593 + - e1a9d6fd258d - 37213cf56392 - 45083d070fb8 - - d03af1c7002c + - 037a11682176 - 200c378d85f3 + - 4839e590cb26 - 51dd22484644 - - 037a11682176 - - e1a9d6fd258d - ac8250086ac3 + - d03af1c7002c + - 809dfc93d593 - ba6f87115e13 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 de82da03a..072bce4b8 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,42 +2,42 @@ tools: - name: abyss owner: iuc revisions: - - 0124fce4654a - 8f1b150a2487 - 0e93176640ac - - a929ce596a34 - - fa5259cc561b - - 553bfe8bd0b5 + - 7547fcab5d19 - 841084c5fc46 + - 0124fce4654a - 890b794c997d - - 7547fcab5d19 + - fa5259cc561b + - a929ce596a34 + - 553bfe8bd0b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 21e491ad532a - - b9e31c5c01c7 - b2860df42e16 - ddddce450736 - 94fe43e75ddc - 067592b6b312 + - 21e491ad532a + - b9e31c5c01c7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 25ca5d73aedf - 321347bd0494 + - 25ca5d73aedf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - 3371c5bdc17a - - faee8629b460 - a7f16f24e9a1 - 22286dab5aa1 + - 3371c5bdc17a + - faee8629b460 - 5258e18bbe23 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -51,30 +51,30 @@ tools: - name: busco owner: iuc revisions: - - 1e62c28ba91d + - 0d243f458b53 + - 2dd755c1c6ff + - 602fb8e63aa7 + - 94170eee0ad8 - 4048d82f0c88 + - 1e62c28ba91d + - 5ecdeca79a0d - bb935709506a + - 46ae58b1d792 - cf13a1e03e5b - - e4bd1e99bacf + - 1440ae06552f - e824f5d958d0 - - 41030a6c03b7 - ea8146ee148f - - 0d243f458b53 - - 94170eee0ad8 - - 602fb8e63aa7 - - 46ae58b1d792 - - 2dd755c1c6ff - - 1440ae06552f + - 41030a6c03b7 - 2babe6d5c561 - - 5ecdeca79a0d + - e4bd1e99bacf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - c5b7390290b1 - - 86f150c8019d - 5732f959936a + - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -86,41 +86,41 @@ tools: - name: flye owner: bgruening revisions: + - 1ce9b1d72ec3 - 276f5d8712d5 - e27815e82dd4 + - cb8dfd28c16f - 3ee0ef312022 - - 291923e6f276 - - 1ce9b1d72ec3 - - 8d4f03b5fe9d - 3e4f8642c77e - - cb8dfd28c16f + - 8d4f03b5fe9d + - 291923e6f276 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 3169a38c2656 - 01210c4e9144 - 460fad600dce - b2f674562a18 + - 3169a38c2656 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 8b330a577046 - 7348b69e5109 - ba88bc5a6446 + - 8b330a577046 - 06bcf65179fb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: + - 690c2caa367e - 3ef480892a9f - 3fba9c77550a - 5127a713de83 - - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -132,23 +132,23 @@ tools: - name: hifiasm owner: bgruening revisions: - - ec9e21e9c71b - - df25d4fb79b7 + - da9d8bf98802 + - 284a1cb82b61 + - 5f625c63b8bc + - 045c7c3d8e59 + - 9ef6920c3089 + - f3c89da3af16 - 366a11d316a7 + - 6505bd37670d + - ec9e21e9c71b + - 60024a528cbd + - 3f7be05a1597 + - 71740308d412 - 5bec28269d95 - - 9ef6920c3089 - - 284a1cb82b61 + - df25d4fb79b7 - 41cea2aa2dce - - 3f7be05a1597 - 0ee0c3089254 - - f3c89da3af16 - - 71740308d412 - - da9d8bf98802 - - 60024a528cbd - - 5f625c63b8bc - - 045c7c3d8e59 - 2061fb3b81b4 - - 6505bd37670d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -172,43 +172,43 @@ tools: - name: megahit owner: iuc revisions: - - 7518ee87b53d - a96f3ad4e0d8 - - 14ddfc8ffb93 - de387b2b2803 + - 14ddfc8ffb93 + - 7518ee87b53d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - d7edbc9c3a07 + - eb7b00ec347d - f8113c25bc6b - 39edec572bae - 9d79beb19ac3 - - eb7b00ec347d + - d7edbc9c3a07 - 09c589057ee8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 51c2360aa807 - 29dabd8db6f2 + - 51c2360aa807 - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 606b09cc9860 + - f338e9942b27 + - 3ca2d2a9068c - 2ecf5a570907 - - f369ef5f210b + - 606b09cc9860 - e731ea24e48d - eb7a370f6588 - - 3ca2d2a9068c - fd128c111ab0 - 99ecfdafc64f - - f338e9942b27 + - f369ef5f210b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -220,11 +220,11 @@ tools: - name: miniasm owner: iuc revisions: - - a7b889b90140 + - 73a3846701e1 + - b799a615995d - 8b6d0d85252b - 8dee0218ac7d - - b799a615995d - - 73a3846701e1 + - a7b889b90140 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -256,35 +256,35 @@ tools: - name: pretext_map owner: iuc revisions: - - bbe19ef04a74 + - 8fef980d48b5 + - 79b48f02db49 - dfb8a4497339 - 2b16ba799da9 - - 02831bf9e95f - d256a51a656b - - 8fef980d48b5 - - 79b48f02db49 + - bbe19ef04a74 + - 02831bf9e95f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - a315c25dc813 - - e9bd16ba5ebd - 76d4cbefff85 + - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 59db8ea8c845 - - 342a1d1fed7b - 3061c8b029e5 - - 7594365c546b + - 6fcbee531de6 - 72472698a2df - - 875d0f36d66f - ebb0dcdb621a + - 7594365c546b + - 342a1d1fed7b + - 59db8ea8c845 - 675488238c96 - - 6fcbee531de6 + - 875d0f36d66f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon @@ -292,10 +292,10 @@ tools: revisions: - 78c533842eeb - 39bed8de8017 - - cd06929b224b - a199cd7ac344 - - aa39b19ca11e + - cd06929b224b - d865b62f501c + - aa39b19ca11e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragtag @@ -307,31 +307,31 @@ tools: - name: raven owner: iuc revisions: - - 33b7d8481a76 - - 2b2a352488fa - - f8564b2d7f63 - - 5c55448d0f33 - 3edba9afc9bc - f11b994b7eb2 + - f8564b2d7f63 + - 2b2a352488fa + - 5c55448d0f33 + - 33b7d8481a76 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast owner: iuc revisions: - - 8e66f695d859 - f73ab5187eed + - 8e66f695d859 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: + - 5fc94b3a4704 - ef69617ecb42 + - 28189050e437 - e122f9101584 - 1d06c8b38e77 - - 53c2bc8c2ae3 - - 28189050e437 - - 5fc94b3a4704 - 378e55aeeb25 + - 53c2bc8c2ae3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -343,13 +343,13 @@ tools: - name: shovill owner: iuc revisions: - - 196a599ec43d - - 865119fcb694 - - 83ead2be47b2 - d9f6a00b6db7 - ad80238462c1 - - ee17a294d3a3 + - 83ead2be47b2 - f698c7604b3b + - 196a599ec43d + - 865119fcb694 + - ee17a294d3a3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot @@ -363,168 +363,168 @@ tools: - name: spades_biosyntheticspades owner: iuc revisions: - - 051fd2db8a27 - - c33a476f4001 - - 1bb12736175c - - 904bf932cf78 - - 7490b213baa9 - 604782a8a53a + - 904bf932cf78 + - 1bb12736175c - 1fc82fe7ebef + - c33a476f4001 + - 051fd2db8a27 + - 7490b213baa9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - ad8b536d1caa + - 808b3a0a6716 - 9678993ca5bd - - 34305b013402 - - 655fa188c3cc - d6e617c4e338 + - ad8b536d1caa + - 655fa188c3cc + - 34305b013402 - fee85957cebe - - 808b3a0a6716 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 7e27faaad80e - - b8002c3f7141 - 037f9927c4ff - - 6b5a5842531e + - e5a3b75a271f - 8d4b90bf9caf - 21da31ed41a1 - - e5a3b75a271f + - b8002c3f7141 + - 6b5a5842531e + - 7e27faaad80e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 5b26685e5d3b + - 2a10645aeadd - 9de69775f512 + - 5b26685e5d3b - 328aa71f0f3c - - 7922870efcca - 86f66ab58e14 - f1532cb33c75 - - 2a10645aeadd + - 7922870efcca tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - 8cc856b935ee + - 1708851f8804 - 340bc17f49cf - - e41dcb0e913b - - 85fb02c43042 - 6aad515a5270 - - 1708851f8804 + - 85fb02c43042 + - e41dcb0e913b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - de1260f8a300 - b3490b036c5a + - d5fb354f745d - d159735a6a9f - 249f6a28c751 - - 6357b127161e - - d5fb354f745d - b65a43f70b99 + - 6357b127161e + - de1260f8a300 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 33368fec3b70 - - dd7ad84f3943 - - b7829778729f - d2d1df21dfb9 - - 7897763d14ec - a90db5dbaaf3 - - 9006e5836729 + - 33368fec3b70 + - 7897763d14ec + - b7829778729f - d5887ace0dd4 + - dd7ad84f3943 + - 9006e5836729 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: + - 505a9833ab5d + - 189e837009c9 - ed2425b9fd27 - - ced385aa976d - 8f631679571f - - 505a9833ab5d + - ced385aa976d - 6f4c8ad6ea01 - - 189e837009c9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e + - 9ded6109434a + - 19bdfd1e6fe3 - f31d376ce725 - e59bee4565b3 - - 19bdfd1e6fe3 + - d40ed4eb0c0e - 356afed970b4 - - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: + - 4688ae3b49b5 + - 6dd935e4984b + - 80a17897564d - ebd801e712bc - af40e971a8cc - - 80a17897564d - - 6dd935e4984b - b23249f81bc4 - - 4688ae3b49b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: + - bb11fefb23a3 - cb1e3db43020 - 59bd28f6265d - b64696992ee9 - - 937ea677d437 - - bb11fefb23a3 - b5e35a2ca4f3 + - 937ea677d437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 6bfab4a4a988 - - 05bd7504fdb2 - - 383bb5ad32e2 + - 2628f6790eda - 6015aa0303f2 - cb4768eeca3b - - 2628f6790eda + - 383bb5ad32e2 + - 05bd7504fdb2 + - 6bfab4a4a988 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: + - e022dff952df + - 0a3a602cd1e3 + - 8f9f06995f98 - 6e26c9afd301 - 3e44ef016b45 - - 8f9f06995f98 - - e92675014ac9 - - 0a3a602cd1e3 - 9e3e80cc4ad4 - - e022dff952df + - e92675014ac9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f - - 8d09f8be269e - 5da9a0e2fb2d - 920677cd220f + - 08256557922f + - 8d09f8be269e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 4a53b89fa703 - 37d88f41c810 + - 4a53b89fa703 - 82398ba86ba7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -537,8 +537,8 @@ tools: - name: yahs owner: iuc revisions: - - 425e63adcc5d - 39495e107274 - ff4031bfaa22 + - 425e63adcc5d 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 1a5edf3ad..681ecc5af 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,18 +2,18 @@ tools: - name: integron_finder owner: iuc revisions: - - 4768f7f8e93f - bfd290fe1588 - - 1ae00120dd24 + - 4768f7f8e93f - 392f100eebcd + - 1ae00120dd24 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - 1f5641a52664 - - ded48b36f3b7 - 8e8dc9a1e3e5 + - ded48b36f3b7 + - 1f5641a52664 - 31812e7a1315 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu @@ -21,7 +21,7 @@ tools: owner: nml revisions: - 17fcac7ddf54 - - 5c8ff92e38a9 - 24a7a95867b0 + - 5c8ff92e38a9 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index a9af80876..93ce7ba00 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,13 +2,13 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 159b04e36791 - - 7beb76ffbc0f - - d1f62024a08b - - 1c427e24fb79 - a9c9d768b751 - 0840ba83860c - 204a131e47db + - d1f62024a08b + - 1c427e24fb79 + - 159b04e36791 + - 7beb76ffbc0f tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge @@ -17,3 +17,9 @@ tools: - cab19c0452c4 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu +- name: bbtools_tadpole + owner: iuc + revisions: + - 0ddf147d1897 + tool_panel_section_label: BB Tools + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index a16adb522..53760bb0c 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - a1a923cd89e8 + - a68aa6c1204a + - 0a5c785ac6db - b28e0cfa7ba1 - 87ee588b3d45 - - 0a5c785ac6db - - dde39ba9c031 - e19bebe96cd2 - - a68aa6c1204a - - ce3c7f062223 - 589e7e57fd6d + - ce3c7f062223 + - a1a923cd89e8 + - dde39ba9c031 - 07e8b80f278c - - a8eabd2838f6 - 64e2edfe7a2c + - a8eabd2838f6 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 e6aaeca38..bf5a60e73 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -9,29 +9,29 @@ tools: owner: bgruening revisions: - e8ac2b53f262 - - 62c9df8382c2 - 54f751e413f4 + - 62c9df8382c2 - f921014aba5a tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - - d999e774072a - - a52d2d93e595 - - cbf3f518b668 - e25d3acf6e68 - - 6f386c5dc4fb - 5edc472ec434 - - 0e3cf9594bb7 - - acf4e47b734c - 2889433c7ae1 + - a52d2d93e595 + - 6f386c5dc4fb + - d999e774072a + - acf4e47b734c + - cbf3f518b668 + - 0e3cf9594bb7 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 87b08ad32..02a42a4b6 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 6ca543ec1bf8 - - da6bd1975a71 - - 095ad4d096d1 - - c8cdde00b105 - 710301bc46fa - - f4230f116196 + - c8cdde00b105 + - 095ad4d096d1 - 27ee142314a9 + - da6bd1975a71 + - f4230f116196 + - 6ca543ec1bf8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -92,8 +92,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 8e214e52e461 - 7255688c77f3 + - 8e214e52e461 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_rxn_maker @@ -125,73 +125,73 @@ tools: owner: chemteam revisions: - 3b8a9d5ced85 + - 88076940fa94 - 79cfd9ead848 - bfb65cb551d8 - 0fac8e2afc13 - - 88076940fa94 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: + - d532b7e5f64b + - 55918daa5651 + - eb6564a60136 - f5d979cb4b54 - 