diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index f84126e8c..912815dfd 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -6136,3 +6136,4 @@ Update 177 20/12/23 22:44:42 sample_seqs False Tests failed peterjc bdaefd241921 Update 177 20/12/23 22:47:34 samtools_split False Tests failed devteam bd850490c7f1 bd850490c7f1 Staging Testing 0/1 SAM/BAM toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_177/install_log.txt Update 177 20/12/23 22:48:19 unicycler False Installed iuc 8f9f06995f98 8f9f06995f98 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_177/install_log.txt Install 1386 22/12/23 09:45:06 seq_filter_by_id False Installed peterjc 85ef5f5a0562 85ef5f5a0562 6/6 6/6 Filter and Sort toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1386/install_log.txt +Install 1388 15/01/24 11:12:44 pharokka True Tests failed iuc 2f40d2ccb0eb latest Staging Testing 0/2 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1388/install_log.txt diff --git a/requests/pharokka.yml b/requests/pharokka.yml deleted file mode 100644 index dfc9ae382..000000000 --- a/requests/pharokka.yml +++ /dev/null @@ -1,4 +0,0 @@ -tools: - - name: pharokka - owner: iuc - tool_panel_section_label: Annotation diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index 816b8b23c..088d12127 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 78c75f134c16 - - 6e9aea89e388 - - 3f3e247c053d - c2ef298da409 + - 3f3e247c053d - 4efdca267d51 + - 78c75f134c16 + - 6e9aea89e388 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -36,15 +36,15 @@ tools: - name: annotatemyids owner: iuc revisions: - - 4f2967b27e67 - - 3e1f6f6d557e - 44018dd6b447 - - 133f36c29579 + - fe3ca740a485 - b5d8e5475247 + - cd2480f35935 + - 133f36c29579 - 1aae04680c4b + - 4f2967b27e67 + - 3e1f6f6d557e - f29602ae449e - - cd2480f35935 - - fe3ca740a485 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -57,17 +57,17 @@ tools: - name: augustus_training owner: bgruening revisions: + - 6519ebe25019 - 7be22100e5e1 - dc027fa56d55 - - 6519ebe25019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: + - 09855551d713 - 28433faa6e42 - ca6d970d931c - - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -79,8 +79,8 @@ tools: - name: barrnap owner: iuc revisions: - - fe48aa4ccd5e - 8fd427007e93 + - fe48aa4ccd5e - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -107,8 +107,8 @@ tools: owner: galaxyp revisions: - 63662ae295d6 - - d9c3016f7283 - 9d1fbff733cf + - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -127,55 +127,55 @@ tools: owner: iuc revisions: - 3bbe70fef6df - - b6b5cd37f2a2 - 14f588312c56 + - 582fd74dc2a1 + - b6b5cd37f2a2 - 9f2455341fac - 756376aeb1ae - - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - a230ea445788 - - 989f7c061f35 - - 0ffe5be70caf - 30fb23d4c31c - 1691af4a0d17 + - 989f7c061f35 - 73428a792541 + - 0ffe5be70caf + - a230ea445788 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 563a19373357 + - e94187d661df - b69c46064ec7 - - 30f08d74024f - 5a5ae61da69c - - e94187d661df + - 563a19373357 - 494f0bb4a993 + - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - 2bba2ff070d9 - - f31125bb85ea - 1bc5a03faf2e - - 7abc5f6dd595 - - f77d7b685bb3 - d6c7106b7b2e + - f31125bb85ea + - 2bba2ff070d9 + - f77d7b685bb3 + - 7abc5f6dd595 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - fed64e676186 - - d3af38b9c7e1 - - 54961e026fe4 - - 52af33194019 - 520e30695ec3 - b3cf4684e9c7 + - 54961e026fe4 + - 52af33194019 + - d3af38b9c7e1 + - fed64e676186 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -201,10 +201,10 @@ tools: - name: goseq owner: iuc revisions: - - 602de62d995b - - ef2ad746b589 - 43798b4caee0 - 8b3e3657034e + - ef2ad746b589 + - 602de62d995b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -222,16 +222,16 @@ tools: - name: infernal owner: bgruening revisions: - - 477d829d3250 - c9e29ac5d099 + - 477d829d3250 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: - - 98cafcbd2578 - c55643c3d813 - 74810db257cc + - 98cafcbd2578 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -249,16 +249,16 @@ 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 - - d46d803ca6cc - 370c210d9541 + - d46d803ca6cc + - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 @@ -286,14 +286,20 @@ tools: - 15cff34c2005 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu +- name: pharokka + owner: iuc + revisions: + - 2f40d2ccb0eb + tool_panel_section_label: Annotation + tool_shed_url: toolshed.g2.bx.psu.edu - name: prokka owner: crs4 revisions: - - bf68eb663bc3 + - 8a22554cdde2 - d643e3b03500 - a17498c603ec - eaee459f3d69 - - 8a22554cdde2 + - bf68eb663bc3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -325,14 +331,14 @@ tools: - name: snpeff owner: iuc revisions: + - 5a29ab10dba6 + - cfcf33df7fc0 + - 268d162b9c49 + - 5c7b70713fb5 + - 8f92c2b26e6d - 9473cd297a76 - 68693743661e - - 8f92c2b26e6d - 5b80f544c67f - - 5c7b70713fb5 - - cfcf33df7fc0 - - 5a29ab10dba6 - - 268d162b9c49 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift @@ -366,21 +372,21 @@ tools: owner: iuc revisions: - 37213cf56392 + - 45083d070fb8 + - ba6f87115e13 + - 809dfc93d593 - 200c378d85f3 + - 037a11682176 - 2c68b0c38785 - - e1a9d6fd258d - ac8250086ac3 - - ba6f87115e13 - - 45083d070fb8 - - 037a11682176 - - 809dfc93d593 + - e1a9d6fd258d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - 8fc50fe60127 - f50807720df1 + - 8fc50fe60127 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: trna_prediction diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index f88c72bc8..2c01e2ab7 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,42 +2,42 @@ tools: - name: abyss owner: iuc revisions: - - 7547fcab5d19 - - 553bfe8bd0b5 - - 841084c5fc46 - a929ce596a34 - - fa5259cc561b + - 841084c5fc46 - 890b794c997d - 8f1b150a2487 + - 7547fcab5d19 - 0e93176640ac + - fa5259cc561b + - 553bfe8bd0b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - b2860df42e16 - - 21e491ad532a + - b9e31c5c01c7 - 067592b6b312 - - 94fe43e75ddc + - b2860df42e16 - ddddce450736 - - b9e31c5c01c7 + - 94fe43e75ddc + - 21e491ad532a 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: + - faee8629b460 + - 22286dab5aa1 - a7f16f24e9a1 - - 3371c5bdc17a - 5258e18bbe23 - - 22286dab5aa1 - - faee8629b460 + - 3371c5bdc17a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -49,30 +49,30 @@ tools: - name: busco owner: iuc revisions: - - 1e62c28ba91d - - 0d243f458b53 - - 602fb8e63aa7 - - e824f5d958d0 - 2a5b8b9936bf + - 602fb8e63aa7 - 5ecdeca79a0d + - 41030a6c03b7 + - 2dd755c1c6ff + - bb935709506a - 94170eee0ad8 + - 0d243f458b53 + - cf13a1e03e5b + - e824f5d958d0 + - 46ae58b1d792 - e4bd1e99bacf + - 1e62c28ba91d - 1440ae06552f - f18f0b887c31 - - 46ae58b1d792 - - 41030a6c03b7 - - cf13a1e03e5b - 4048d82f0c88 - - bb935709506a - - 2dd755c1c6ff tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: + - 5732f959936a - c5b7390290b1 - 86f150c8019d - - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -84,37 +84,37 @@ tools: - name: flye owner: bgruening revisions: - - 8d4f03b5fe9d - - cb8dfd28c16f - 3ee0ef312022 - 276f5d8712d5 + - 8d4f03b5fe9d - 1ce9b1d72ec3 - e27815e82dd4 + - cb8dfd28c16f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - b2f674562a18 - 3169a38c2656 - 01210c4e9144 + - b2f674562a18 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 7348b69e5109 - - 06bcf65179fb - 8b330a577046 + - 06bcf65179fb + - 7348b69e5109 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 5127a713de83 - - 3ef480892a9f - 3fba9c77550a + - 3ef480892a9f - 690c2caa367e + - 5127a713de83 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -126,21 +126,21 @@ tools: - name: hifiasm owner: bgruening revisions: - - 71740308d412 - - 366a11d316a7 + - 6505bd37670d + - 3f7be05a1597 - 9ef6920c3089 - - f3c89da3af16 - - 41cea2aa2dce + - 5bec28269d95 - 2061fb3b81b4 - da9d8bf98802 - - 3f7be05a1597 + - f3c89da3af16 + - 5f625c63b8bc - 0ee0c3089254 - - 60024a528cbd - - 5bec28269d95 + - 41cea2aa2dce - ec9e21e9c71b - - 5f625c63b8bc + - 366a11d316a7 - 045c7c3d8e59 - - 6505bd37670d + - 60024a528cbd + - 71740308d412 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -158,39 +158,39 @@ tools: - name: megahit owner: iuc revisions: - - 7518ee87b53d + - 14ddfc8ffb93 - de387b2b2803 + - 7518ee87b53d - a96f3ad4e0d8 - - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: + - 9d79beb19ac3 - f8113c25bc6b - 09c589057ee8 - 39edec572bae - - 9d79beb19ac3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - eadfd71dde37 - - 29dabd8db6f2 - 51c2360aa807 + - 29dabd8db6f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - 3ca2d2a9068c + - e731ea24e48d - f338e9942b27 - - fd128c111ab0 - - 606b09cc9860 - eb7a370f6588 - - e731ea24e48d + - 3ca2d2a9068c + - fd128c111ab0 - 2ecf5a570907 + - 606b09cc9860 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -202,10 +202,10 @@ tools: - name: miniasm owner: iuc revisions: + - a7b889b90140 + - 8dee0218ac7d - 80d1250bd5fd - 73a3846701e1 - - 8dee0218ac7d - - a7b889b90140 - 8b6d0d85252b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -218,9 +218,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 64a1c751d99b - - 15200570e926 - 7c2f5268d01c + - 15200570e926 + - 64a1c751d99b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -232,74 +232,74 @@ tools: - name: pretext_map owner: iuc revisions: - - 511e5e3cd55e - - 2b16ba799da9 - bbe19ef04a74 - 02831bf9e95f - - 8fef980d48b5 - - d256a51a656b + - 2b16ba799da9 + - 511e5e3cd55e - dfb8a4497339 + - d256a51a656b + - 8fef980d48b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - e9bd16ba5ebd - a315c25dc813 - 76d4cbefff85 + - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: + - 72472698a2df + - 875d0f36d66f - 675488238c96 - - 59db8ea8c845 - - 7594365c546b - ebb0dcdb621a - - 6fcbee531de6 - 3061c8b029e5 - - 72472698a2df - 342a1d1fed7b - - 875d0f36d66f + - 59db8ea8c845 + - 6fcbee531de6 + - 7594365c546b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - cd06929b224b - 78c533842eeb + - d865b62f501c + - cd06929b224b - 39bed8de8017 - - a199cd7ac344 - aa39b19ca11e - - d865b62f501c + - a199cd7ac344 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - - f8564b2d7f63 - - 33b7d8481a76 - 2b2a352488fa - - 3edba9afc9bc + - 33b7d8481a76 - f11b994b7eb2 + - f8564b2d7f63 + - 3edba9afc9bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: + - 53c2bc8c2ae3 + - 1d06c8b38e77 - ef69617ecb42 - e122f9101584 - 378e55aeeb25 - - 1d06c8b38e77 - - 53c2bc8c2ae3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - f77f7a7f3b83 - - ba7b0f11e470 - ab5b7f6b7198 + - ba7b0f11e470 - 9a22227bb6d0 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -312,168 +312,168 @@ tools: - name: shovill owner: iuc revisions: + - d9f6a00b6db7 + - f698c7604b3b + - ee17a294d3a3 - 83ead2be47b2 - - 865119fcb694 - ad80238462c1 - - d9f6a00b6db7 + - 865119fcb694 - 196a599ec43d - - ee17a294d3a3 - - f698c7604b3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - 5a0ddb4dc3a4 - - 24e471d13fe9 - 5e0825476fb7 + - 24e471d13fe9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 051fd2db8a27 + - 1bb12736175c - 904bf932cf78 - - 1fc82fe7ebef - 7490b213baa9 - - 1bb12736175c + - 051fd2db8a27 + - 1fc82fe7ebef tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - 808b3a0a6716 - - fee85957cebe - 34305b013402 - - d6e617c4e338 + - 808b3a0a6716 - ad8b536d1caa + - d6e617c4e338 + - fee85957cebe tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 21da31ed41a1 - - 8d4b90bf9caf - - b8002c3f7141 - e5a3b75a271f - 6b5a5842531e + - b8002c3f7141 + - 21da31ed41a1 + - 8d4b90bf9caf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - f1532cb33c75 - - 328aa71f0f3c - - 9de69775f512 - 86f66ab58e14 - 2a10645aeadd + - 9de69775f512 + - 328aa71f0f3c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - e41dcb0e913b - - 6aad515a5270 + - 1708851f8804 - 340bc17f49cf - 85fb02c43042 - - 1708851f8804 + - 6aad515a5270 + - e41dcb0e913b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - b65a43f70b99 + - b3490b036c5a - d159735a6a9f - d5fb354f745d - - b3490b036c5a + - b65a43f70b99 - 249f6a28c751 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 7897763d14ec + - 33368fec3b70 - 9006e5836729 - b7829778729f - - d2d1df21dfb9 - - 33368fec3b70 + - 7897763d14ec - dd7ad84f3943 + - d2d1df21dfb9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - ced385aa976d - - 189e837009c9 - - 6f4c8ad6ea01 - 8f631679571f + - 6f4c8ad6ea01 - 505a9833ab5d + - 189e837009c9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 19bdfd1e6fe3 - - e59bee4565b3 - - 9ded6109434a - d40ed4eb0c0e + - e59bee4565b3 - 356afed970b4 + - 19bdfd1e6fe3 + - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: + - 6dd935e4984b + - 4688ae3b49b5 - b23249f81bc4 - 80a17897564d - - 4688ae3b49b5 - - 6dd935e4984b - ebd801e712bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - b64696992ee9 - - b5e35a2ca4f3 - - 937ea677d437 - cb1e3db43020 - 59bd28f6265d + - 937ea677d437 + - b5e35a2ca4f3 + - b64696992ee9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 2628f6790eda - - 05bd7504fdb2 - cb4768eeca3b - - 6015aa0303f2 + - 05bd7504fdb2 - 383bb5ad32e2 + - 6015aa0303f2 + - 2628f6790eda tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - 6e26c9afd301 - - 9e3e80cc4ad4 - 8f9f06995f98 - - 0a3a602cd1e3 + - 9e3e80cc4ad4 - e92675014ac9 + - 0a3a602cd1e3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 08256557922f - - 920677cd220f - 8d09f8be269e + - 08256557922f - 5da9a0e2fb2d + - 920677cd220f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 37d88f41c810 - 82398ba86ba7 + - 37d88f41c810 - 0e2b4e3f9ca1 - 4a53b89fa703 - d81360ea69d8 diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index efef178f8..6f5b4d803 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -15,17 +15,17 @@ tools: - name: mlst owner: iuc revisions: - - 8e8dc9a1e3e5 - - 1f5641a52664 - 31812e7a1315 + - 1f5641a52664 - ded48b36f3b7 + - 8e8dc9a1e3e5 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 5c8ff92e38a9 - 24a7a95867b0 - 17fcac7ddf54 + - 5c8ff92e38a9 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bb_tools.yml b/staging.gvl.org.au/bb_tools.yml index 05eb64807..70adf3e9d 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,8 +2,8 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - 159b04e36791 - 204a131e47db + - 159b04e36791 - a9c9d768b751 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index 833911b1e..b8ba27613 100644 --- a/staging.gvl.org.au/bed.yml +++ b/staging.gvl.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: - - e19bebe96cd2 - - a8eabd2838f6 + - a68aa6c1204a + - 0a5c785ac6db + - 589e7e57fd6d - ce3c7f062223 - - dde39ba9c031 - b28e0cfa7ba1 - - 0a5c785ac6db + - dde39ba9c031 - 87ee588b3d45 - a1a923cd89e8 + - e19bebe96cd2 + - a8eabd2838f6 - 07e8b80f278c - - 589e7e57fd6d - - a68aa6c1204a 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 652e71f9e..6af0bccc6 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -8,10 +8,10 @@ tools: - name: diamond owner: bgruening revisions: - - f921014aba5a - e8ac2b53f262 - - 62c9df8382c2 - 54f751e413f4 + - 62c9df8382c2 + - f921014aba5a tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,14 +23,14 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: + - 0e3cf9594bb7 - d999e774072a - 5edc472ec434 - - e25d3acf6e68 - 2889433c7ae1 + - a52d2d93e595 - acf4e47b734c - 6f386c5dc4fb - - 0e3cf9594bb7 - - a52d2d93e595 + - e25d3acf6e68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index ff968f895..20e412eda 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -2,13 +2,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 6ca543ec1bf8 - - 27ee142314a9 - - 095ad4d096d1 - da6bd1975a71 - - f4230f116196 - c8cdde00b105 + - f4230f116196 - 710301bc46fa + - 6ca543ec1bf8 + - 095ad4d096d1 + - 27ee142314a9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -80,15 +80,15 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 7255688c77f3 - 8e214e52e461 + - 7255688c77f3 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: enumerate_charges owner: bgruening revisions: - - 67ee76f0e497 - 2a868592ebcb + - 67ee76f0e497 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -106,84 +106,84 @@ tools: - name: gmx_editconf owner: chemteam revisions: + - 0fac8e2afc13 + - 88076940fa94 - bfb65cb551d8 - 3b8a9d5ced85 - 79cfd9ead848 - - 88076940fa94 - - 0fac8e2afc13 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - 55918daa5651 + - d532b7e5f64b - f5d979cb4b54 - eb6564a60136 - - d532b7e5f64b - - b46d4b4d995c - 715cd0e87781 + - 55918daa5651 + - b46d4b4d995c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - d2f955aea23a - 5579659312e6 - - f26afd1b7104 - - fdf2cc80adb5 - 97872d87ba80 + - fdf2cc80adb5 + - 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 - ed736e6eee39 + - 070e3ecc3fda - cac1886249a2 - - 4da9ee404eab tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - da8753545526 - - f197e34c33a9 - - d1f803b5943c - - 525ca7c8065f - - 807aa4c9293d + - 73008ef1f487 - c0c9a5024177 + - f197e34c33a9 - 2e219a2d9327 - - 73008ef1f487 + - 807aa4c9293d + - 525ca7c8065f + - d1f803b5943c + - da8753545526 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - c4fbab8e03c5 - - 61094e01eff9 + - 27ea4e1a3f95 - 1809414a9454 + - 61094e01eff9 + - c4fbab8e03c5 - 7568ae18908a - - 27ea4e1a3f95 - 2c8ed1b52bf7 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: + - ba83f0923369 - 79e8ab8f1e81 + - 730ef07b90ae - ccfbd956a2d3 - d7ec25187599 - - ba83f0923369 - - 730ef07b90ae tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -202,8 +202,8 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: - - b59c91adeac1 - 1400d1977e7b + - b59c91adeac1 - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -234,9 +234,9 @@ 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 31370c2ce..3bc42ef7c 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -2,9 +2,9 @@ tools: - name: diffbind owner: bgruening revisions: - - 163688bb8f73 - fa56d93f7980 - c97a786e8fb5 + - 163688bb8f73 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -22,17 +22,17 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 11cf21ee4242 - 4124781932db + - 11cf21ee4242 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: - - 86e2413cf3f8 - f5d67c722d67 - - 495a4173006f + - 86e2413cf3f8 - 424aefbd7777 + - 495a4173006f - 640d3af5d833 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -52,9 +52,9 @@ tools: - name: sicer owner: devteam revisions: - - 74c9214cc8e6 - - 5c2cc3b58c7d - 4a14714649b4 + - 5c2cc3b58c7d + - 74c9214cc8e6 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 996452b4d..2703a8f7e 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 - - 33151a38533a - 830961c48e42 - 25136a2b0cfe + - 90981f86000f + - 33151a38533a tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -26,14 +26,14 @@ tools: owner: bgruening revisions: - baabc30154cd - - 6cbe2f30c2d7 - 0046692724f9 + - 6cbe2f30c2d7 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 57f0914ddb7b - 38eec75fbe9b + - 57f0914ddb7b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index b5f962286..7e6cbb4f7 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -8,37 +8,37 @@ tools: - name: biom_add_metadata owner: iuc revisions: - - f3a19509108a + - 5e1240a87bcb + - 4a6ee918c13a - a3b86937ead6 - - 6ef0b5664c69 + - 367b1ed91207 - dad9da48a09a - - 4a6ee918c13a - e3cbd2287f63 - - 367b1ed91207 + - f3a19509108a - 0b3c3ad92827 - - 5e1240a87bcb + - 6ef0b5664c69 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - bd46669113b9 - - 33c99804a32f - 584008e574b2 - - 501c21cce614 - - 1b5fc03380d4 + - 54ccb7e1f49a + - e525f9ffb9ac + - 33c99804a32f - 72ed72122deb + - bd46669113b9 + - 1b5fc03380d4 + - 501c21cce614 - e177a8ea0bf1 - a4db66553a61 - - e525f9ffb9ac - - 54ccb7e1f49a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 owner: iuc revisions: - - 11c3eb512633 - a0d092f27fdf + - 11c3eb512633 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: compress_file @@ -50,16 +50,16 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - e7ed3c310b74 - 7e801ab2b70e + - e7ed3c310b74 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: - 8979c288aefb - - 186b8d913e6c - 77b41c89d856 + - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular @@ -78,8 +78,8 @@ 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 @@ -91,9 +91,9 @@ tools: - name: gffread owner: devteam revisions: - - 3e436657dcd0 - - 154d00cbbf2d - 4dea02886337 + - 154d00cbbf2d + - 3e436657dcd0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -111,8 +111,8 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - 8190f6083c0d - f5c632894818 + - 8190f6083c0d tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - 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- 32e451def88c - - f264afa9fa6f - - 2c66e43f1c86 - - bad3ca889618 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 56bce3c82278 - - 7fda5607e777 - 231994413f89 - - 3b9d990a0a0e - 4e12ea27f788 + - 3b9d990a0a0e + - 7fda5607e777 - 7e361d147872 + - 56bce3c82278 - 9368fbc49c8b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - 4431f39ede55 - - ce4ce3316f74 - - d9114ef1c8a5 - - b1779366c8e9 - 94ca68515826 + - b1779366c8e9 - c03c3384cd81 + - ce4ce3316f74 - e65d16fb2724 + - 4431f39ede55 + - d9114ef1c8a5 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 793665fff0f8 - d57251071381 + - 23f7c5f1fdaf + - 793665fff0f8 + - 4ed32329e0ed - b88ebb3672a1 - 2da482e408b8 - f8fc4e5aff9d - - 4ed32329e0ed - - 23f7c5f1fdaf tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: + - a7849312d328 - a4dfb122e52b - - ba6efa77fb79 + - 512155688d98 - e4c7985d4585 - - a7849312d328 - 010e58e9d822 - - 512155688d98 + - ba6efa77fb79 - 25d830337d31 - c60570fa602f tool_panel_section_label: DeepTools @@ -184,23 +184,23 @@ tools: - name: deeptools_plot_pca owner: bgruening revisions: - - c899e0ccff8c - - aa200e4f3939 - - 00d869ea03a1 - 4d678170d29b - - 443d9a9d6d11 - 69264da0ce77 + - 443d9a9d6d11 - 38e3f226248b + - c899e0ccff8c + - 00d869ea03a1 + - aa200e4f3939 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - aac8444d6681 - - 10301d137111 + - d806504e96d9 - 6662b1a8d326 + - 10301d137111 + - aac8444d6681 - c361b12d207a - - d806504e96d9 - a2d70c4fd406 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 c4dc1576b..6bf9a8305 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -51,15 +51,15 @@ tools: - name: obi_stat owner: iuc revisions: - - 39320fee9d70 - 723a93febe89 + - 39320fee9d70 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab owner: iuc revisions: - - 5f7003111e32 - 3299c7d5268f + - 5f7003111e32 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index 42a614fb1..9e65a9209 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -3,8 +3,8 @@ tools: owner: devteam revisions: - ce385837c160 - - dba489bfcd62 - 832c20329690 + - dba489bfcd62 - 63dd26468588 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index 1d62e8a20..e7f187ab1 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -3,9 +3,9 @@ tools: owner: iuc revisions: - 29bdbc353f20 - - d82648ad25a3 - 62f5fab76dfb - 6da3972210ee + - d82648ad25a3 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -17,7 +17,7 @@ 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/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 02dca4000..88366bc18 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -8,22 +8,22 @@ tools: - name: cutadapt owner: lparsons revisions: - - 8665bcc8b847 - - de6cebe3c043 - 4e5056fefd88 - - 44e2cc14f75b - - c4b82dce8335 - - c053d4cad713 + - 5915ea1ec9b1 - 135b80fb1ac2 - - e4691e1589d3 - - 49370cb85f0f - 093678460093 - - 48f587c13075 - - 5915ea1ec9b1 - 8c0175e03cee + - 8665bcc8b847 - 288f97432497 - - 660cffd8d92a + - c053d4cad713 - c5e2e5902201 + - c4b82dce8335 + - 49370cb85f0f + - 48f587c13075 + - 660cffd8d92a + - e4691e1589d3 + - 44e2cc14f75b + - de6cebe3c043 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -36,8 +36,8 @@ tools: owner: devteam revisions: - 8889eb864cef - - 9db07fd39f85 - f666895cbebd + - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -49,15 +49,15 @@ 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 owner: devteam revisions: - - 25b8736c627a - 717aee069681 + - 25b8736c627a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_extract @@ -76,9 +76,9 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 516b97a23d7e - 859422bcb689 - 9457a20156db + - 516b97a23d7e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -97,9 +97,9 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: - - f773e98b26cf - - ec0b5076173a - f81d4362b6c1 + - ec0b5076173a + - f773e98b26cf tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -111,10 +111,10 @@ tools: - name: fasta_stats owner: iuc revisions: + - 56022eb50bbd - 0dbb995c7d35 - cd0874854f51 - 9c620a950d3a - - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -126,8 +126,8 @@ tools: - name: fastp owner: iuc revisions: - - dbf9c561ef29 - 65b93b623c77 + - dbf9c561ef29 - 1d8fe9bc4cb0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -154,8 +154,8 @@ tools: - name: fastq_groomer owner: devteam revisions: - - 8611b80a14d6 - 47e5dbc3e790 + - 8611b80a14d6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation @@ -175,30 +175,30 @@ 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 owner: devteam revisions: - - 2ccb8dcabddc - 3e396e702cea + - 2ccb8dcabddc tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner owner: devteam revisions: - - 09a2199cd356 - c885369b207b + - 09a2199cd356 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - - 249c8393f2d4 - - 35e38452bb3f - e39cc71d3ed6 + - 35e38452bb3f + - 249c8393f2d4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -211,8 +211,8 @@ tools: owner: devteam revisions: - 045f0e1043f7 - - 54053ea6c77e - 74db4cffab1f + - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -224,8 +224,8 @@ 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 @@ -244,10 +244,10 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 567d5b3c52b1 + - 09070cacefd8 - 529bccd5e4a1 + - 567d5b3c52b1 - d5e9e83cd3d8 - - 09070cacefd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter @@ -259,9 +259,9 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: + - 8abdedf55101 - 4bedca26c133 - 0b7ec11b3c7c - - 8abdedf55101 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter @@ -273,10 +273,10 @@ tools: - name: fastx_clipper owner: devteam revisions: - - bdf1ce174e39 + - 90858c306551 - 736b8f6ee456 - cb1e251cac37 - - 90858c306551 + - bdf1ce174e39 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -302,8 +302,8 @@ tools: - name: fastx_renamer owner: devteam revisions: - - 3599f5451ee2 - f984bb114520 + - 3599f5451ee2 - 02f8a17a4ebd - b29d37ca9e41 tool_panel_section_label: FASTA/FASTQ @@ -317,10 +317,10 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: - - 177f0621c266 - - 6027ef51ef91 - e246088b6e34 + - 177f0621c266 - 0c2907307ba4 + - 6027ef51ef91 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement @@ -332,10 +332,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: - - 73194cdd4f57 - 377ac2829eac - - 547e8d00f11c + - 73194cdd4f57 - 61b4cedc8934 + - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -359,8 +359,8 @@ tools: - name: pear owner: iuc revisions: - - b4c6f054210a - 2f804526f5fd + - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -379,8 +379,8 @@ tools: - name: seqtk owner: iuc revisions: - - 3da72230c066 - 4b494533146a + - 3da72230c066 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -398,8 +398,8 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - 51b771646466 - dfa082f84068 + - 51b771646466 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -418,11 +418,11 @@ tools: - name: umi_tools_count owner: iuc revisions: - - e654095ab143 + - a535cf1e5da4 - b557acca0b56 - 8250ea3a1501 - - a535cf1e5da4 - 24013bf85a6f + - e654095ab143 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -440,12 +440,12 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - f3759eec3018 - - 6a675c3aa610 - 828dba98cdb4 - - 7accf7407811 - 9fa7803d1c51 - 27ac32a22ad2 + - 7accf7407811 + - f3759eec3018 + - 6a675c3aa610 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 1575b13b5..f408cdd49 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,28 +2,28 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - e41385662e5e - - ce9cd02d5b88 - - 7b4468117008 - 64e9a6afdd0c + - 7b4468117008 + - ce9cd02d5b88 + - e41385662e5e tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - 8050e091e99b - c64d534a763c + - 8050e091e99b tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - 3d0c7bdf12f5 + - 9da02be9c6cc - 2b0c9d9fc6ca + - ff9530579d1f - f2e8552cf1d0 - e7b2202befea - - ff9530579d1f - - 9da02be9c6cc - 5ec9f6bceaee tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu @@ -37,46 +37,46 @@ 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: - cc0fd298cc17 - - 7306ec78632a - 59003d0543cd + - 7306ec78632a 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: - 75c93c70d094 + - 1c2db0054039 - abfd8a6544d7 - bf675f34b056 - b2f1f75d49c4 - - 5e33b465d8d5 - 9a913cdee30e - 3d93dd18d9f8 - - 1c2db0054039 - f7985e0479b9 + - 5e33b465d8d5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - cd7e644cae1d - - 949f01671246 - 084bbd8ba7b8 + - 949f01671246 + - cd7e644cae1d tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/filter_and_sort.yml b/staging.gvl.org.au/filter_and_sort.yml index d934ded82..9243d596c 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: - - 85ef5f5a0562 - 141612f8c3e3 + - 85ef5f5a0562 - 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 4358a06b3..78a05789a 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -2,8 +2,8 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 142d95ab942e - 3630a6e624d4 + - 142d95ab942e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend @@ -16,16 +16,16 @@ tools: - name: gemini_annotate owner: iuc revisions: - - f2f3bc622a16 - - 8f53b238a360 - 0c8f7322f8fc + - 8f53b238a360 + - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden owner: iuc revisions: - - 1a4c5adcd587 - df57188562f0 + - 1a4c5adcd587 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets @@ -45,8 +45,8 @@ tools: - name: gemini_de_novo owner: iuc revisions: - - 9db3e299b1c8 - d5b01cc263be + - 9db3e299b1c8 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -86,16 +86,16 @@ tools: - name: gemini_load owner: iuc revisions: - - cf61daf064fe - 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 @@ -108,8 +108,8 @@ tools: - name: gemini_pathways owner: iuc revisions: - - 9199331c3421 - 6b09debcfc49 + - 9199331c3421 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -122,8 +122,8 @@ tools: - name: gemini_query owner: iuc revisions: - - da74170c55c7 - 840fb4850be3 + - da74170c55c7 - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu @@ -144,28 +144,28 @@ tools: - name: gemini_roh owner: iuc revisions: - - 345d41f3f574 - 93967598e18e + - 345d41f3f574 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic owner: iuc revisions: - - e4e2128460e3 - ef9991a4a9a7 + - e4e2128460e3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats owner: iuc revisions: - - 5c9efee9cb1e - ee894347fcd6 + - 5c9efee9cb1e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower owner: iuc revisions: - - 8f04952b8882 - 0c58ba91d018 + - 8f04952b8882 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 6e2bcd639..c5b84e945 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.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 @@ -16,15 +16,15 @@ tools: - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway owner: iuc revisions: - - 39a996d44e16 - 9744e1124d0f + - 39a996d44e16 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index 9a72cb3ea..69d1fca8b 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,56 +2,56 @@ tools: - name: dbbuilder owner: galaxyp revisions: + - c1b437242fee - 983bf725dfc2 - e9df53a75f3c - b39347891609 - - c1b437242fee tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download owner: iuc revisions: + - 28587613264f - 1c58de56d587 - e063168e0a81 - - 28587613264f tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - f5ea3ce9b9b0 - 6ea73833cf67 - - 4317d3cb6cba - - 83c7d564b128 - - c441583adae5 - - aad3885b3216 - - 4df8de2d0e48 + - f5ea3ce9b9b0 - 69ebb7f46e45 - - 653e89d73fc4 - - 9a776b080193 - - e407b9da183a - 6591f049cf7e - - 7068f48d0ef9 - - e08a7ad4378b + - 4df8de2d0e48 + - 653e89d73fc4 - 5e6237d58b0c + - 83c7d564b128 + - aad3885b3216 - 1790dcf3c32d + - 7068f48d0ef9 + - 4317d3cb6cba + - c441583adae5 - 734abc7ac21d + - e407b9da183a + - 9a776b080193 + - e08a7ad4378b tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 7863f1abcdda - 34758ab8aaa4 - - 75b3b3d0adbf - 9aaa46d45472 + - 75b3b3d0adbf + - 7863f1abcdda tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - bfdc6a7ffd3a - - 054483e27a35 - af5eccf83605 + - 054483e27a35 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index 3bf9fe99a..9df186d2f 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -4,12 +4,12 @@ tools: revisions: - 7f13dc906cb9 - ae9994cf526f - - 4b519282a05b - df7356989ac1 - - c4bde687c846 - 290a11559985 - - fd59d783248a - a64dc31ab7f2 + - fd59d783248a + - c4bde687c846 + - 4b519282a05b - 740057a5126d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -34,9 +34,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - f95284aa2946 - - 7cf5b1d072b5 - 867ab348287d + - 7cf5b1d072b5 + - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -49,30 +49,30 @@ tools: owner: iuc revisions: - 53460afd5115 - - ca7cb0eaad62 - - 3b37b1b1c3a7 - '566197475670' + - 3b37b1b1c3a7 + - ca7cb0eaad62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - d3a9e32672ec - da4c086cff5b - 10515715c940 - 391a4cc45fea - 3d059e9c2fba + - d3a9e32672ec tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 299307abd804 - - 3b12bf9b4b87 - - d0fc8b746d57 - 5fe1dc76176e - - 1acf88921176 - e3a675da7fd0 + - 3b12bf9b4b87 + - 1acf88921176 + - d0fc8b746d57 + - 299307abd804 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -84,8 +84,8 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - cf1df6b2220a - 5d6f8f0bef7c + - cf1df6b2220a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan @@ -98,24 +98,24 @@ tools: - name: histogram owner: devteam revisions: - - 6f134426c2b0 - cdb9e89e2970 + - 6f134426c2b0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: jbrowse owner: iuc revisions: - a6e57ff585c0 - - 667e17248bfe - - 4542035c1075 - - 6cd09d7b5f37 - - 2bb2e07a7a21 - 1cfc579079a6 - - 836d1aa3e89a + - fd5dbf0f732e + - 667e17248bfe - ca2def38369c - 112eb40ba6cf + - 4542035c1075 - 17359b808b01 - - fd5dbf0f732e + - 6cd09d7b5f37 + - 836d1aa3e89a + - 2bb2e07a7a21 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -133,9 +133,9 @@ tools: - name: pathview owner: iuc revisions: + - 03c13085aecc - f1691de443a7 - fe154a7af404 - - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -167,8 +167,8 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 0a10fddd97d2 - 44c66e8d21e6 + - 0a10fddd97d2 - 7c9417381ad5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -181,22 +181,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 360df4999907 - - 14e7c35f3d00 - 326a3db8d9d1 + - 2824d77cd8f8 + - 59fd173ac850 - 7dd841a32245 - - 4ac4e7083b7e - a1abfa420d9d - - 59fd173ac850 - - 2824d77cd8f8 + - 14e7c35f3d00 + - 4ac4e7083b7e + - 360df4999907 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: + - 83c573f2e73c - 73b8cb5bddcd - 44608d0193ed - - 83c573f2e73c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index 787c2a488..48e3e9ec5 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph @@ -82,8 +82,8 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 94697510d55f - 9a2f72d7dbd2 + - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet @@ -173,8 +173,8 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - 0f98603d0116 - 767a675b5254 + - 0f98603d0116 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 00ca6470e..4a584124c 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,17 +2,17 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: + - 921a2da49a0c - ed2cca6b5de4 - 29f66c353bcb - 9edf8894a22d - - 921a2da49a0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 5746d61f0a91 - ec4b948dc6f0 + - 5746d61f0a91 - 78fb5e286609 - d404277cc87a tool_panel_section_label: HiCExplorer @@ -20,27 +20,27 @@ tools: - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: + - 03dd3c16ae4e - 4d511437b1e5 - - 977dc15add20 - 9e357a8b2ec3 - - 03dd3c16ae4e + - 977dc15add20 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - 77919cc3618e + - 0ba4f56a3613 - 3b5b54ed6392 - 41dbf4d162a2 - - 0ba4f56a3613 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - 5308ca68ef3d - - b63363075c2e - - 9939786dd9c9 - 7babd8a46fe0 + - 9939786dd9c9 + - b63363075c2e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index 6ee6e963d..398b937d9 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,23 +2,23 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: + - 81f0cbca04a7 - 3df9f0a4bf34 - 0c777d708acc - - 81f0cbca04a7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 0a53256b48c6 - 5791a7f65275 + - 0a53256b48c6 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - e576b73a2e2f - 6ad1d3cfdea1 + - e576b73a2e2f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization @@ -31,16 +31,16 @@ tools: - name: 2d_simple_filter owner: imgteam revisions: - - f70b215d155c - dba87c4b32d3 + - f70b215d155c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - - 10eed33aa9b2 - 85edbb7a436b - f3360fbeda64 + - 10eed33aa9b2 - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -54,17 +54,17 @@ tools: - name: count_objects owner: imgteam revisions: - - b58447a2eed2 - - 5bf8eb50b280 - 664232d2a3f7 + - 5bf8eb50b280 + - b58447a2eed2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - e917a2424690 - eb6c08714244 - 0e4dccaafef5 + - e917a2424690 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -77,8 +77,8 @@ tools: - name: cp_common owner: bgruening revisions: - - 6070780813d9 - 670975e92458 + - 6070780813d9 - e7273daa5ae2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -93,8 +93,8 @@ tools: - name: cp_display_data_on_image owner: bgruening revisions: - - 5d28ac336861 - 6a7da2e5f696 + - 5d28ac336861 - 2484086dee41 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -109,25 +109,25 @@ tools: - name: cp_export_to_spreadsheet owner: bgruening revisions: - - d0178bdcd00e - f24c370e5ea4 + - d0178bdcd00e - f8fa0f6718a3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: + - 31d195bedf6d - ad271f78a87a - 3245681b2f6d - - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - b6eec6087271 - 87d4d92d7487 - 993faa34333b + - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math @@ -150,55 +150,55 @@ tools: owner: bgruening revisions: - 2564f461de62 - - a1a961c46d4b - ac5bea85a391 + - a1a961c46d4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 91e03287f285 - 20dbb1f7ec7b - a32c3f810ade + - 91e03287f285 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - 5499dc6f8ac1 - - b64af54c5c09 - 8536b1ae0254 + - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - d3890df07463 - - 6f4715b8540a - e972e07c7845 + - 6f4715b8540a + - d3890df07463 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - e52c75a28c4b - 407925835dd9 - 980aed9e8fd5 + - e52c75a28c4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - d85f11570109 - - acf3aa487283 - 79e10d12d90a + - acf3aa487283 + - d85f11570109 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - b76841ee5560 - 80b200ae516b + - b76841ee5560 - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -212,16 +212,16 @@ tools: owner: bgruening revisions: - 48102a685037 - - 3a3033222f61 - 8083a87d2fdf + - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - - 4ecf93628f97 - - 33f4fa1413fb - 27edbb90ab2b + - 33f4fa1413fb + - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -233,21 +233,21 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 972d2c365739 - 1fd453cd757b + - 972d2c365739 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info owner: imgteam revisions: - - 236ec78b2e53 - 7b6d9412c7f8 + - 236ec78b2e53 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_segmentation_mask owner: imgteam revisions: - - 22e573b7dcb1 - 8ad39f493587 + - 22e573b7dcb1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index c349e8307..e4691cbcf 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,29 +2,29 @@ tools: - name: ivar_consensus owner: iuc revisions: - - f362150bef41 - 3e4f434a69c6 - - e4ee04da1c19 - - 1069f6db0a0e - - 78bbd17d0703 - - 17f911830a8c - a38934e303b9 - - e319b5b65879 + - 78bbd17d0703 - d6e72da3ec35 + - e319b5b65879 + - 17f911830a8c + - f362150bef41 + - e4ee04da1c19 + - 1069f6db0a0e tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: + - 2b95d5c04908 + - f91cfb73d369 + - c88553ec696e + - 72ddd32392cd - 7fe36019c073 - 8f8df367470d - - 0135f1d487a0 - 9537184d421f - - c88553ec696e - - f91cfb73d369 - 1ef5b6e3e09d - - 72ddd32392cd - - 2b95d5c04908 + - 0135f1d487a0 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked @@ -39,51 +39,51 @@ tools: - name: ivar_removereads owner: iuc revisions: - - bd2a7d1316b9 - - 7f1cfa4c0e32 - ee29337f905c - - 94df24c6bc00 - - 9eaadf03e0df - - 8c05afb547fa - - 3d18f8c3c0f6 - - ee2beb764a7b - - 28a6f1908fcc - - 69797fa273c3 - 43aac8d29685 - 6a1515bb0687 + - 28a6f1908fcc + - 69797fa273c3 + - ee2beb764a7b + - 94df24c6bc00 + - 3d18f8c3c0f6 + - 8c05afb547fa + - 7f1cfa4c0e32 + - 9eaadf03e0df + - bd2a7d1316b9 - 8d36959b000d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - c092052ed673 - - 364f4ffec275 + - db536ad45f28 - e3bb03cf207a + - 0893a1dbb807 + - 364f4ffec275 - d37ede8589b2 - 8858fa037a15 + - 5671e1d3d5ee - 9f978da6528a - - db536ad45f28 + - c092052ed673 - cb903c9dc33d - - bcaa0d571ce2 - - 5671e1d3d5ee - 5d6ed46cc101 - - 0893a1dbb807 + - bcaa0d571ce2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - c5c9f02b6167 - - 3b6a16d82c1b - - e1a015876aa9 - - 045d6d00f606 - ed28dd32141c - - f95f403841ad - - 12d66d0d05ac + - 045d6d00f606 - 230b05597996 - 49236b03e4fd + - c5c9f02b6167 + - 12d66d0d05ac - 584beffa972b + - f95f403841ad + - 3b6a16d82c1b + - e1a015876aa9 - 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 84681fd6c..6b29f0d02 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: - - 0f1724dd59d2 - - f198773344e4 - b8a457820315 + - f198773344e4 - 17e3b698dd52 + - 0f1724dd59d2 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - a513e3fbb4c5 - - 22c2a1ac7ae3 - ac092723240d - 374cb875d38a + - 22c2a1ac7ae3 - 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 ce31ebc2c..3fb3aa762 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,36 +2,36 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 772e0e89fc68 - 522137aaa9c4 - 66d7efc06000 + - 772e0e89fc68 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - f22a9297440f - - 4d81e3e2fb63 - 8a794e6d3388 + - 4d81e3e2fb63 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - b6ef6d0cb6b7 - - 818f9b69d8a0 - f1b9a42d6809 - - 2af1346e68c9 - e1317b5502fa + - 818f9b69d8a0 + - 2af1346e68c9 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 05143043ca13 - c80db5d6fd8c - 8334dc98c48e - 1588f9076e32 + - 05143043ca13 - 947c2eacccb8 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -39,62 +39,62 @@ tools: owner: bgruening revisions: - 25b46af53232 - - 83228baae3c5 + - 9991c4ddde14 - 29e4122c90de + - 83228baae3c5 - 1552b8cb4a94 - - 9991c4ddde14 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 1a53edc4b438 + - a07ab242b0b5 - 841a6cc5fc58 - f3dfa4bdf87e - - a07ab242b0b5 - - 060ca94ac049 + - 1a53edc4b438 - 53616c8b0865 + - 060ca94ac049 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 91c4e3331208 - - 927586a18553 - - 2fc89dcd41c8 + - dc4b5fd604a6 - d4808d5b83da - 40f4447733b2 - - dc4b5fd604a6 + - 2fc89dcd41c8 + - 927586a18553 + - 91c4e3331208 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 301e07345c93 - 7626ea9c2e1b - - 25ab6b4e376e + - 301e07345c93 - e5a5ad882f1f - - 36e8d6d5d01b + - 25ab6b4e376e - c6ae57f774c6 + - 36e8d6d5d01b tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: + - 02d2be90dedb - f9639b488779 - - 0630258dcf35 - 4ed102b922cb - - b7c3e9a3b954 - - 02d2be90dedb - 80852884053f + - b7c3e9a3b954 + - 0630258dcf35 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 14180f9c831e + - caeb57858702 - ec69cbe34b73 + - 14180f9c831e - 61634a87efc7 - - 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 9ee132b10..076d039d8 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -6,11 +6,11 @@ tools: - a6d65b0c67af - cd659e8cc5fa - 017aba02828d - - 17062a0decb7 - - 749c918495f7 + - 937aa69e715f - f6877ad76b00 - 03e9b2fbc005 - - 937aa69e715f + - 749c918495f7 + - 17062a0decb7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -30,8 +30,8 @@ tools: owner: devteam revisions: - e188dc7a68e6 - - 3fe632431b68 - 64f11cf59c6e + - 3fe632431b68 - 53646aaaafef - dfd8b7f78c37 tool_panel_section_label: Mapping @@ -45,43 +45,43 @@ tools: - name: lastz owner: devteam revisions: - - 37b497aa133f - - 3e1ea2facca6 - - e7f19d6a9af8 - 2ff111fac1d7 - 60afcc2c1d05 + - 3e1ea2facca6 + - 37b497aa133f + - e7f19d6a9af8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: + - be1d967337e4 - 11a0d50a54e6 - - 8c6cd2650d1f - 6b1e195506a3 - f54f5baedfdd - - b3eab4b67562 - - 3f4d6399997b - - c0c2d0941de8 - 037c6e54df11 - - 77b2770508f6 - - be1d967337e4 - 09b53c1d4ab1 + - 3f4d6399997b + - 77b2770508f6 + - b3eab4b67562 + - c0c2d0941de8 + - 8c6cd2650d1f - 53c0b7a1a0c3 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 178bdbdb6d24 - 1cd2511a396e - - 5ef7ec16b04f - - 00fbfac99d39 - - 13022c3d3076 - - ec9cbd6b9a49 - - 79b885ce78d7 - - e403d27e8f24 - b8f5f6e87f5c + - 79b885ce78d7 - 9ee34ba73ebf + - ec9cbd6b9a49 + - 00fbfac99d39 + - 5ef7ec16b04f + - 178bdbdb6d24 + - e403d27e8f24 + - 13022c3d3076 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index e33b23f41..85d8ce24a 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -35,17 +35,17 @@ tools: owner: iuc revisions: - 7c2100246a2f - - 76d3d2b10738 - 63f86089423e - 5b5a7af9fbb4 + - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: + - 1c35dadbe76f - 84fd33a60b35 - 18a502a9d287 - - 1c35dadbe76f - 96336c6a2bb7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -62,70 +62,70 @@ tools: owner: iuc revisions: - 0776d824d896 - - 75403243703a - 04c15826a0b8 + - 75403243703a - 8c202e741d68 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: + - 43c99742158b + - 8470de786d47 - 1c9b3bcd4261 - e96bbb9e24ea - - 8470de786d47 - - 43c99742158b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 84743da21318 - 1d75bd0595e2 - 306a40d4bb8f + - 84743da21318 - 5c865a382933 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - 555ccac8a4c5 + - 8daf4564ccda - 78faebd0879c - ac72310b038a - - 8daf4564ccda + - 555ccac8a4c5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - a58e4a43f49c - d60df8727f59 - f947b4bb5107 + - a58e4a43f49c - 7b8cb2b02978 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 7f3b59dee073 - 04144473e59e - - 1bc3657cd694 - 7136e9ab70db + - 1bc3657cd694 + - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - 0a1224c4b781 - - 9058d8943303 - 19299bb1c6af + - 9058d8943303 - d943081510da tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - e005e659ae21 - c7e73acfa3eb + - e005e659ae21 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf @@ -139,16 +139,16 @@ tools: - name: hifiasm_meta owner: galaxy-australia revisions: - - fa35f1106d3e - 15dbb444df71 + - fa35f1106d3e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: - 654548ae1357 - - 6d364c65c946 - 6c84982ee6f7 + - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -160,25 +160,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - e66ab198ec15 - 6aad8ca3918b + - e66ab198ec15 - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - d77397f09da1 - c6676a890f50 - b084117133af + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - 7f208f1eb64f - - cad93abecac9 - 9704f1a3b32d + - cad93abecac9 + - 7f208f1eb64f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -190,51 +190,51 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - 31c6d107e7a5 - - e88b731dad59 - 79706f10d680 + - e88b731dad59 + - 31c6d107e7a5 - c409a495841f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: + - 172920f67a84 + - 714d5a28cc5c - 71ea608ddfa3 - 094ad9c068af - - 714d5a28cc5c - d24841f5c3d2 - - 172920f67a84 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - a4d7148ccee4 + - d7e9a3c41657 + - 12fb63b5f63f - 4137b492233e - a293a742194f - - 12fb63b5f63f - - d7e9a3c41657 + - a4d7148ccee4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: - - e2c71b852aba + - 97f7bb0851e7 - 64bc7acc22a9 - 75bedfb2078b - - 6fcb8ac37a3e - - 97f7bb0851e7 - cf87759761eb + - e2c71b852aba + - 6fcb8ac37a3e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - - 080ea153677c - c82508e76ad1 + - 080ea153677c - 5e5a999ffaa9 - - 2d35528d2141 - 4033827c76b8 + - 2d35528d2141 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann @@ -242,8 +242,8 @@ tools: revisions: - 95bf7479d53c - 2cd76b089570 - - fc6c328c292f - 6b7622dda516 + - fc6c328c292f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan5 @@ -309,8 +309,8 @@ tools: - name: kraken2 owner: iuc revisions: - - 4a9da2b6c2e3 - 328c607150ff + - 4a9da2b6c2e3 - e674066930b2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -337,8 +337,8 @@ tools: - name: kraken_report owner: devteam revisions: - - 6c09bed3444f - 1902d3de4a4f + - 6c09bed3444f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -350,8 +350,8 @@ tools: - name: kraken owner: devteam revisions: - - 8ba2174315aa - aec58624706f + - 8ba2174315aa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -388,19 +388,19 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 27250f92a01a - - 4fd3b5d8706b - 0270541aaf46 - - 2cff76cf35c6 - e073891b2afc + - 4fd3b5d8706b + - 27250f92a01a + - 2cff76cf35c6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: + - 708abf08a626 - 76bc4efa1aeb - eb50e7eca3dc - - 708abf08a626 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -466,19 +466,19 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - fdbd63e92b01 - ebb74774457e + - fdbd63e92b01 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - 2131d7dca455 - - 1a6cdf55390f - - ff8f55893e7d - - a16313517e55 - a92a632c4d9b + - a16313517e55 - 6dee4abadccb + - 2131d7dca455 + - ff8f55893e7d + - 1a6cdf55390f - b89b0765695d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -551,8 +551,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 9168545e09df - 0ba7dfaa941d + - 9168545e09df tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -570,8 +570,8 @@ tools: - name: picrust_normalize_by_copy_number owner: iuc revisions: - - 2e62e32d4f33 - 3bd5f5afb9b1 + - 2e62e32d4f33 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_predict_metagenomes @@ -601,13 +601,13 @@ tools: - name: staramr owner: nml revisions: - - 141afacabcfa - 4d83eccf5f81 - - 3b22de20bd4b - 2fd4d4c9c5c2 - - aeaa20b96ef2 + - 3b22de20bd4b + - 141afacabcfa - be818ae858e4 - 4b9a8031ab74 + - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -638,7 +638,7 @@ tools: owner: iuc revisions: - 9495df9dd6ef - - b3c7199d8786 - 576963db5f1b + - b3c7199d8786 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 9b6a140d4..46e11a4be 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - 12e856482d26 - de3cfb122105 + - 12e856482d26 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - f4d7d5755f01 - 63b74bfc8052 + - f4d7d5755f01 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 2553ea7d5..6c7b9cad1 100644 --- a/staging.gvl.org.au/multiple_alignments.yml +++ b/staging.gvl.org.au/multiple_alignments.yml @@ -2,37 +2,37 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: + - 2263989660f5 - a74dbfee5a86 + - 9eeb13a92d79 + - 80f03df2e2ce + - 8b67dd48fec1 + - 94b8c6013083 - 6ae5a7b5a0a2 + - 9422c5a87ee2 - bdfbaf0c10aa - - 94b8c6013083 - 9baa871cb1d1 - 48c13389050d - - 8b67dd48fec1 - - 2263989660f5 - - 9422c5a87ee2 - cd07731e4434 - - 9eeb13a92d79 - - 80f03df2e2ce tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - 3ff17bad4006 + - bc3831dd65c1 + - f14193ec1f50 - aaa0d6a8b808 - - c18157c68134 - - d7ce0ec78e51 - 2e093badc689 - - f14193ec1f50 + - f0af8936ed41 + - d7ce0ec78e51 - fc2e49f91e52 - 4a60927aaca5 - 5abf2c2249aa + - d390fe1567dc + - c18157c68134 + - 3ff17bad4006 - be78f13134e2 - '764845535798' - - d390fe1567dc - - f0af8936ed41 - - bc3831dd65c1 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -44,8 +44,8 @@ tools: - name: chromeister owner: iuc revisions: - - e483be1014b6 - b768cc4cca40 + - e483be1014b6 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -65,18 +65,18 @@ tools: owner: rnateam revisions: - f1a5908ea2cb + - a65296ffb4a0 - 15974dd17515 + - c5908940967d - 6f28e90db932 - - a65296ffb4a0 - f0d493f8f84f - - c5908940967d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - fbca557a4847 - b3acbb3a6af0 + - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff @@ -110,7 +110,7 @@ tools: - name: mummer_show_coords owner: iuc revisions: - - 959c1f8dae95 - b4124df98b26 + - 959c1f8dae95 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index ff6ca2e46..f8599c399 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,42 +8,42 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: + - 72b5e9dda577 - 0e9e7fcdd543 - fc8804320156 - - 79e9a869f40e - - a7228a7ea146 - - 72b5e9dda577 - cb34f00cc10f + - a7228a7ea146 + - 79e9a869f40e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - 18505fe2bdb1 - d6cddc06aeae - - fa11aa8103b2 - db25ec99c3ea + - fa11aa8103b2 + - 18505fe2bdb1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: - - 222669c4afb6 - - 0f5f4a208660 + - 43815fa60f3a - 2bf63b38ee9b - - ec699520444c - - edf6d4003fad - eb746fa6f514 - - 43815fa60f3a - cc36773a3681 + - 0f5f4a208660 + - edf6d4003fad - 19f3b583a9b3 + - ec699520444c + - 222669c4afb6 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - c0fb573c1e8d - b833eff63b10 + - c0fb573c1e8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -56,8 +56,8 @@ tools: owner: iuc revisions: - 645159bcee2d - - edbb6c5028f5 - a3c4fe6f49ab + - edbb6c5028f5 - 0f1c34698076 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -65,47 +65,47 @@ tools: owner: bgruening revisions: - 85a394edc247 - - d219b6d8158a - 3b6f94fc7e1d + - d219b6d8158a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - 90a922f32523 - - a8d4be409446 - be95355fef8d + - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: + - 4857d5bcce52 - 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 + - a3afc5f0a96c + - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - 5f76b20953e5 - - 93d623d9979c - 543cbeef3949 + - 93d623d9979c 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 @@ -130,8 +130,8 @@ 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 @@ -150,8 +150,8 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - ce8af9373061 - 34553d0caa5e + - ce8af9373061 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index 9b1349e61..921e41712 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -14,8 +14,8 @@ tools: - name: bcftools_plugin_color_chrs owner: iuc revisions: - - 71186bb66ca2 - 4e85a3a5dbd1 + - 71186bb66ca2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_frameshifts @@ -53,16 +53,16 @@ tools: owner: iuc revisions: - 3e73c97f025d - - adfd6bf710bd - d74850cf4e42 + - adfd6bf710bd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: + - 9dd107db92c2 - 83da94c0e4a6 - 1586b111d2a3 - - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -74,10 +74,10 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - edacc4bcd3cb - - ed1518ce2237 - e4b4837f06f5 + - edacc4bcd3cb - 2f27f3b86827 + - ed1518ce2237 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -103,9 +103,9 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 5711fc06a63e - - 48a42ca61006 - 38ccd4589990 + - 48a42ca61006 + - 5711fc06a63e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -145,16 +145,16 @@ 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: - 172815da3d41 - - 27a6a256cd23 - 5bcf0e24f42c + - 27a6a256cd23 - b4b2b284230a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -167,8 +167,8 @@ 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 @@ -180,9 +180,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 19bbd19b74b3 - fea85c467896 - 87febc68b45b + - 19bbd19b74b3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -213,10 +213,10 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 0cb27ea69dc1 - - 4ba60cb14cb0 - 9c43baa60906 + - 0cb27ea69dc1 - 5fe20c915fa6 + - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -228,18 +228,18 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - 0db22932bc39 - 9d09724f2bf1 - aec831b54a5b + - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - df30a2f1db55 - - 29c738066906 - ed7a967cb11b - 6e24e79d3d69 + - df30a2f1db55 + - 29c738066906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sam_fasta_index_builder @@ -253,8 +253,8 @@ tools: - 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 @@ -266,16 +266,16 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - d63c1442407f - - c520a52b5174 - 64deddb6a8ec + - c520a52b5174 + - d63c1442407f tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 9946bc39c834 - 94a50db37d1a + - 9946bc39c834 - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -1034,9 +1034,9 @@ tools: - name: rdock_rbdock owner: bgruening revisions: - - c362398df83b - - a22969b08177 - e4b7d1507a75 + - a22969b08177 + - c362398df83b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index 8d01f9858..b2c75e22f 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -34,86 +34,86 @@ tools: owner: iuc revisions: - 26de3a7b1cb9 - - 6a457678efcb + - f04a1264e2a2 - 5a7c56a5cc08 + - 3b8b5bde0bd9 - cce7b18495e4 - - d7c7ef3353fe + - '841557158611' + - 6a457678efcb - 8834daeb9892 - - f73435dc282b - - 3b8b5bde0bd9 - - 3f59ebfbfe3d - - c78f3d7dd1db - - f04a1264e2a2 - - b89cac5156ec - 107d3ba7024a - d033ffc1c161 + - c78f3d7dd1db + - d7c7ef3353fe + - f73435dc282b - a6619171428e + - 3f59ebfbfe3d - 