715cd0e87781 - b46d4b4d995c - - 55918daa5651 - - eb6564a60136 - - d532b7e5f64b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - dae135dfd519 - - f26afd1b7104 - - d2f955aea23a - fdf2cc80adb5 + - d2f955aea23a + - f26afd1b7104 + - dae135dfd519 - 5579659312e6 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - 319a28774da9 - bc31d02be922 - d1d0efda35c0 + - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - 2c349b027a01 - 4da9ee404eab - - 070e3ecc3fda - ed736e6eee39 + - 2c349b027a01 + - 070e3ecc3fda - cac1886249a2 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - 525ca7c8065f - 807aa4c9293d - - c0c9a5024177 - - 2e219a2d9327 - 73008ef1f487 + - da8753545526 - f197e34c33a9 + - 525ca7c8065f - d1f803b5943c - - da8753545526 + - c0c9a5024177 + - 2e219a2d9327 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - c4fbab8e03c5 - - 2c8ed1b52bf7 - 1809414a9454 - - 7568ae18908a - 27ea4e1a3f95 + - 2c8ed1b52bf7 - 61094e01eff9 + - c4fbab8e03c5 + - 7568ae18908a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -203,18 +203,18 @@ tools: - name: md_converter owner: chemteam revisions: - - ba83f0923369 + - 79e8ab8f1e81 - 730ef07b90ae - - ccfbd956a2d3 + - ba83f0923369 - d7ec25187599 - - 79e8ab8f1e81 + - ccfbd956a2d3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 48d6a6eb438b - 9a3a1f698fc6 + - 48d6a6eb438b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_dihedral @@ -262,9 +262,9 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: + - 4242b4d68e9c - e2c36f62e22f - e6011617c748 - - 4242b4d68e9c - b59c91adeac1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -344,10 +344,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 9b48456a96fe - d4c67ced6abc - bf99565cec1f - 85fad59f8168 + - 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 787904659..fc33ae9ee 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -18,31 +18,31 @@ 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: - - 495a4173006f - 86e2413cf3f8 + - f5d67c722d67 - 424aefbd7777 + - 495a4173006f - 640d3af5d833 - - 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 owner: devteam revisions: - - 74c9214cc8e6 - 5c2cc3b58c7d + - 74c9214cc8e6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index eab346784..08115b8b9 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -2,16 +2,16 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - - 25136a2b0cfe - - 90981f86000f - 830961c48e42 + - 90981f86000f + - 25136a2b0cfe - 33151a38533a tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu @@ -31,10 +31,10 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - baabc30154cd - 6cbe2f30c2d7 - - 2dae863c8f42 - 0046692724f9 + - baabc30154cd + - 2dae863c8f42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index 41e60df8b..b5d078341 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -2,8 +2,8 @@ tools: - name: agat owner: bgruening revisions: - - e7449b2c14bf - abba05ead5d7 + - e7449b2c14bf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -15,32 +15,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: + - e3cbd2287f63 - ab9350a8ab4d - - 6ef0b5664c69 - - 367b1ed91207 + - 5e1240a87bcb - 0b3c3ad92827 - 4a6ee918c13a - - f3a19509108a + - 6ef0b5664c69 - 3b6f97e7094c - - 5e1240a87bcb + - f3a19509108a - a3b86937ead6 - - e3cbd2287f63 + - 367b1ed91207 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - e525f9ffb9ac + - 33c99804a32f + - 091bb5922a82 + - 1b5fc03380d4 - 501c21cce614 - - d4d4e9febf5c + - e525f9ffb9ac + - 72ed72122deb + - bd46669113b9 - 54ccb7e1f49a + - d4d4e9febf5c - 584008e574b2 - - bd46669113b9 - e177a8ea0bf1 - - 33c99804a32f - - 72ed72122deb - - 091bb5922a82 - - 1b5fc03380d4 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -65,9 +65,9 @@ tools: - name: fastq_to_fasta owner: devteam revisions: + - 8979c288aefb - 77b41c89d856 - 186b8d913e6c - - 8979c288aefb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular @@ -94,8 +94,8 @@ tools: owner: devteam revisions: - 4dea02886337 - - 154d00cbbf2d - 3e436657dcd0 + - 154d00cbbf2d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -140,11 +140,11 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: + - 92ac8e086317 - 63769c4217a7 - - 26c6706bfb07 - 19e45916daf9 + - 26c6706bfb07 - b9b385097f13 - - 92ac8e086317 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index 1143920d9..77ee3cd2d 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,70 +2,70 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - e821645ef8fc - de72ba3ed6f2 - c929a006727f - 5f6d123679f4 - - a1ca9bccc7f2 - - 29451af70c52 - 268e91e540ee + - 29451af70c52 + - a1ca9bccc7f2 + - e821645ef8fc tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 2d2cf5c1ea8a - - 0e143b4c3987 + - 0e49b109abc2 + - 12af64f93288 - 5d11599b8a7d + - 0e143b4c3987 - 7a7fd0f5f15d - bb1e4f63e0e6 - - 12af64f93288 - - 0e49b109abc2 + - 2d2cf5c1ea8a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: + - c06951d10364 - dc059492a995 + - 1d848bc4585f - 195e98217334 - - c06951d10364 - - 81b1e3e1fc6c - 7c1beb6d6eca - - 1d848bc4585f + - 81b1e3e1fc6c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: + - 26e7304d6737 + - 3d211717a775 + - a67ac707496a - 71aa86af6762 - - 93eb012d9eed - bfff7454b59a + - 93eb012d9eed - 07418a30ed01 - - a67ac707496a - - 26e7304d6737 - - 3d211717a775 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: - - 2bc10a9ca58b - - b8858746dc1f - - 29fcfd36e90a - - 5be24eba848d - 56d5b797ce84 - - 26983857c91a - dd0b7398bb96 + - b8858746dc1f + - 2bc10a9ca58b + - 26983857c91a + - 5be24eba848d + - 29fcfd36e90a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: + - ee3a1b0f45f1 - 72bfafe3330b - 7e6bcd2e5128 - - c3e012dfe21f - - ee3a1b0f45f1 - 9384cd033f30 + - c3e012dfe21f - 7ef978dc1b8a - e6d0bff01239 tool_panel_section_label: DeepTools @@ -73,14 +73,14 @@ tools: - name: deeptools_compute_matrix owner: bgruening revisions: + - 167788df3b46 - 514fa53b5efb - 9470f29702f8 - - b73e213add0c - - fd1275e01605 - d9a637e83828 - - 167788df3b46 - - fb9cf9c97ec4 + - fd1275e01605 - a60c359ec43c + - b73e213add0c + - fb9cf9c97ec4 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias @@ -89,8 +89,8 @@ tools: - c34d11ea4ba6 - ca0616bb2cdf - 2c37ce318bc3 - - 5bffaa8354a1 - e479c7ca5570 + - 5bffaa8354a1 - 86febdcc4283 - a02cfa31e9cb tool_panel_section_label: DeepTools @@ -98,109 +98,109 @@ tools: - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 004aea905d4d - - 01fb6a7654e6 + - 69a8621ca2f0 - 1fcb7adc39b8 + - 004aea905d4d - 192ef85c0b0b - - 2d466b530754 - 78f405266706 - - 69a8621ca2f0 + - 2d466b530754 + - 01fb6a7654e6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 459cfa861f0b - - db940c262830 - d580d6acd1df - - 9ecba5e225a6 - 137c4beed34b + - 3c9f0c486cca + - 459cfa861f0b - d9ce4897dbb2 + - db940c262830 + - 9ecba5e225a6 - 2f9e4843f480 - - 3c9f0c486cca tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - bad3ca889618 - - f264afa9fa6f - fbe773640707 - - 32e451def88c + - 2c66e43f1c86 - bd7db9e2f2cb - fd408d755394 - - 2c66e43f1c86 + - f264afa9fa6f + - 32e451def88c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 231994413f89 - 7e361d147872 - 7fda5607e777 - - 4e12ea27f788 - - 9368fbc49c8b - - 56bce3c82278 + - 231994413f89 - 3b9d990a0a0e + - 56bce3c82278 + - 9368fbc49c8b + - 4e12ea27f788 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - 4431f39ede55 + - 94ca68515826 + - d9114ef1c8a5 + - c03c3384cd81 - e65d16fb2724 - ce4ce3316f74 - - c03c3384cd81 - - d9114ef1c8a5 - - 94ca68515826 - b1779366c8e9 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 4ed32329e0ed + - 23f7c5f1fdaf + - 2da482e408b8 - d57251071381 + - f8fc4e5aff9d - b88ebb3672a1 - - 2da482e408b8 - - 23f7c5f1fdaf + - 4ed32329e0ed - 793665fff0f8 - - f8fc4e5aff9d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - 512155688d98 - - a7849312d328 + - a4dfb122e52b + - c60570fa602f - 010e58e9d822 + - a7849312d328 - ba6efa77fb79 - - a4dfb122e52b + - 512155688d98 - 25d830337d31 - - c60570fa602f - e4c7985d4585 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: + - 443d9a9d6d11 + - 38e3f226248b - 69264da0ce77 + - aa200e4f3939 - c899e0ccff8c - 4d678170d29b - 00d869ea03a1 - - aa200e4f3939 - - 443d9a9d6d11 - - 38e3f226248b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: + - d806504e96d9 - a2d70c4fd406 - - aac8444d6681 - - 10301d137111 - - c361b12d207a - 6662b1a8d326 - - d806504e96d9 + - c361b12d207a + - 10301d137111 + - 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 09b891ed3..20e04f7bb 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -16,8 +16,8 @@ tools: - name: obi_convert owner: iuc revisions: - - 4d705e3443a7 - e328ced6cf0a + - 4d705e3443a7 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep @@ -30,22 +30,22 @@ 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 owner: iuc revisions: - - 91a1ed0b486f - 76e69de726b2 + - 91a1ed0b486f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort owner: iuc revisions: - - b6d9ea2fb41b - 12b9e285ca1c + - b6d9ea2fb41b tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_stat diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index aaf7a1b11..c87ebd957 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - dba489bfcd62 - 63dd26468588 - - ce385837c160 + - dba489bfcd62 - 832c20329690 + - ce385837c160 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index 451908f2d..748775435 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -9,10 +9,10 @@ tools: owner: iuc revisions: - 29bdbc353f20 - - cf1322aeb137 + - 62f5fab76dfb - d82648ad25a3 + - cf1322aeb137 - 6da3972210ee - - 62f5fab76dfb tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -24,7 +24,7 @@ tools: - name: pileometh owner: bgruening revisions: - - 183cb55b1729 - d6787bab7b11 + - 183cb55b1729 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 6c02db1ad..19aea1e28 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,34 +8,34 @@ tools: - name: cutadapt owner: lparsons revisions: - - c053d4cad713 - - de6cebe3c043 - - 5915ea1ec9b1 - - 49370cb85f0f - 48f587c13075 - - c4b82dce8335 - - 64172f1c1202 + - 49370cb85f0f + - 5eb7e84243f2 - c5e2e5902201 - - 4e5056fefd88 + - 5915ea1ec9b1 + - 44e2cc14f75b + - 093678460093 + - 64172f1c1202 + - b1c926deaa2d + - de6cebe3c043 + - c053d4cad713 + - c4b82dce8335 - 288f97432497 - 8665bcc8b847 + - fe74900d6dc7 + - 8c0175e03cee - 135b80fb1ac2 - - e4691e1589d3 - 660cffd8d92a - - 44e2cc14f75b - - b1c926deaa2d - - 8c0175e03cee - - fe74900d6dc7 - - 5eb7e84243f2 - - 093678460093 + - 4e5056fefd88 + - e4691e1589d3 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 @@ -60,50 +60,50 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 859422bcb689 - 9457a20156db + - 859422bcb689 - 516b97a23d7e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - f546e7278f04 - 2904d46167da + - f546e7278f04 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: - - ec0b5076173a - - f773e98b26cf - f81d4362b6c1 + - f773e98b26cf + - ec0b5076173a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: - - 9c620a950d3a + - 56022eb50bbd - 0dbb995c7d35 - cd0874854f51 - - 56022eb50bbd + - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - d60c3f704da0 - - dbf9c561ef29 - 65b93b623c77 - - 1d8fe9bc4cb0 - c59d48774d03 + - dbf9c561ef29 + - 1d8fe9bc4cb0 + - d60c3f704da0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - f1dc2a761c30 - b05e39b9c170 + - f1dc2a761c30 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -137,8 +137,8 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - f3936d0632cb - 03d57fea6482 + - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -158,8 +158,8 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - 35e38452bb3f - e39cc71d3ed6 + - 35e38452bb3f - 249c8393f2d4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -174,8 +174,8 @@ tools: - name: fastq_stats owner: devteam revisions: - - f0e7deab6518 - b1cea1b2fcd0 + - f0e7deab6518 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer @@ -194,34 +194,34 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - d5e9e83cd3d8 - 529bccd5e4a1 - 09070cacefd8 - 567d5b3c52b1 + - d5e9e83cd3d8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 0b7ec11b3c7c - 4bedca26c133 + - 0b7ec11b3c7c - 8abdedf55101 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: - - 90858c306551 + - 736b8f6ee456 - cb1e251cac37 - bdf1ce174e39 - - 736b8f6ee456 + - 90858c306551 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: - - 07497255281e - 421f0af4ee95 + - 07497255281e - 7ce1891db6f5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -229,27 +229,27 @@ tools: owner: devteam revisions: - 02f8a17a4ebd - - f984bb114520 - - 3599f5451ee2 - b29d37ca9e41 + - 3599f5451ee2 + - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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_trimmer owner: devteam revisions: - - 73194cdd4f57 - 547e8d00f11c - 61b4cedc8934 - 377ac2829eac + - 73194cdd4f57 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -261,24 +261,24 @@ tools: - name: pear owner: iuc revisions: - - 037f0acc7830 - 2f804526f5fd - b4c6f054210a + - 037f0acc7830 - f69501361cec 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 - 61eb4cfc7313 + - fdc21382376d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats @@ -291,8 +291,8 @@ tools: - name: seqtk owner: iuc revisions: - - 4b494533146a - 3da72230c066 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic @@ -312,10 +312,10 @@ tools: - name: umi_tools_count owner: iuc revisions: + - e654095ab143 + - 8250ea3a1501 - b557acca0b56 - a535cf1e5da4 - - 8250ea3a1501 - - e654095ab143 - 24013bf85a6f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -328,12 +328,12 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 9fa7803d1c51 - - f3759eec3018 - 7accf7407811 + - f3759eec3018 + - 9fa7803d1c51 - 6a675c3aa610 - - 828dba98cdb4 - 27ac32a22ad2 + - 828dba98cdb4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group diff --git a/usegalaxy.org.au/fastq_quality_control.yml b/usegalaxy.org.au/fastq_quality_control.yml index 8c6d1449a..093910d0c 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,30 +2,30 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - e41385662e5e - - 7b4468117008 - ce9cd02d5b88 + - 7b4468117008 - 64e9a6afdd0c + - e41385662e5e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - c64d534a763c - 8050e091e99b + - c64d534a763c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - - 2c64fded1286 - 3d0c7bdf12f5 - - e7b2202befea - - 2b0c9d9fc6ca - - 9da02be9c6cc - - f2e8552cf1d0 + - 2c64fded1286 - ff9530579d1f + - f2e8552cf1d0 + - 2b0c9d9fc6ca - 5ec9f6bceaee + - 9da02be9c6cc + - e7b2202befea tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -47,39 +47,39 @@ tools: - 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: - - a72af9de6bf5 - 1f296803dfa3 - 8880fb74ef56 + - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - b2f1f75d49c4 - - 5e33b465d8d5 - - bf675f34b056 - - 9a913cdee30e - - abfd8a6544d7 - f7e2f1eb3a16 - c1a4b5f3b432 - 1c2db0054039 - 3d93dd18d9f8 + - 9a913cdee30e + - 5e33b465d8d5 + - b2f1f75d49c4 - 75c93c70d094 + - abfd8a6544d7 + - bf675f34b056 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: + - cd7e644cae1d - 084bbd8ba7b8 - 949f01671246 - - cd7e644cae1d tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index b329fac45..2a6aade30 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -2,15 +2,15 @@ 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 owner: peterjc revisions: - - 7c40a1fbc82e - bdaefd241921 + - 7c40a1fbc82e tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_filter_by_id diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index d3193ef10..b893e494c 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 @@ -31,8 +31,8 @@ tools: - name: gemini_comp_hets owner: iuc revisions: - - 7cf9bc210044 - 62647e2637f6 + - 7cf9bc210044 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info @@ -45,8 +45,8 @@ tools: - name: gemini_de_novo owner: iuc revisions: - - d5b01cc263be - 9db3e299b1c8 + - d5b01cc263be tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -59,15 +59,15 @@ tools: - name: gemini_fusions owner: iuc revisions: - - 91d53f89ca54 - 8151a5a0e4f6 + - 91d53f89ca54 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -79,37 +79,37 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 184aa4e686e2 - 2550239feed5 + - 184aa4e686e2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load owner: iuc revisions: - - b2c25142267e - - cf61daf064fe - 45296e47d565 + - cf61daf064fe + - 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 owner: iuc revisions: - - 61343646155c - 00c2734b3bea + - 61343646155c tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways owner: iuc revisions: - - 9199331c3421 - 6b09debcfc49 + - 9199331c3421 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -123,29 +123,29 @@ tools: owner: iuc revisions: - 840fb4850be3 - - 666f60a9331a - da74170c55c7 + - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant owner: iuc revisions: - - 05124dc72dba - 86f3aac4418d + - 05124dc72dba tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region owner: iuc revisions: - - 33efe43c1dbb - 601b70d10d92 + - 33efe43c1dbb tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh owner: iuc revisions: - - 93967598e18e - 345d41f3f574 + - 93967598e18e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic @@ -165,7 +165,7 @@ tools: - name: gemini_windower owner: iuc revisions: - - 0c58ba91d018 - 8f04952b8882 + - 0c58ba91d018 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 5d63fa522..301093442 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -2,8 +2,8 @@ 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 @@ -23,14 +23,14 @@ tools: - name: mageck_pathway owner: iuc revisions: - - 9744e1124d0f - 39a996d44e16 + - 9744e1124d0f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test owner: iuc revisions: - - 9b4f4533c9ee - 688a8eccea71 + - 9b4f4533c9ee tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index b1d6f2748..5e3a5f78a 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - 983bf725dfc2 - b39347891609 - e9df53a75f3c - c1b437242fee + - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -18,53 +18,53 @@ tools: owner: iuc revisions: - 1c58de56d587 - - e063168e0a81 - 28587613264f + - e063168e0a81 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 1ec814014652 - 83c7d564b128 - - ba931a59dd59 - - aad3885b3216 - - f8054ea1c365 - - c441583adae5 + - 653e89d73fc4 - 1790dcf3c32d - 69ebb7f46e45 - - 734abc7ac21d + - e407b9da183a + - c441583adae5 + - 4317d3cb6cba + - f5ea3ce9b9b0 + - 9a776b080193 + - 7068f48d0ef9 - 6591f049cf7e + - ba931a59dd59 + - 1ec814014652 - 8848455c0270 - - 653e89d73fc4 - 6ea73833cf67 - - 4317d3cb6cba - - f5ea3ce9b9b0 + - 734abc7ac21d - 5e6237d58b0c + - f8054ea1c365 + - 4df8de2d0e48 - e08a7ad4378b + - aad3885b3216 - 516a54ddf218 - - 4df8de2d0e48 - - e407b9da183a - - 7068f48d0ef9 - - 9a776b080193 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 75b3b3d0adbf - 34758ab8aaa4 - - 9aaa46d45472 - 21a560af5913 + - 75b3b3d0adbf + - 9aaa46d45472 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - 468c71dac78a - - 95fb5712344f - - af5eccf83605 - 054483e27a35 - bfdc6a7ffd3a + - 95fb5712344f + - af5eccf83605 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 039affe97..4c6021e44 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: - - df7356989ac1 - - c4bde687c846 - - 4b519282a05b - a64dc31ab7f2 - - 740057a5126d - - fd59d783248a - - 290a11559985 + - 4b519282a05b - ae9994cf526f + - 290a11559985 + - 740057a5126d + - df7356989ac1 - 7f13dc906cb9 + - fd59d783248a + - c4bde687c846 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -29,8 +29,8 @@ tools: owner: devteam revisions: - 7cf5b1d072b5 - - 867ab348287d - f95284aa2946 + - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -42,9 +42,9 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: + - 374e9062d874 - '566197475670' - 53460afd5115 - - 374e9062d874 - ca7cb0eaad62 - 3b37b1b1c3a7 tool_panel_section_label: Graph/Display Data @@ -53,10 +53,10 @@ tools: owner: iuc revisions: - 10515715c940 - - d3a9e32672ec - 391a4cc45fea - 3d059e9c2fba - da4c086cff5b + - d3a9e32672ec tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -74,12 +74,12 @@ tools: - name: ggplot2_point owner: iuc revisions: - - 1acf88921176 + - e3a675da7fd0 - 3b12bf9b4b87 + - 5fe1dc76176e + - 1acf88921176 - 299307abd804 - d0fc8b746d57 - - 5fe1dc76176e - - e3a675da7fd0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin @@ -97,15 +97,15 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - 97e3b735ed22 + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan owner: iuc revisions: - - 6e8eb0c0d91f - 8f62f666dcb6 + - 6e8eb0c0d91f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -123,17 +123,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 6cd09d7b5f37 - - 1cfc579079a6 - 836d1aa3e89a - - a6e57ff585c0 - - 2bb2e07a7a21 - ca2def38369c + - 112eb40ba6cf - 4542035c1075 - 17359b808b01 - - 112eb40ba6cf - - fd5dbf0f732e + - 1cfc579079a6 - 667e17248bfe + - 6cd09d7b5f37 + - 2bb2e07a7a21 + - fd5dbf0f732e + - a6e57ff585c0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -151,8 +151,8 @@ tools: - name: pathview owner: iuc revisions: - - f1691de443a7 - fe154a7af404 + - f1691de443a7 - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -165,17 +165,17 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 1c5dcef5ce0f + - f234e2e59d76 - 85da91bbdbfb - 62e3a4e8c54c - - f234e2e59d76 + - 1c5dcef5ce0f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 9958188c6195 - 7b21a9b5922f + - 9958188c6195 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -187,8 +187,8 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 44c66e8d21e6 - 6c571966cfb9 + - 44c66e8d21e6 - 7c9417381ad5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -201,23 +201,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - a1abfa420d9d - 14e7c35f3d00 - - 360df4999907 + - 4ac4e7083b7e + - 326a3db8d9d1 + - a1abfa420d9d - 7dd841a32245 + - 360df4999907 - 36b848d5f3ec - - 326a3db8d9d1 - 2824d77cd8f8 - - 4ac4e7083b7e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 2f557f6abbfb - 73b8cb5bddcd - - 44608d0193ed - 83c573f2e73c + - 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 91be5deed..3fcf4a120 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 1a642de6db01 - 14b3f2a4523b + - 1a642de6db01 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -28,8 +28,8 @@ tools: - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 22bd5861706d - 7779b9dcf040 + - 22bd5861706d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells @@ -42,8 +42,8 @@ tools: - name: scanpy_filter_genes owner: ebi-gxa revisions: - - cc64914b0cf4 - 23d838d1569d + - cc64914b0cf4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_cluster @@ -63,22 +63,22 @@ tools: - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 79da59a0b180 - 64dd8bb151e1 + - 79da59a0b180 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 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 @@ -91,8 +91,8 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 94697510d55f - ff6decc0f432 + - 94697510d55f - 9a2f72d7dbd2 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -113,8 +113,8 @@ tools: - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - 73d43034c860 - 0387a2179f88 + - 73d43034c860 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed @@ -134,8 +134,8 @@ tools: - name: scanpy_plot_trajectory owner: ebi-gxa revisions: - - cb1992d1804b - d3df472a21dc + - cb1992d1804b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x @@ -162,8 +162,8 @@ tools: - name: scanpy_run_dpt owner: ebi-gxa revisions: - - 12f67b0c1a94 - 03921aa8b29c + - 12f67b0c1a94 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_fdg @@ -190,22 +190,22 @@ tools: - name: scanpy_run_tsne owner: ebi-gxa revisions: - - 3fb53f5e46ea - abdb61e4afa3 + - 3fb53f5e46ea tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_umap owner: ebi-gxa revisions: - - 767a675b5254 - - ea91cfd0444e - 0f98603d0116 + - ea91cfd0444e + - 767a675b5254 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 + - 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 1e95cac6f..5815bab75 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -3,50 +3,50 @@ tools: owner: bgruening revisions: - 9edf8894a22d - - 921a2da49a0c - - ed2cca6b5de4 - a4c13ddcc8ee + - ed2cca6b5de4 + - 921a2da49a0c - 29f66c353bcb tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 78fb5e286609 - 5746d61f0a91 - - ec4b948dc6f0 - - d404277cc87a - 755df866ad0c + - d404277cc87a + - 78fb5e286609 + - ec4b948dc6f0 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - 03dd3c16ae4e - - 9e357a8b2ec3 + - 977dc15add20 - 11fa44ee0603 + - 9e357a8b2ec3 - 4d511437b1e5 - - 977dc15add20 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 0ba4f56a3613 - c3e5e2cf12b7 + - 41dbf4d162a2 + - 0ba4f56a3613 - 3b5b54ed6392 - 77919cc3618e - - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 5308ca68ef3d - - 7babd8a46fe0 - - b63363075c2e - 12d51d7be66f - 9939786dd9c9 + - 7babd8a46fe0 + - 5308ca68ef3d + - b63363075c2e 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 389ee4d3b..6ca248f63 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -4,18 +4,18 @@ tools: revisions: - 7db4fc31dbee - 0c777d708acc - - 8bccb36e055a - - 3df9f0a4bf34 - 699a5e9146b3 + - 3df9f0a4bf34 - 81f0cbca04a7 + - 8bccb36e055a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 0a53256b48c6 - 2436a8807ad1 - 5791a7f65275 + - 0a53256b48c6 - 5bc8cdc17fd0 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -30,17 +30,17 @@ tools: - name: 2d_histogram_equalization owner: imgteam revisions: - - b1c2c210813c - - 70316d792fc9 - 77f7159d775a + - 70316d792fc9 + - b1c2c210813c 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: 2d_split_binaryimage_by_watershed @@ -62,23 +62,23 @@ tools: - 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 - 664232d2a3f7 + - b58447a2eed2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - 0e4dccaafef5 - e917a2424690 + - 0e4dccaafef5 - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -100,16 +100,16 @@ tools: - name: cp_convert_objects_to_image owner: bgruening revisions: - - df3ad3ba5c6f - - ef4aed1d34c4 - cdf8e3c57dae + - ef4aed1d34c4 + - df3ad3ba5c6f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - - 5d28ac336861 - 2484086dee41 + - 5d28ac336861 - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -117,16 +117,16 @@ tools: owner: bgruening revisions: - bace5a93a97c - - 11f177b1a59e - f2ed92b011a9 + - 11f177b1a59e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - f24c370e5ea4 - d0178bdcd00e - f8fa0f6718a3 + - f24c370e5ea4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color @@ -141,16 +141,16 @@ tools: owner: bgruening revisions: - 993faa34333b - - b6eec6087271 - 87d4d92d7487 + - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - c09dcda1143f - - 6100a22bf4f2 - ff1a86a87364 + - 6100a22bf4f2 + - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image @@ -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: - - 91e03287f285 - 20dbb1f7ec7b + - 91e03287f285 - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -181,8 +181,8 @@ tools: owner: bgruening revisions: - b64af54c5c09 - - 8536b1ae0254 - 5499dc6f8ac1 + - 8536b1ae0254 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality @@ -196,9 +196,9 @@ tools: - name: cp_measure_object_intensity owner: bgruening revisions: - - e52c75a28c4b - 980aed9e8fd5 - 407925835dd9 + - e52c75a28c4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape @@ -213,31 +213,31 @@ tools: owner: bgruening revisions: - b76841ee5560 - - 035a58c7f54a - 80b200ae516b + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines owner: bgruening revisions: - - b44b081bcf37 - 91560258e972 + - b44b081bcf37 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_relate_objects owner: bgruening revisions: - - 8083a87d2fdf - 48102a685037 + - 8083a87d2fdf - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 27edbb90ab2b - 33f4fa1413fb - 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: - - 1fd453cd757b - 972d2c365739 + - 1fd453cd757b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: idr_download_by_ids @@ -262,8 +262,8 @@ tools: - name: image_info owner: imgteam revisions: - - f8b4eada923c - 7b6d9412c7f8 + - f8b4eada923c - 236ec78b2e53 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index 03c897c86..2cee87c18 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 78bbd17d0703 - - 1069f6db0a0e - - e319b5b65879 - - f362150bef41 + - 3e4f434a69c6 - 3a72fede57ce + - 40737febe339 + - 78bbd17d0703 - d6e72da3ec35 - a38934e303b9 - - 40737febe339 - - 3e4f434a69c6 + - f362150bef41 + - 1069f6db0a0e + - e319b5b65879 - e4ee04da1c19 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - fcbeda41d0ac - - 9537184d421f + - 7fe36019c073 - 2b95d5c04908 - - 0135f1d487a0 + - 72ddd32392cd - c88553ec696e - - f91cfb73d369 + - 9537184d421f - 618297d23022 - 8f8df367470d - - 7fe36019c073 - - 72ddd32392cd + - f91cfb73d369 + - 0135f1d487a0 + - fcbeda41d0ac tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - 2cf4a1cafc16 - - d7e79eb3bcb3 - fafb3d685fa9 - ad0dc9f4c9e2 + - d7e79eb3bcb3 + - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 8c05afb547fa - - 7f1cfa4c0e32 + - 5dc33613c288 + - ee29337f905c - 8d36959b000d - - 3d18f8c3c0f6 - - 9eaadf03e0df + - 28a6f1908fcc + - 7f1cfa4c0e32 + - ee2beb764a7b - 94df24c6bc00 + - 9eaadf03e0df + - a1c2aecd7a0d + - 8c05afb547fa - 43aac8d29685 - - ee29337f905c - bd2a7d1316b9 - - 28a6f1908fcc - - ee2beb764a7b + - 3d18f8c3c0f6 - 6a1515bb0687 - - a1c2aecd7a0d - - 5dc33613c288 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: + - 364f4ffec275 + - bcaa0d571ce2 + - 5671e1d3d5ee + - 9f978da6528a - a250929be21b - - c092052ed673 + - 8858fa037a15 - e3bb03cf207a - - 364f4ffec275 - - db536ad45f28 - 5d6ed46cc101 - - 9f978da6528a - - 5671e1d3d5ee + - cb903c9dc33d - d37ede8589b2 - 86a20ae274fc - - cb903c9dc33d - - bcaa0d571ce2 - - 8858fa037a15 + - db536ad45f28 + - c092052ed673 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: + - ed28dd32141c + - 49236b03e4fd - 12d66d0d05ac - - c5c9f02b6167 + - 38b91a3190cd - 584beffa972b + - 230b05597996 - abbc8041e8ec + - c5c9f02b6167 - e1a015876aa9 - - 38b91a3190cd - - f95f403841ad - - 230b05597996 - - ed28dd32141c - - 49236b03e4fd - 194e3ceee923 + - f95f403841ad - 3b6a16d82c1b 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 09c5ac1ab..e096a0f0c 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,18 +2,18 @@ tools: - name: datamash_reverse owner: iuc revisions: + - 17e3b698dd52 + - 0f1724dd59d2 - b8a457820315 - f198773344e4 - - 0f1724dd59d2 - - 17e3b698dd52 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - ba0c40780ecf - ac092723240d - 374cb875d38a + - ba0c40780ecf - 22c2a1ac7ae3 - a513e3fbb4c5 tool_panel_section_label: Join, Subtract and Group diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index 10532a585..e1029375a 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -19,81 +19,81 @@ tools: owner: bgruening revisions: - b6ef6d0cb6b7 - - 2af1346e68c9 - 818f9b69d8a0 - - f1b9a42d6809 - e1317b5502fa + - f1b9a42d6809 + - 2af1346e68c9 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - c80db5d6fd8c - - 05143043ca13 - - 8334dc98c48e - 1588f9076e32 + - 05143043ca13 - 947c2eacccb8 + - c80db5d6fd8c + - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - 29e4122c90de - - 9991c4ddde14 - - 25b46af53232 - 83228baae3c5 + - 9991c4ddde14 - 1552b8cb4a94 + - 25b46af53232 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 841a6cc5fc58 - 1a53edc4b438 - a07ab242b0b5 - - 060ca94ac049 - 53616c8b0865 + - 060ca94ac049 - f3dfa4bdf87e + - 841a6cc5fc58 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 927586a18553 - 91c4e3331208 - - dc4b5fd604a6 - - 2fc89dcd41c8 + - 927586a18553 - d4808d5b83da + - dc4b5fd604a6 - 40f4447733b2 + - 2fc89dcd41c8 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 36e8d6d5d01b - - e5a5ad882f1f - - 301e07345c93 - - c6ae57f774c6 - 25ab6b4e376e + - c6ae57f774c6 + - e5a5ad882f1f - 7626ea9c2e1b + - 36e8d6d5d01b + - 301e07345c93 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - b7c3e9a3b954 - - 02d2be90dedb - 4ed102b922cb - 80852884053f - - f9639b488779 - 0630258dcf35 + - 02d2be90dedb + - f9639b488779 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 14180f9c831e - ec69cbe34b73 + - 14180f9c831e - 61634a87efc7 - caeb57858702 tool_panel_section_label: Machine Learning diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index 77ffd4d4b..9c1d4034e 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - d5ceb9f3c25b - - 03e9b2fbc005 - - 0d4acadabb04 - - a6d65b0c67af - 017aba02828d - cd659e8cc5fa - - 17062a0decb7 - - 749c918495f7 + - 03e9b2fbc005 - 937aa69e715f - - f6877ad76b00 - 3ba8d4563129 + - 17062a0decb7 + - d5ceb9f3c25b + - 0d4acadabb04 + - f6877ad76b00 + - a6d65b0c67af + - 749c918495f7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -24,19 +24,19 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - bfaa0d22c2e4 - b4a22d90cce9 + - bfaa0d22c2e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - - 2477830927ec - - dfd8b7f78c37 - - e188dc7a68e6 - 3fe632431b68 - - 53646aaaafef - 64f11cf59c6e + - e188dc7a68e6 + - dfd8b7f78c37 + - 2477830927ec + - 53646aaaafef 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: - - 3e1ea2facca6 - - e7f19d6a9af8 - 37b497aa133f - 60afcc2c1d05 + - 3e1ea2facca6 - 2ff111fac1d7 + - e7f19d6a9af8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 11a0d50a54e6 - - 8c6cd2650d1f - f54f5baedfdd - - 6b1e195506a3 - - 09b53c1d4ab1 - - b3eab4b67562 - - 53c0b7a1a0c3 - - be1d967337e4 - - 5cc34c3f440d - c0c2d0941de8 - - 037c6e54df11 + - be1d967337e4 - 3f4d6399997b + - 6b1e195506a3 - 77b2770508f6 + - 8c6cd2650d1f + - 53c0b7a1a0c3 + - 037c6e54df11 + - 5cc34c3f440d + - 09b53c1d4ab1 + - 11a0d50a54e6 + - b3eab4b67562 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 178bdbdb6d24 - - e403d27e8f24 + - 5ef7ec16b04f - 79b885ce78d7 + - 1cd2511a396e - b8f5f6e87f5c - - 5ef7ec16b04f + - 9ee34ba73ebf + - 00fbfac99d39 + - 178bdbdb6d24 - 13022c3d3076 - - ec9cbd6b9a49 - 45795f582ae9 + - e403d27e8f24 - 42ce70172b72 - - 1cd2511a396e - - 9ee34ba73ebf - - 00fbfac99d39 + - ec9cbd6b9a49 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 c803606ef..29a5d4217 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -82,8 +82,8 @@ tools: - name: matchms_filtering owner: recetox revisions: - - 00e66c401366 - a177ac3c752c + - 00e66c401366 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity @@ -103,15 +103,15 @@ tools: - name: matchms_metadata_export owner: recetox revisions: - - b576ed720711 - f04610d25411 + - b576ed720711 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match owner: recetox revisions: - - 1d443ed476a1 - 03bc9b7f40f6 + - 1d443ed476a1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge @@ -148,15 +148,15 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: - - 7627b40601f6 - 9ff95a1a2705 + - 7627b40601f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split owner: recetox revisions: - - 0cf68b536cd1 - 500f473df7e4 + - 0cf68b536cd1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting @@ -168,8 +168,8 @@ tools: - name: msmetaenhancer owner: recetox revisions: - - 90745ecc5e9f - b5467dead5b1 + - 90745ecc5e9f tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msnbase_readmsdata @@ -232,12 +232,14 @@ tools: owner: recetox revisions: - 79ad928a0dae + - c53a97599181 - 7b42ee54d757 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: + - 18ec7635bac6 - f3a18e020cdd - 149b9cc7499b tool_panel_section_label: Metabolomics @@ -246,6 +248,7 @@ tools: owner: recetox revisions: - dfebc82ba1f0 + - 134be5abb208 - 481d769e2f7a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -254,34 +257,39 @@ tools: revisions: - 9064aecc78a7 - 02c772a49998 + - 51332c2520c7 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - b3413f335327 - e7305ba0dd38 + - b341cfd4baf8 + - b3413f335327 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - 17a48d0a80f4 - dd7bbc2b99d1 + - cf061712a184 + - 17a48d0a80f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - 99d118321d5f + - 24278c6b6d1c - d7f5878a98c3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - d90187b0f247 - ffbabefbd2e2 + - ea0758b41473 + - d90187b0f247 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -293,8 +301,8 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 6b5dec818827 - 2c6fa447f6a0 + - 6b5dec818827 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index 0fea92d2a..8484c764b 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -9,9 +9,9 @@ tools: - name: cat_bins owner: iuc revisions: - - 18676df0cb3a - 0e63d03c8790 - 0094893f5001 + - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise @@ -30,101 +30,101 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 65db807336bc + - 5b5a7af9fbb4 - 76d3d2b10738 - - 63f86089423e - 7c2100246a2f - - 5b5a7af9fbb4 + - 65db807336bc + - 63f86089423e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 00f5005840fa - 96336c6a2bb7 - - 1c35dadbe76f - 84fd33a60b35 - 18a502a9d287 + - 1c35dadbe76f + - 00f5005840fa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: + - 34e55239e68b - e8fba04706d3 - f732237754fc - addaf9d22850 - - 34e55239e68b - a9f4a217dcd6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 8c202e741d68 - - 0776d824d896 - 04c15826a0b8 - - 75403243703a - 5fe3edf19b9c + - 0776d824d896 + - 75403243703a + - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 1c9b3bcd4261 - - 75c8945b0da2 - 43c99742158b - 8470de786d47 + - 1c9b3bcd4261 + - 75c8945b0da2 - e96bbb9e24ea tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: + - 5c865a382933 + - 84743da21318 - 35176674168c - - 1d75bd0595e2 - 306a40d4bb8f - - 84743da21318 - - 5c865a382933 + - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 32c9ea835770 - - 78faebd0879c - - 8daf4564ccda - 555ccac8a4c5 + - 8daf4564ccda + - 32c9ea835770 - ac72310b038a + - 78faebd0879c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - 7b8cb2b02978 + - d60df8727f59 - cae017b76acb - f947b4bb5107 - a58e4a43f49c - - d60df8727f59 + - 7b8cb2b02978 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - 1bc3657cd694 - - 073608a50ac3 - - 7f3b59dee073 - 04144473e59e - 7136e9ab70db + - 073608a50ac3 + - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: + - 19299bb1c6af + - a7817705348e - 0a1224c4b781 - d943081510da - - 19299bb1c6af - 9058d8943303 - - a7817705348e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -137,26 +137,27 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - c4db8c4de66f - f8f56dd6449f - a68b985913ab + - b907a3c0434f - 65d52c693b8e + - c4db8c4de66f - dbf1798c0dcc 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: - - 6d364c65c946 - 6c84982ee6f7 - 654548ae1357 + - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -168,9 +169,9 @@ tools: - name: humann2_regroup_table owner: iuc revisions: + - bd7a9c6efb10 - e66ab198ec15 - 6aad8ca3918b - - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table @@ -184,9 +185,9 @@ tools: - name: humann2_unpack_pathways owner: iuc revisions: - - cad93abecac9 - - 7f208f1eb64f - 9704f1a3b32d + - 7f208f1eb64f + - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -223,28 +224,28 @@ tools: owner: iuc revisions: - 31c6d107e7a5 - - 79706f10d680 - - e88b731dad59 - c409a495841f + - e88b731dad59 + - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - 714d5a28cc5c - - 71ea608ddfa3 - - d24841f5c3d2 - 172920f67a84 - 094ad9c068af + - d24841f5c3d2 + - 71ea608ddfa3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - a4d7148ccee4 + - d7e9a3c41657 - a293a742194f - 4137b492233e - - d7e9a3c41657 - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -258,11 +259,11 @@ tools: owner: iuc revisions: - 64bc7acc22a9 - - 75bedfb2078b - cf87759761eb - - 6fcb8ac37a3e - 97f7bb0851e7 - e2c71b852aba + - 75bedfb2078b + - 6fcb8ac37a3e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table @@ -281,10 +282,10 @@ tools: owner: iuc revisions: - 4033827c76b8 - - 080ea153677c - - 2d35528d2141 - - c82508e76ad1 - 5e5a999ffaa9 + - c82508e76ad1 + - 2d35528d2141 + - 080ea153677c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann @@ -354,17 +355,17 @@ tools: - name: kraken2 owner: iuc revisions: - - 20e2f64aa1fe - 4a9da2b6c2e3 - - 328c607150ff + - 20e2f64aa1fe - cdee7158adf3 + - 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 @@ -383,8 +384,8 @@ tools: - name: kraken_report owner: devteam revisions: - - 6c09bed3444f - 1c677354ab18 + - 6c09bed3444f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_taxonomy_report @@ -403,8 +404,8 @@ 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 @@ -435,8 +436,8 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 2deaada69b14 - 88d274322340 + - 2deaada69b14 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa @@ -473,13 +474,13 @@ tools: owner: iuc revisions: - 2cff76cf35c6 - - 0270541aaf46 - - 7f5d7b0e9884 - e073891b2afc - 27250f92a01a + - 0270541aaf46 + - 327d9f4cc95f + - 7f5d7b0e9884 - 3cc4a60615c0 - 4fd3b5d8706b - - 327d9f4cc95f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 @@ -560,24 +561,24 @@ tools: - name: metaphlan owner: iuc revisions: - - 1a037928504c - - 289b3807e80c - - ff8f55893e7d - - fd69c607b43f - - a16313517e55 - a92a632c4d9b - - 2131d7dca455 - - ef65b083bd0c + - a16313517e55 + - 6dee4abadccb + - ff8f55893e7d + - 1a037928504c - 1a6cdf55390f + - ef65b083bd0c - b89b0765695d - - 6dee4abadccb + - fd69c607b43f + - 289b3807e80c + - 2131d7dca455 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning owner: galaxy-australia revisions: - - e3a64a1d2a6e - 2a8bc1d26d06 + - e3a64a1d2a6e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_filter @@ -608,8 +609,8 @@ tools: - name: picrust2_hsp owner: iuc revisions: - - 3b133b8d578a - 6eafc1e01a8c + - 3b133b8d578a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline @@ -629,15 +630,15 @@ tools: - name: picrust2_pipeline owner: iuc revisions: - - d6bb2e3febda - 540aedfc81c7 + - d6bb2e3febda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs owner: iuc revisions: - - 73b56418e7f4 - 680fb3eb574c + - 73b56418e7f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions @@ -706,20 +707,20 @@ tools: - name: staramr owner: nml revisions: + - aeaa20b96ef2 + - 141afacabcfa - 3b22de20bd4b - be818ae858e4 - - 2fd4d4c9c5c2 - 4b9a8031ab74 + - 2fd4d4c9c5c2 - 4d83eccf5f81 - - 141afacabcfa - - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - - b3c7199d8786 - - 9495df9dd6ef - 576963db5f1b + - 9495df9dd6ef + - b3c7199d8786 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index e826cebe9..c8656b62d 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - bdb4a58a2025 - 12e856482d26 + - bdb4a58a2025 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -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: - - 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 b409e2138..c90d5cf02 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 + - 2263989660f5 + - 098506c54016 + - 8b67dd48fec1 + - 6ae5a7b5a0a2 + - cd07731e4434 + - a74dbfee5a86 - 9eeb13a92d79 - - bdfbaf0c10aa - 9baa871cb1d1 - 80f03df2e2ce - - 48c13389050d - - 2263989660f5 - - a74dbfee5a86 - - 6ae5a7b5a0a2 - - 8b67dd48fec1 - - 098506c54016 - 9422c5a87ee2 - - cd07731e4434 + - bdfbaf0c10aa + - 94b8c6013083 + - 48c13389050d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - '764845535798' - - f0af8936ed41 - - aaa0d6a8b808 - - d390fe1567dc + - c44f824c051a - c18157c68134 + - bc3831dd65c1 - 3ff17bad4006 + - '764845535798' + - 5abf2c2249aa - f14193ec1f50 + - f0af8936ed41 + - 2e093badc689 - be78f13134e2 - fc2e49f91e52 - - 5abf2c2249aa + - aaa0d6a8b808 - d7ce0ec78e51 - - 2e093badc689 + - d390fe1567dc - 4a60927aaca5 - - c44f824c051a - - bc3831dd65c1 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: - - d6694932c5e0 - 5b097fde95dd + - d6694932c5e0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -66,14 +66,14 @@ tools: - name: mafft owner: rnateam revisions: - - f0d493f8f84f - - bf28a8cff401 + - 6f28e90db932 - 8e649f27aa0d - - 15974dd17515 - - c5908940967d - a65296ffb4a0 + - c5908940967d - f1a5908ea2cb - - 6f28e90db932 + - 15974dd17515 + - f0d493f8f84f + - bf28a8cff401 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter @@ -88,39 +88,39 @@ tools: owner: iuc revisions: - c9685bc0407c - - 60698466facd - 5561a1193611 + - 60698466facd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - 48823c9635a4 - 57f042937ba7 - bcd65de9725b + - 48823c9635a4 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: + - 4fc0cb2ac8ae - fb43e8887350 - ebe3b0f84de9 - - 4fc0cb2ac8ae tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: + - e18267f90096 - 7cd7a55a678d - 636b049e6141 - - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: + - cf3c9489c088 - 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 425e67516..27fcd4871 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -16,8 +16,8 @@ tools: - name: dorado owner: galaxy-australia revisions: - - 99c9427219d3 - fc5b6491cf78 + - 99c9427219d3 - 63d8ecfcfab1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -25,20 +25,20 @@ tools: owner: iuc revisions: - 72b5e9dda577 - - 79e9a869f40e - - a7228a7ea146 - - fc8804320156 - cb34f00cc10f - 0e9e7fcdd543 + - a7228a7ea146 + - fc8804320156 + - 79e9a869f40e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: + - d6cddc06aeae + - db25ec99c3ea - 18505fe2bdb1 - fa11aa8103b2 - - db25ec99c3ea - - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -50,22 +50,22 @@ tools: - name: medaka_variant owner: iuc revisions: - - edf6d4003fad - - 19f3b583a9b3 - 2bf63b38ee9b + - 19f3b583a9b3 - 0f5f4a208660 - - ec699520444c - - 43815fa60f3a - eb746fa6f514 - - cc36773a3681 - 222669c4afb6 + - 43815fa60f3a + - edf6d4003fad + - cc36773a3681 + - ec699520444c 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 @@ -77,60 +77,60 @@ tools: - name: nanoplot owner: iuc revisions: + - 645159bcee2d + - 0f1c34698076 - a3c4fe6f49ab - a02b8b3f5a0c - - 0f1c34698076 - - edbb6c5028f5 - - 7b379e98b9a9 - - 645159bcee2d - a38bdcec9e4c + - 7b379e98b9a9 + - edbb6c5028f5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - d219b6d8158a - 85a394edc247 - 3b6f94fc7e1d + - d219b6d8158a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - 90a922f32523 - - be95355fef8d - a8d4be409446 + - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 4857d5bcce52 - - 449e9aeded2d - d376944466bf + - 449e9aeded2d + - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - de5b3d8f5b90 - a3afc5f0a96c - bec636361cfd + - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: + - 543cbeef3949 - 5f76b20953e5 - 93d623d9979c - - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 1d835c691480 - 28d7819c312f + - 1d835c691480 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_extract @@ -142,8 +142,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - 47936349f3e9 - 5a82eb9e1b89 + - 47936349f3e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -155,8 +155,8 @@ tools: - name: poretools_occupancy owner: iuc revisions: - - 338d15b8d6fb - 336791b5665f + - 338d15b8d6fb tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_qualdist diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index 19f5b1230..0a2c06cb2 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -6,12 +6,6 @@ tools: - 592ef3959907 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu -- name: bbtools_tadpole - owner: iuc - revisions: - - 0ddf147d1897 - tool_panel_section_label: None - tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes owner: devteam revisions: @@ -34,18 +28,18 @@ tools: owner: iuc revisions: - 3e73c97f025d - - d74850cf4e42 - adfd6bf710bd - - baceff842902 + - d74850cf4e42 - 97b1b5ad1cda + - baceff842902 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 1586b111d2a3 - - 9dd107db92c2 - 83da94c0e4a6 + - 9dd107db92c2 + - 1586b111d2a3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -57,12 +51,12 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 19b6a2f0dbe2 - 13851aefa67a - - 2f27f3b86827 + - ed1518ce2237 + - 19b6a2f0dbe2 - e4b4837f06f5 - 1e34d2e3d285 - - ed1518ce2237 + - 2f27f3b86827 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -81,16 +75,16 @@ 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 - 5711fc06a63e - - 48a42ca61006 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -110,8 +104,8 @@ tools: - name: data_manager_fetch_busco owner: iuc revisions: - - 15b97817550a - 2b4526fdf7fb + - 15b97817550a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta @@ -137,10 +131,10 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: - - b4b2b284230a - - 27a6a256cd23 - - 52b6a4d98009 - 172815da3d41 + - 52b6a4d98009 + - 27a6a256cd23 + - b4b2b284230a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -152,8 +146,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d210e1f185bd - d74c740bdb25 + - d210e1f185bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -165,9 +159,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: + - 87febc68b45b - fea85c467896 - 19bbd19b74b3 - - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -180,8 +174,8 @@ tools: - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 4c7ebbad42cf - 15c2fc266540 + - 4c7ebbad42cf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -199,26 +193,26 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 0cb27ea69dc1 - 2c61c30a57e7 - - 4ba60cb14cb0 - 5fe20c915fa6 - - d8dc037e3c13 + - 4ba60cb14cb0 - 9c43baa60906 + - d8dc037e3c13 + - 0cb27ea69dc1 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: - - aec831b54a5b - 9d09724f2bf1 + - aec831b54a5b - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -226,9 +220,9 @@ tools: owner: iuc revisions: - 6e24e79d3d69 + - df30a2f1db55 - ed7a967cb11b - 29c738066906 - - df30a2f1db55 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -240,16 +234,16 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - ad90c2da4f38 - 3e4d45aca422 + - ad90c2da4f38 - 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 @@ -269,9 +263,9 @@ tools: - name: data_manager_twobit_builder owner: devteam revisions: - - 9946bc39c834 - 625fd9476402 - 94a50db37d1a + - 9946bc39c834 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -795,10 +789,10 @@ tools: - name: salsa owner: iuc revisions: - - ba7b0f11e470 - - 9a22227bb6d0 - f77f7a7f3b83 - 58a870ef434c + - ba7b0f11e470 + - 9a22227bb6d0 - ab5b7f6b7198 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index c5c7d898c..4bbe68e72 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -20,8 +20,8 @@ tools: - name: gubbins owner: iuc revisions: - - 96e6283e4745 - 637ec5d5368c + - 96e6283e4745 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -34,54 +34,54 @@ tools: owner: iuc revisions: - c78f3d7dd1db - - '841557158611' - - 8834daeb9892 - - d7c7ef3353fe - - 6a457678efcb - - cce7b18495e4 - - f73435dc282b - - 26de3a7b1cb9 - - 3f59ebfbfe3d - - 3b8b5bde0bd9 - 107d3ba7024a + - 3f59ebfbfe3d - 5a7c56a5cc08 - - 81e66674859e + - '841557158611' - f04a1264e2a2 - d033ffc1c161 - - b89cac5156ec + - 3b8b5bde0bd9 - a6619171428e + - 8834daeb9892 + - f73435dc282b + - 81e66674859e + - cce7b18495e4 + - d7c7ef3353fe + - b89cac5156ec + - 26de3a7b1cb9 + - 6a457678efcb tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 6223845127ea + - 5b777002c2de + - 6a726db04d4b - b0af57c1a968 - - 5fcd1ece3a6e - 3b96e92e8ec3 - - 02b8758214b0 - - a185b079b095 + - 4755f52427c4 + - df47d4845b62 + - 5fcd1ece3a6e + - 7a2092844346 - 88c4aa435ded - - e75442c7f4da + - 659517798cc4 - aa8cc71438cf - - 7a2092844346 - 6283babe736e - - 659517798cc4 - - df47d4845b62 - - 6a726db04d4b - - 5b777002c2de - - 4755f52427c4 + - 02b8758214b0 + - 6223845127ea + - e75442c7f4da + - a185b079b095 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - 111bd54f6bc4 - d1c340a5664b + - 111bd54f6bc4 + - 24d024316465 - f97743d52b87 - 0878b7fd5260 - c1d53e95327f - - 24d024316465 - b8476e82ac20 - 70acec670c30 tool_panel_section_label: Phylogenetics @@ -89,10 +89,10 @@ tools: - name: nextclade owner: iuc revisions: - - 4f6349228462 - - daddf188c13f - 9e10ba792be2 - feb40665d7cd + - daddf188c13f + - 4f6349228462 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -104,26 +104,26 @@ tools: - name: pangolin owner: iuc revisions: - - 9d61d3fa046c - - 8ad84c5753ea - ca337cce3888 - - abf6dbe8c9d7 - - 03ed9524dcd1 - b7e297c2ede6 - - 42a174224817 - - ca0d8cf80567 - - 5f8727ff21e7 - - a2099fb98cdb - - 83a69484cb87 - - 7bb8726be37c - - 437e28791761 - - 2fa9d4f1b48f - 3a43c3982401 - - b6abccb1f25b - - 81804a978fc0 - - 2f1019071464 + - 8ad84c5753ea - 36912871ccdc - 14ae456b8cc5 + - 2fa9d4f1b48f + - 2f1019071464 + - 437e28791761 + - b6abccb1f25b + - 5f8727ff21e7 + - 03ed9524dcd1 + - 7bb8726be37c + - 81804a978fc0 + - abf6dbe8c9d7 + - ca0d8cf80567 + - a2099fb98cdb + - 9d61d3fa046c + - 83a69484cb87 + - 42a174224817 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -142,9 +142,9 @@ tools: - name: raxml owner: iuc revisions: - - 29ff6a849eac - - ea30d3089354 - a4b71be30c3c + - ea30d3089354 + - 29ff6a849eac - 73a469f7dc96 - ba29b5e2a4be - b1e68bbe4cef @@ -153,12 +153,12 @@ tools: - name: roary owner: iuc revisions: - - e88a7de55d6e - - dbe2b2204555 - - f1ccc8a6eb05 - - 91887494eb97 - - 9b2b122d0415 - 809e42326fc2 + - 9b2b122d0415 + - 91887494eb97 + - dbe2b2204555 - 15ac71df11a0 + - f1ccc8a6eb05 + - e88a7de55d6e 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 91aa1e357..911eafa44 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - b502c227b5e6 - 1aac2a13842a - - 3f254c5ced1d + - b502c227b5e6 - a1f0b3f4b781 - 881d7645d1bf - f6ced08779c4 - fc288950c3b7 - - 7d34178f2812 + - 3f254c5ced1d - f9242e01365a + - 7d34178f2812 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 32459355d..38075a105 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,16 +2,16 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - d00e15139065 - - eb085b3dbaf8 - - 5b85006245f3 - - ca90d17ff51b - - c0e71cb2bd1b - - 6ab1a261520a - e4a053d67e24 - - 3bd420ec162d - - a58f7eb0df2c + - 6ab1a261520a + - ca90d17ff51b - 7fbec959cf2b + - a58f7eb0df2c + - 3bd420ec162d - 2f7702fd0a4c + - c0e71cb2bd1b + - d00e15139065 + - 5b85006245f3 + - eb085b3dbaf8 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 593719665..b528c0149 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -4,61 +4,61 @@ tools: revisions: - 277dc652246e - ece627528a78 - - 4c177985028a - - 0a18ac48ac53 - - f28ad96b76dc - b18329a8ac14 - b574b84afc4d + - 0a18ac48ac53 + - f28ad96b76dc + - 4c177985028a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: + - bf06d196e23d + - e988563cc6e5 - 525f201b86c1 + - b41107d8fe89 - a9a28e46d54a - e215f71d7983 - - b41107d8fe89 - - bf06d196e23d - - e988563cc6e5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 4fbffddde8cd - 56da27be956a - - 8da3511c9467 - bb6397b94018 + - 4fbffddde8cd + - 8da3511c9467 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: + - b8c79e70516d + - a8157342d9a3 - f23d67e28cc8 - 890845926d4b - 528fb09022be - - b8c79e70516d - - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 80600735685d - - ae304a72db7b - - a95a82eb4d50 - 59e85306eae5 - - 25b83cbd596a + - a95a82eb4d50 + - ae304a72db7b + - 80600735685d - a69865da6f80 + - 25b83cbd596a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - ed9ed1e6cca2 - 83aac7741200 - - 798da6bdff3d - 611d80c0e29d + - 798da6bdff3d + - ed9ed1e6cca2 - f1897eb07081 - e0669b1854b1 tool_panel_section_label: Proteomics @@ -67,9 +67,9 @@ tools: owner: galaxyp revisions: - 5a35e3a8d013 - - a7fb9b395ddf - 74b61bf5bc4b - d426a9107a6c + - a7fb9b395ddf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations @@ -77,19 +77,19 @@ tools: revisions: - 91f0f5922011 - df2187f9013b - - cc430977c8ff - 82f6c2f4332d + - cc430977c8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 1693b2126f30 - - c5aa9fca18c6 - - 10566783d718 - ba92b59cd529 + - 10566783d718 - d2483487e077 - 043f9c91f686 + - c5aa9fca18c6 + - 1693b2126f30 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -107,9 +107,9 @@ tools: - name: diann owner: galaxyp revisions: - - ff8c9e0e8a7b - ae4dc0c041f9 - 9fa3dbf06f17 + - ff8c9e0e8a7b - bf0728e000cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -122,32 +122,32 @@ tools: - name: encyclopedia_encyclopedia owner: galaxyp revisions: + - d263296cd73e - d0ea7589e95f - eac99effe86f - - d263296cd73e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: - - 0fa397f4f40b - - 4081e4faa4ab - 1c5cbf8f79ce + - 4081e4faa4ab + - 0fa397f4f40b 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 owner: galaxyp revisions: - 0d2e93e01e68 - - d6a4dfdad269 - ce1a157a41bd + - d6a4dfdad269 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -159,16 +159,16 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: + - d286ff4600dd - 160538a890a6 - e66f552a3c47 - - d286ff4600dd 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 @@ -181,16 +181,16 @@ tools: - name: maxquant owner: galaxyp revisions: - - 1f39c833f65f + - f522c08e900c + - 4d17fcdeb8ff - 9c52362ae7bb - - 2133b0be850a + - 97a7f34fcb6a - e42225f8a659 - - 4d17fcdeb8ff - - f522c08e900c - 837224ad1694 - - 97a7f34fcb6a - - 7f432d87c82c + - 1f39c833f65f - 37d669de2828 + - 7f432d87c82c + - 2133b0be850a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -203,77 +203,77 @@ tools: owner: galaxyp revisions: - 0ed07016d668 - - a72ac2c7cc5b - - e63db1aa82ee - 85b8866f06d7 + - e63db1aa82ee + - a72ac2c7cc5b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 990b4560ead7 - - 1974224d63c2 - 767c1d761aaf + - 1974224d63c2 - 352b37c66d97 + - 990b4560ead7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - 4f359549383c - - 99450519d727 - 35cc7ca0bdc7 + - 99450519d727 - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - c1343e3389ca - c7745841de24 - - e79958768a2c + - c1343e3389ca - 06f6826d380c + - e79958768a2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: + - b9d453dca8d3 + - d2eac53666f0 - d46d64e7964d - da986f83631b - - d2eac53666f0 - - b9d453dca8d3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 8bd7734309f6 - - 944b43462104 - 1199751329b0 - 9bf325045235 + - 8bd7734309f6 + - 944b43462104 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus owner: galaxyp revisions: - - e0104a9f20f0 - 8295d959ca28 + - e0104a9f20f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert 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 - - de7593c29499 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -286,36 +286,36 @@ tools: - name: openms_consensusid owner: galaxyp revisions: + - 01dbaf6a57e0 + - f4be248c3d47 - 4e77b8f12cd3 - 8960fb791701 - - f4be248c3d47 - - 01dbaf6a57e0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - 06cca574e337 - - 25529df60a81 - 370141bc0da3 + - 25529df60a81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 6ccbf9a2072c - - 518b1730cf2a - - f7fef900f5b2 - 9cdf15d3cfc8 - c9eff69a7c62 + - f7fef900f5b2 + - 6ccbf9a2072c + - 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tool_panel_section_label: Proteomics @@ -395,119 +395,119 @@ tools: - name: openms_idmapper owner: galaxyp revisions: - - b5d0905419da - - adca857b4884 - - 39caaa778d2e - 8ddb7bab1138 + - 39caaa778d2e + - adca857b4884 + - b5d0905419da tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 1c5f31b8d632 - - f817513840a9 - - 18f93351f8b6 - 34e7afee141d + - f817513840a9 - 8d4db262964c + - 18f93351f8b6 + - 1c5f31b8d632 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - 5d9f175dff81 - - 986e03d3201e - - c69f69d7867a - 111c3a00136d + - c69f69d7867a + - 986e03d3201e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - be74a8cd7d66 + - 4204882495f2 - 476b5e296979 - 0e52c85f3b15 - - 4204882495f2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - - 2b2a7551a857 - - f5ec766d80cf - c18d8efa4474 + - 2b2a7551a857 - a407b6790342 + - f5ec766d80cf 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: - - 2735db4dd8d9 - - bf32e0bcf554 - 8098330f6d91 + - 2735db4dd8d9 - ee860980edc6 + - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - 0ced5bc9f4dd - - a2a6e9551046 - 08488066d588 + - a2a6e9551046 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - - de7a553552a6 - 2a9ff56cb279 - 8c01da82292c + - 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+ - 05ec9fb05ed1 - f9ed7e074900 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -515,35 +515,35 @@ tools: owner: galaxyp revisions: - 6e8cc5ed2a9b - - d31426ef20f6 - 18826fb8e5db + - d31426ef20f6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: + - bc63b4d12779 - 4a7b96835140 - 2aebe58de46e - - bc63b4d12779 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - 5ae104d0da6e + - 3d8d4ada5405 - 6b01678ec2fc - decc397c3b7e - - 3d8d4ada5405 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: + - 5182338d5e7c - 539a3a4dcc9e - - dd173849c3d8 - d6aca689dd48 - - 5182338d5e7c - e039cc5c7aed + - dd173849c3d8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier @@ -557,9 +557,9 @@ tools: - name: openms_targetedfileconverter owner: galaxyp revisions: + - 43b9ed22e8ce - 9c70a651a53e - dd71e020e2aa - - 43b9ed22e8ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter @@ -573,18 +573,18 @@ tools: - name: openms_xmlvalidator owner: galaxyp revisions: + - f036e8cf1a55 - 78c080d36945 - ad2ba3a95a02 - - f036e8cf1a55 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - 7f6a1f27553e - - fb52e95a370c - - c8b225c69a7f - 5c2a97a234d6 + - c8b225c69a7f + - fb52e95a370c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -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: - - 3ec27b4cee7c + - da885ca16cb2 - 7fdd9119cc4f - - 07ff622ec007 - 1beff3ddce58 - - a72c48001f7c - 3634c90301af + - 3ec27b4cee7c + - 07ff622ec007 - 943a34df6047 - - da885ca16cb2 + - a72c48001f7c 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: - - a371252a2cf6 + - 265c35540faa - 12692567c7f9 + - a371252a2cf6 - 1a5690a5eedc - - 265c35540faa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index a4a91ae00..9c09e117d 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,131 +2,131 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: + - 42201b90e3f4 + - cd5f98911089 - 110a346daf36 - - e345aadf914f - 289b7d6b69a4 - - cd5f98911089 - - 42201b90e3f4 - 2f1d464ebfd2 + - e345aadf914f tool_panel_section_label: RAD-seq tool_shed_url: 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d504d945a655 - 95286af4139b - - d1fad35bdb4a 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: - - 563af4497055 - 96de7538bf0c + - 563af4497055 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 3253beab0..3690c8186 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,24 +2,24 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - cf01dd6c6b1f - - 31f8063eedea - 2d4e3aff9dc7 + - 31f8063eedea + - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: + - 703a2cb3fb38 - 125d20cb23d7 - 32e542c2a773 - - 703a2cb3fb38 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 01ccd366690d - 3d61a698e5e1 + - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -31,8 +31,8 @@ tools: - name: blockclust owner: rnateam revisions: - - aab6cf87b40a - dbb6ee3179bc + - aab6cf87b40a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: chira_collapse @@ -87,23 +87,23 @@ tools: - name: cufflinks owner: devteam revisions: - - e04dbae2abe0 - d080005cffe1 + - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: + - 86285ddd4512 - cf747d1bd79a - 6a6717a5f421 - - 86285ddd4512 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - 9a854107dbb2 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -128,55 +128,55 @@ tools: owner: iuc revisions: - e3b16fd7dd08 - - 0693ccd171c4 - 3b36efd62b3e + - 0693ccd171c4 - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - 24a09ca67621 + - 6a3a025714d3 - 8fe98f7094de - - 9a882d108833 + - d027d1f4984e - 0696db066a5b - cd9874cb9019 - - 6a3a025714d3 - - d027d1f4984e + - 24a09ca67621 + - 9a882d108833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - 62adf13b86ea - - b47c006d90c5 - df929f257179 + - b47c006d90c5 - 2872c633f07e - 9a7c5b6d8f1e + - 62adf13b86ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 070900306913 - - 0cb907a2a810 - - a8305cf0c951 - - 3d89af8a44f0 - ae2aad0a6d50 - - 5bf899c13979 + - 3d89af8a44f0 + - 555659de7321 + - a8305cf0c951 + - df0c8d0a5992 - 6e53e565fc6a + - 0cb907a2a810 + - 070900306913 - f2843df56434 - - 334ce9b1bac5 - 9bdff28ae1b1 - - 555659de7321 - - df0c8d0a5992 + - 334ce9b1bac5 + - 5bf899c13979 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea owner: iuc revisions: - - fba1660fb717 - 31ea4992b948 + - fba1660fb717 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: express @@ -188,16 +188,16 @@ tools: - name: featurecounts owner: iuc revisions: - - af814359d244 - - e6a2a912677a - - 6f66ae7c5f7a + - 7db9d3ea71c9 - 90d16db017d7 - f9d49f5cb597 - - ea04b737afa0 - a56fbe2d6ba7 - - 7db9d3ea71c9 + - af814359d244 + - e6a2a912677a - 38b6d12edc68 - a37612abf7f9 + - ea04b737afa0 + - 6f66ae7c5f7a - f3a5f075498f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -222,9 +222,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 3c97c841a443 - 0f710191a66d - f99dd58de04f + - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -237,20 +237,20 @@ tools: owner: iuc revisions: - f4af63aaf57a + - 6c19daec423d - 26371a1df031 - - 6ab42baa56e9 - 3fb01a8c902d - a86e80d3c09c - - 6c19daec423d - d4b55e2beb12 + - 6ab42baa56e9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: + - 4418229c501e - 916cb26bd9d3 - 67b0b160903a - - 4418229c501e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -262,33 +262,33 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - ce5d418183c5 - - 1c75aa5de15e - 5ae5c312d718 - 01247aaf0a10 + - 1c75aa5de15e - 87c11c05d238 + - ce5d418183c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - c971db6f0fe5 - 40985510cd98 - 10c98fab6c5a - 4f9c4e6566e5 + - c971db6f0fe5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 32511f586472 - - 119b069fc845 - 0921444c832d - - 97e06a4c7c75 - - 58c35179ebf0 + - 119b069fc845 - e827f9aae031 - 708348a17fa1 + - 32511f586472 + - 97e06a4c7c75 - d6f5fa4ee473 + - 58c35179ebf0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -344,21 +344,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 980d2a2e1180 - - c772497b2c32 + - 99b17b74a8cd - 4df95e2d7f61 - - 0a563fd2f22e - 5ec75f5dae3c - - 3ea5a2a63fa2 - c7c55b694974 - - 4074fc1940e2 - - 7ed2edc1337f + - e132e7d02a3e - b9e04854e2bb + - 3ea5a2a63fa2 + - 4014de1b6daf + - 980d2a2e1180 - b0f2be869d6d - - e132e7d02a3e + - 4074fc1940e2 - 79de45b5069b - - 4014de1b6daf - - 99b17b74a8cd + - 0a563fd2f22e + - c772497b2c32 + - 7ed2edc1337f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -370,36 +370,36 @@ tools: - name: salmon owner: bgruening revisions: + - e3d32471da11 + - cc05793bb896 - 49121db48873 - 53e9709776a0 - - cc05793bb896 - - e3d32471da11 - - 2c0ca397d302 - f4d5237a84f6 - - 15cd64d7c58b + - 2c0ca397d302 - ebab418107f5 + - 15cd64d7c58b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: + - fab6ff46e019 - 56242ff81c84 - c0fd285eb553 - 8c28affc7c48 - - fab6ff46e019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - 258d696dbd7e + - 76d290331481 + - ae618321f34a + - 914cfcba0ec8 + - cbf488da3b2c - cef79931dda5 - dd4df992d93d - - cbf488da3b2c - 1ebd14235b92 - - 914cfcba0ec8 - - ae618321f34a - - 76d290331481 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -429,28 +429,28 @@ tools: - name: transdecoder owner: iuc revisions: - - 0db979fead3a - - c6334cb383ff - d0d4cef4f967 + - c6334cb383ff + - 0db979fead3a - ffd1300599a1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - bcc5f03f1900 - d6a479fd4281 - - ba3720d7e68b + - bcc5f03f1900 - 74217fbfba4d + - ba3720d7e68b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 2fb4ee002432 - c2b82a94493e - 56162e446004 - 478f36effca1 + - 2fb4ee002432 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -465,55 +465,55 @@ tools: owner: iuc revisions: - 34a018cbee9c - - be3f26533209 - 4687ecf0eb2d + - 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: - - 65e7dea767ea - 5192f657f305 - - 05ab8d5e04a2 - c5fbddcac63a - 33406f5a445c + - 05ab8d5e04a2 + - 65e7dea767ea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d - - a35cba31d904 - e406ac71165d - 6f0fb35b799c + - a35cba31d904 + - 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 - c2c039e421af - - 7c7fbf13aadd - 37a1129c89d2 + - 7c7fbf13aadd + - 964b7efe2639 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - 047c22569787 - - 1d689e4e1caf - - 24e94d84adc9 - eafea3083352 + - 24e94d84adc9 + - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: - - 3a4ac03d1266 - - 9871104ea630 - 1812dbc5bb7b - 04bb8bb7c198 + - 9871104ea630 + - 3a4ac03d1266 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_stats @@ -532,14 +532,14 @@ tools: owner: iuc revisions: - 32b86cd8eb50 - - 48636f857c4b - - db1f362cca3e - - c9cfec002f71 - - d2bc35f3d1c5 - - 8f1c3df4dd49 - d84caa5a98ad - - 9fa24d5aac68 - cee61b3fcf78 + - 8f1c3df4dd49 + - c9cfec002f71 + - 9fa24d5aac68 + - db1f362cca3e + - 48636f857c4b + - d2bc35f3d1c5 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 dfa03fca7..ee91e8906 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: - - 080fd5739bb4 - - 473382134e56 - 1a052c827e88 + - 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 45be7f098..c311b4a01 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,8 +2,8 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 3c661e57a88f - 10184eaa85fc + - 3c661e57a88f - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -32,8 +32,8 @@ tools: - name: bamtools_split_tag owner: iuc revisions: - - e30af4e78cd3 - e9b9c489aacc + - e30af4e78cd3 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: - - 30a201c9c310 - 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: - - e38af83df163 - 17b35d23731f + - e38af83df163 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam2interval @@ -123,15 +123,15 @@ 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 + - 9149ad20699a - 46c6639921f1 - 12749212f61b tool_panel_section_label: SAM/BAM @@ -139,10 +139,10 @@ tools: - name: samtools_calmd owner: devteam revisions: - - 33208952b99d - - 92ec40abcdcf - 06dc50b7b711 + - 33208952b99d - 26b4f9f98aca + - 92ec40abcdcf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_coverage @@ -160,11 +160,11 @@ tools: - name: samtools_fastx owner: iuc revisions: + - b906586a6596 - 720217c23995 + - 66e23b11feae - b3d99709fe1a - a8d69aee190e - - 66e23b11feae - - b906586a6596 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fixmate @@ -177,64 +177,64 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - fe34990e5ce7 - db17d5321bad - fefd89ab563c - - 22970df7a40e + - fe34990e5ce7 - cc61ade70eb8 + - 22970df7a40e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - 88b8c2916784 - - 7def34e6cf4d - fa5d3e61e429 + - 88b8c2916784 - 811fc2d75ad4 - 7a6034296ae9 + - 7def34e6cf4d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - 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: + - b40e2d865d52 - 65a38e8c8e2a - - 740ce0a18f0d - 36677f429310 - - b40e2d865d52 - cae2794d2deb + - 740ce0a18f0d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: + - 583abf29fc8e - b61f5d6a7f25 + - 329deb17a9f7 - 9da0311ab1dd - 8da515fbc1bf - - 329deb17a9f7 - - 583abf29fc8e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase owner: devteam revisions: - - 1e5880498f52 - b5c3b1856370 + - 1e5880498f52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader owner: devteam revisions: - - 30388d878f81 + - 85e38b31e8b3 - bb8cfc6f6e0c - db000c6007a0 - - 85e38b31e8b3 + - 30388d878f81 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -254,46 +254,46 @@ tools: - name: samtools_sort owner: devteam revisions: - - e613c1ad4c4c - - cab3f8d35989 - d54a4df48867 + - cab3f8d35989 + - e613c1ad4c4c - 6c2c1836728b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - 135c85f4cfaf - 5d9ae78f34d3 + - b7f7826ef1cd + - 135c85f4cfaf - bcedabb53ddf - 818030fa6bbf - - b7f7826ef1cd - bd850490c7f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 3a0efe14891f + - 5a08c09b9311 + - 541082d03bef - 1cc79f49b8d5 + - 3a0efe14891f - 145f6d74ff5e - 24c5d43cb545 - - 5a08c09b9311 - - 541082d03bef tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - 2dce91e11ca7 - - 5826298f6a73 - - 32dc5f781059 - - b01db2684fa5 - - 350bbc5c2ffd - 0dbf49c414ae + - 350bbc5c2ffd + - b01db2684fa5 - c370440f901e + - b72793637686 + - 5826298f6a73 + - 32dc5f781059 - bf328cec6a42 - 6be888be75f9 - - b72793637686 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 aeaa39b96..98aad2b71 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -2,13 +2,13 @@ tools: - name: ena_upload owner: iuc revisions: + - 480d9e9d156b + - d147d6455873 + - 5cb6146337d8 - ea5e944f447d - a62c4a11a67d - - 6f6537780379 - 4aab5ae907b6 - - 5cb6146337d8 - - 480d9e9d156b + - 6f6537780379 - 59bb6d34fca6 - - d147d6455873 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 55dcf5312..c96f87907 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -8,96 +8,100 @@ tools: - name: alevin owner: bgruening revisions: - - f2000bc73102 + - e4c01dcece8b - e32b215b7c04 - ecb9ea6269ee - - e4c01dcece8b - c9944a2600f1 + - f2000bc73102 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_export owner: iuc revisions: - - e1c3c2f2a834 - 707023fa62fe + - e1c3c2f2a834 + - cfaf5a405371 - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 32e547223c9e - - cfc3f5a57dc6 + - 55e35e9203cf + - d330b3082107 - 00712416fdaa - fb9e030ffae4 - 93dd15e13e6a - - 55e35e9203cf + - 32e547223c9e + - cfc3f5a57dc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: + - 39e945f0b2c1 - 688357ad5e61 - 038e32885fec - b9fac48532eb - - 39e945f0b2c1 - - ee98d611afc6 + - 0bf7fddf90c7 - 6f0d0c784f09 + - ee98d611afc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - 9bd945a03d7b + - b85871dd69f9 - 43cb7b5a6fe7 + - 3d748954434b + - 9bd945a03d7b + - 7e8c677a7b71 - d4af736e7b83 - ed4996a16f7f - - 3d748954434b - - b85871dd69f9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops owner: ebi-gxa revisions: - - fe75d2414dc0 - 2e8022f1923c - a4774b7b2e85 + - fe75d2414dc0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 0e70b2dfe4be - - 769d815e4b0d - 02b1fe7aed76 + - 0e70b2dfe4be - 4fff5a293013 + - 769d815e4b0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: - - aa4a6f0916b4 - - c29e7bb492bf - 344c2af50552 - a90f8efe08b4 + - c29e7bb492bf + - aa4a6f0916b4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - 050cf43887d3 - - c32347702e12 - b13d3e4c48e1 - 5b7c81b35b89 + - 050cf43887d3 + - c32347702e12 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - ae969fdb8442 + - 1d77986f9ddc - 02fc39c8610d - 239193b96d72 - - 1d77986f9ddc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -133,9 +137,9 @@ tools: - name: dropletutils owner: iuc revisions: - - 2c1200fba922 - cfe1e6c28d95 - 8855361fcfc5 + - 2c1200fba922 - cdf4443d5625 - a9caad671439 tool_panel_section_label: Single-cell @@ -223,15 +227,15 @@ tools: - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - - 2dccb6bb0add - e06265d204f6 + - 2dccb6bb0add tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - b05f662f9f35 - f0216498a666 + - b05f662f9f35 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions @@ -244,50 +248,50 @@ tools: - name: hicexplorer_hiccomparematrices owner: bgruening revisions: - - 3ee5332bf57c - e03780179ee5 + - 3ee5332bf57c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: - - 4401ed529d2c - 3a6a5381db36 + - 4401ed529d2c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - c0737631eea1 - 2ba6cee8e4db + - c0737631eea1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - 62b720dceb56 - ea19190ce5e0 + - 62b720dceb56 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - 2b4d6a8dab36 - 2786a931cad2 + - 2b4d6a8dab36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops owner: bgruening revisions: - - ffc33339cd3e - 0410b6aada45 + - ffc33339cd3e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: - - 77d8e0fd162a - 5dfba24d7bdd + - 77d8e0fd162a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites @@ -300,15 +304,15 @@ tools: - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 7f7c6ead2d0d - 409396ea5cf0 + - 7f7c6ead2d0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinfo owner: bgruening revisions: - - 51e40e9b6c3c - e4f8fceab96a + - 51e40e9b6c3c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad @@ -328,22 +332,22 @@ tools: - name: hicexplorer_hicmergeloops owner: bgruening revisions: - - 1511a8ebe906 - ed900cd4a0a9 + - 1511a8ebe906 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - - f34ab9882252 - 6d042c96aceb + - f34ab9882252 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: - - ea5d67ec94ab - dd9988943f53 + - ea5d67ec94ab tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotdistvscounts @@ -356,8 +360,8 @@ tools: - name: hicexplorer_hicplotsvl owner: bgruening revisions: - - b4e780e93c91 - 337705015ee8 + - b4e780e93c91 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint @@ -377,8 +381,8 @@ tools: - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - 36dfa2825a59 - 1d6af10874d5 + - 36dfa2825a59 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -396,25 +400,26 @@ tools: - name: hicexplorer_hictransform owner: bgruening revisions: - - 27fe5cd1729c - f36828ebdc54 + - 27fe5cd1729c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 11a3385e03b5 - 1d201e8378b3 + - 11a3385e03b5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: + - e98619de2776 + - 7784821452ac - 4b0adaa31c95 - eeab712b0b99 - 59be31ac9dc3 - - e98619de2776 - - 7784821452ac + - 0f1aaff9b22d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -426,9 +431,9 @@ tools: - name: music_construct_eset owner: bgruening revisions: + - 7ffaa0968da3 - 2cfd0db49bbc - 282819d09a4f - - 7ffaa0968da3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution @@ -460,20 +465,20 @@ tools: - name: raceid_clustering owner: iuc revisions: - - 0bff0ee0683a - a4b734cd253b - 7e014059a88d - - c4f39bf4a068 - f911a64454fb + - 0bff0ee0683a + - c4f39bf4a068 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: - - b83fbc90161e - - 7608d5faee41 - - d45f092caf24 - 43c146e25a43 + - d45f092caf24 + - 7608d5faee41 + - b83fbc90161e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -495,9 +500,9 @@ tools: - name: raceid_trajectory owner: iuc revisions: + - 44b935f2271b - 2af7c5086a96 - e93b008c637a - - 44b935f2271b - c92d0f9338c5 - 72979cac22b2 tool_panel_section_label: Single-cell @@ -517,94 +522,100 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - b2df381a6004 - - 77b91b9bdf52 - - aaa5da8e73a9 - - 4d8f983cd751 - - 6f83f8fd381f - 6acb08931836 + - aaa5da8e73a9 + - 77b91b9bdf52 - f9353ee6a0d4 + - 178242b82297 + - 6f83f8fd381f + - b2df381a6004 + - 4d8f983cd751 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - 72a6bebab2a5 + - a97abb8cd15b - a03ff8633507 - - 277313130da5 + - 72a6bebab2a5 + - 713a0c65b1fe + - b409c2486353 - 3c86f71498bc - - a97abb8cd15b - d636ce5cde16 - - b409c2486353 + - 277313130da5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - - 5c3ebe2adc77 - - c5d3684f7c4c - - f54f0f0598ad - - 6bd82ed14acd - - c0a80a16560f - 6c145a6868cc + - c0a80a16560f - 3081ff5c84a3 + - 6bd82ed14acd + - 18262103fa61 - 5e9171dc8244 + - 5c3ebe2adc77 + - c5d3684f7c4c + - f54f0f0598ad tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - 7b9fafe32c86 - - 94c19fb1281c - - ab55fe8030b6 - - c9cb76cf8d6c - - a407e7f8bdc1 + - 5dada6f76047 - d844935c906c + - 7b9fafe32c86 - 9f354c7c8c92 - 3bcd5445cd7a + - c9cb76cf8d6c + - a407e7f8bdc1 + - 94c19fb1281c + - ab55fe8030b6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - aa0c474463c2 - - 6adf98e782f3 - - dbbe1ea8ecb1 - - 7647e5cd1b8b - - 9b0cdb8cf6be - 6f5349dd5c49 - 95777145cb92 + - 7647e5cd1b8b + - dbbe1ea8ecb1 + - aa0c474463c2 + - 9b0cdb8cf6be - f7446fd8d5e7 + - 2dfb2227a16c - 1072ce66b426 + - 6adf98e782f3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - d18e7a6e5cd4 - - 73ab2ac53d06 - - 215733a383f2 - c65fce500915 - bf2017df9837 - - 458e8f43a775 + - 73ab2ac53d06 + - d18e7a6e5cd4 - f2f6c703da06 + - 215733a383f2 + - 458e8f43a775 - a39040ae0a38 + - b70219da4a96 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_filter owner: iuc revisions: - - b7ea9f09c02f - 7a365ec81b52 - 652923ce664f + - b7ea9f09c02f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_normalize @@ -616,9 +627,9 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: + - 81e5bdff4853 - 2e41b35b5bdd - ef4c80837bc5 - - 81e5bdff4853 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_exprs_freq @@ -630,9 +641,9 @@ 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_tsne @@ -872,22 +883,22 @@ tools: - name: snapatac2_clustering owner: iuc revisions: - - 8f8bef61fd0b - afb90d3485df + - 8f8bef61fd0b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 588c811fdd48 - 88192fe25375 + - 588c811fdd48 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting owner: iuc revisions: - - 370d45e0d1a8 - fecf9664c885 + - 370d45e0d1a8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing @@ -906,8 +917,8 @@ tools: - name: velocyto_cli owner: iuc revisions: - - 883c33ef3372 - 90e95e9ee190 + - 883c33ef3372 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: vitessce_spatial diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index 1d5e6ed77..2afb9693b 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,11 +32,11 @@ tools: - name: datamash_ops owner: iuc revisions: - - 746e8e4bf929 + - 2f3c6f2dcf39 - 4c07ddedc198 - 562f3c677828 - 419027d822d6 - - 2f3c6f2dcf39 + - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass @@ -49,15 +49,15 @@ tools: - name: dwt_cor_avb_all owner: devteam revisions: - - e01e8a9a82f4 - 8564f6927b87 + - e01e8a9a82f4 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all owner: devteam revisions: - - 0b89b03ad760 - 506ae7b0d85d + - 0b89b03ad760 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass @@ -114,43 +114,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: + - 840f29aad145 - 9c3e1d3235c8 + - 4c4ec859c31a - 7442b94d6a1e - aef56d0e7a61 - - 840f29aad145 - b1eda492f063 - - 4c4ec859c31a tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - d0352e8b4c10 - - 07843f917990 - - 30d21a6041f6 - 9fda0b82f419 + - 07843f917990 - 375bbd555f4a + - d0352e8b4c10 + - 30d21a6041f6 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 7ae443e6217d + - 8b1b2b91f8d0 - cd02bf168d23 - 4cc980df6265 - 2c58b83c9bad - - 8b1b2b91f8d0 + - 7ae443e6217d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - ad7e0b4291ee - 4bbaf77573ef - - 1dd433d2c92c - - e10e776f2109 + - ad7e0b4291ee - bb9fc9d46ea4 + - 1dd433d2c92c - 7dd3fb35904f + - e10e776f2109 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 b7ecc883b..61ed2bd79 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -34,14 +34,14 @@ tools: - name: column_maker owner: devteam revisions: - - be25c075ed54 - - 9cd341095afd + - 6e8d94597139 - aff5135563c6 - - 02026300aa45 + - 13b6f0007d9e + - be25c075ed54 - 464b9305180e + - 02026300aa45 - 6595517c2dd8 - - 13b6f0007d9e - - 6e8d94597139 + - 9cd341095afd tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -78,11 +78,11 @@ tools: - name: filter_tabular owner: iuc revisions: - - 557ec8d7087d - - 9cc411a62277 - - 90f657745fea - 37cde8134c6a + - 90f657745fea - 34d29339abab + - 557ec8d7087d + - 9cc411a62277 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -106,28 +106,28 @@ tools: - name: merge_cols owner: devteam revisions: - - ae7843d06f8f - dd40b1e9eebe + - ae7843d06f8f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: + - 3a6b78c39dca - 2e8f945f7285 - - cf4397560712 + - 83069b38aa85 - 1ea4e668bf73 + - cf4397560712 + - 623f3eb7aa48 - cf34c344508d - - 3a6b78c39dca - 33d61c89fb8d - - 623f3eb7aa48 - - 83069b38aa85 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - 503bcd6ebe4b - ae8c4b2488e7 + - 503bcd6ebe4b - 399da6b5ec21 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -140,30 +140,30 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - b722161a845a - - bce29ec10b78 - c4d18aa4ec4a + - b722161a845a - f768f6183386 + - bce29ec10b78 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute owner: iuc revisions: - - 60ff16842fcd - 3bf5661c0280 + - 60ff16842fcd tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: - - 12615d397df7 - - ddf54b12c295 + - fbf99087e067 + - 86755160afbf + - 74a8bef53a00 + - d698c222f354 - f46f0e4f75c4 + - ddf54b12c295 - a6f147a050a2 - - 86755160afbf - - fbf99087e067 - 9ff72e942410 - - d698c222f354 - - 74a8bef53a00 + - 12615d397df7 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 d3c10be72..e4cd7ac5a 100644 --- a/usegalaxy.org.au/variant_calling.yml +++ b/usegalaxy.org.au/variant_calling.yml @@ -8,9 +8,9 @@ tools: - name: breseq owner: iuc revisions: + - 82fb5e3bb93e - 85c57cc9b558 - 0d18a3ba2d1c - - 82fb5e3bb93e tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: control_freec @@ -28,32 +28,32 @@ tools: - name: freebayes owner: devteam revisions: + - 57def2d7c093 - ef2c525bd8cd - - 156b60c1530f - a5937157062f - - 57def2d7c093 - 04fa42777df9 + - 156b60c1530f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 435b157bed6d + - 791f73caa0c8 - 09d6e4693887 + - 435b157bed6d - e61c9ac190ad - - 791f73caa0c8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - 074d44697036 + - 03627f24605f - 65432c3abf6c - - 3b4b2121842f + - 4805fe3d8fda - e1461b5c52a0 + - 074d44697036 - dfadc322b065 - - 4805fe3d8fda - - 03627f24605f + - 3b4b2121842f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter @@ -67,18 +67,18 @@ tools: - name: lofreq_indelqual owner: iuc revisions: + - f4473557ffc7 - 971e07ca4456 - - 426d707dfc47 - c27549b9aa1f - - f4473557ffc7 + - 426d707dfc47 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - dbd9f2db9ed8 - - aa35ee7f3ab2 - cdaab621d454 + - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -96,9 +96,9 @@ tools: - name: snippy owner: iuc revisions: - - d220115f882b - - 5bbf9eada9c2 - fa016f1eea1a + - 5bbf9eada9c2 + - d220115f882b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -134,21 +134,21 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - 40f0591deda0 - 32f14a2723ec - - 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