81e66674859e - - '841557158611' + - b89cac5156ec tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 5b777002c2de - - 3b96e92e8ec3 - - df47d4845b62 - - 6283babe736e - - 659517798cc4 - - b0af57c1a968 - 6a726db04d4b - - aa8cc71438cf + - 88c4aa435ded - e75442c7f4da + - 5b777002c2de + - 659517798cc4 + - 3b96e92e8ec3 + - a185b079b095 - 4755f52427c4 - - 02b8758214b0 - 6223845127ea - - 7a2092844346 - - 88c4aa435ded + - aa8cc71438cf + - 6283babe736e + - b0af57c1a968 - 5fcd1ece3a6e - - a185b079b095 + - 7a2092844346 + - 02b8758214b0 + - df47d4845b62 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - 524d31add34a + - b8476e82ac20 - 9b892d7f82cc - f97743d52b87 - d1c340a5664b - - b8476e82ac20 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - daddf188c13f - - 128ba8da994f - 9e10ba792be2 - feb40665d7cd + - daddf188c13f + - 128ba8da994f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - 2f1019071464 + - b7e297c2ede6 + - 81804a978fc0 + - a2099fb98cdb + - 36912871ccdc - ca0d8cf80567 - - b6abccb1f25b - 83a69484cb87 - - abf6dbe8c9d7 - - a2099fb98cdb - 2fa9d4f1b48f - - 7bb8726be37c - - 81804a978fc0 - - 36912871ccdc + - abf6dbe8c9d7 + - b6abccb1f25b + - ca337cce3888 - 5f8727ff21e7 - 42a174224817 - - ca337cce3888 - - b7e297c2ede6 - 14ae456b8cc5 - - 9d61d3fa046c - - 437e28791761 - 3a43c3982401 - 03ed9524dcd1 + - 9d61d3fa046c + - 437e28791761 + - 2f1019071464 + - 7bb8726be37c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -126,21 +126,21 @@ tools: - name: raxml owner: iuc revisions: - - ea30d3089354 + - 73a469f7dc96 - a4b71be30c3c - ba29b5e2a4be + - ea30d3089354 - b1e68bbe4cef - 29ff6a849eac - - 73a469f7dc96 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 809e42326fc2 - 15ac71df11a0 - - f1ccc8a6eb05 - e88a7de55d6e + - 809e42326fc2 + - f1ccc8a6eb05 - 91887494eb97 - dbe2b2204555 tool_panel_section_label: Phylogenetics diff --git a/staging.gvl.org.au/picard.yml b/staging.gvl.org.au/picard.yml index d3170c43d..e5b9ae428 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -3,12 +3,12 @@ tools: owner: devteam revisions: - f6ced08779c4 - - a1f0b3f4b781 - 1aac2a13842a - - f9242e01365a - fc288950c3b7 - - b502c227b5e6 - 881d7645d1bf + - a1f0b3f4b781 + - b502c227b5e6 + - f9242e01365a - 7d34178f2812 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 5d7d87c63..5e927b386 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -2,14 +2,14 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: + - ca90d17ff51b - d00e15139065 - - 5b85006245f3 - - e4a053d67e24 - - a58f7eb0df2c - c0e71cb2bd1b - - ca90d17ff51b + - e4a053d67e24 + - eb085b3dbaf8 + - 5b85006245f3 - 7fbec959cf2b + - a58f7eb0df2c - 3bd420ec162d - - eb085b3dbaf8 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 49bffec43..2c84eaccb 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,85 +2,85 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - ece627528a78 - 0a18ac48ac53 + - 277dc652246e + - b18329a8ac14 + - ece627528a78 - f28ad96b76dc - b574b84afc4d - - b18329a8ac14 - - 277dc652246e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - e988563cc6e5 - - bf06d196e23d - b41107d8fe89 - - e215f71d7983 + - bf06d196e23d - 525f201b86c1 + - e215f71d7983 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 4fbffddde8cd - 8da3511c9467 - bb6397b94018 + - 4fbffddde8cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - a8157342d9a3 - f23d67e28cc8 - - 528fb09022be - b8c79e70516d + - 528fb09022be + - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - a95a82eb4d50 + - 80600735685d - 25b83cbd596a - a69865da6f80 - 59e85306eae5 - - 80600735685d + - a95a82eb4d50 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: + - 611d80c0e29d - ed9ed1e6cca2 - - e0669b1854b1 - f1897eb07081 - - 611d80c0e29d - 798da6bdff3d + - e0669b1854b1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 5a35e3a8d013 - a7fb9b395ddf - 74b61bf5bc4b + - 5a35e3a8d013 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - cc430977c8ff - - 82f6c2f4332d - df2187f9013b + - 82f6c2f4332d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 10566783d718 - 043f9c91f686 - - 1693b2126f30 - - d2483487e077 - c5aa9fca18c6 + - 10566783d718 + - d2483487e077 + - 1693b2126f30 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -98,9 +98,9 @@ tools: - name: diann owner: galaxyp revisions: + - bf0728e000cd - 9fa3dbf06f17 - ae4dc0c041f9 - - bf0728e000cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -119,8 +119,8 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 0fa397f4f40b - 4081e4faa4ab + - 0fa397f4f40b - 1c5cbf8f79ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -148,8 +148,8 @@ tools: owner: galaxyp revisions: - d286ff4600dd - - e66f552a3c47 - 160538a890a6 + - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing @@ -162,40 +162,40 @@ tools: - name: maxquant_mqpar owner: galaxyp revisions: - - 3fc2116ac6d9 - 9cb7dcc07dae + - 3fc2116ac6d9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - e42225f8a659 - - 97a7f34fcb6a + - 1f39c833f65f - 2133b0be850a + - 7f432d87c82c - 8934bc76bb52 + - 837224ad1694 + - 4d17fcdeb8ff + - 97a7f34fcb6a + - e42225f8a659 - f522c08e900c - 37d669de2828 - - 4d17fcdeb8ff - - 1f39c833f65f - - 7f432d87c82c - - 837224ad1694 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - - a72ac2c7cc5b - - '860429737408' - 0ed07016d668 + - '860429737408' + - a72ac2c7cc5b - 85b8866f06d7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: + - 1974224d63c2 - 990b4560ead7 - 352b37c66d97 - - 1974224d63c2 - 4187b6df1a40 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -203,36 +203,36 @@ tools: owner: galaxyp revisions: - 4f359549383c - - deaf035bbe9f - 99450519d727 - a1daafbf5233 + - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - c1343e3389ca - - 40ca115438d2 - c7745841de24 - e79958768a2c + - 40ca115438d2 + - c1343e3389ca tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - da986f83631b - - b648e45fd3cf - - d46d64e7964d - d2eac53666f0 + - d46d64e7964d + - b648e45fd3cf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - eb811f3018ea - - 1199751329b0 - 9bf325045235 - 944b43462104 + - eb811f3018ea + - 1199751329b0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -250,25 +250,25 @@ tools: - name: msstats owner: galaxyp revisions: - - 8212e342e482 - - 593839e1f2c3 - 28434abe6c5c - b7034eff0db1 + - 593839e1f2c3 + - 8212e342e482 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt owner: galaxyp revisions: - - bd1535813cfe - a5e394b36d87 + - bd1535813cfe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_consensusid owner: galaxyp revisions: - - 4e77b8f12cd3 - - 8960fb791701 - 01dbaf6a57e0 + - 8960fb791701 + - 4e77b8f12cd3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -281,74 +281,74 @@ tools: - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 9cdf15d3cfc8 - 518b1730cf2a - - f7fef900f5b2 + - 9cdf15d3cfc8 - c9eff69a7c62 + - f7fef900f5b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - dff6c756eee5 - - 5e948629bc73 - ca88bd28f116 + - 5e948629bc73 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - 658494a2cb00 - - 890025d6e426 - 41859bbdc16e + - 890025d6e426 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: + - 6634cad7d797 - 5ad0b5bf1deb - 9b7977080f6d - - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: - - 0bb5056cb775 - - 05d5e1ddc985 - d6878d27f051 + - 05d5e1ddc985 + - 0bb5056cb775 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 52ba9695e752 - febd569ad26f + - 52ba9695e752 - 5ad830edc021 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: + - 39e8fde08881 - 27cba4c5fc42 - 92352a475eed - - 39e8fde08881 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - 0efbc235f314 - - 9e26f5c770f8 - d413dc49d650 + - 9e26f5c770f8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 8a04ed1c1d1b - 3720e349ba2a - c28f13cab67a + - 8a04ed1c1d1b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter @@ -356,33 +356,33 @@ tools: revisions: - c55dddc5844a - 382cde407f81 - - c427a8628cbe - ca799a7246e7 + - c427a8628cbe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - 39caaa778d2e - - 8ddb7bab1138 - b5d0905419da + - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - 1c5f31b8d632 + - 8d4db262964c - 18f93351f8b6 - f817513840a9 - - 8d4db262964c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - 111c3a00136d - - c69f69d7867a - 5d9f175dff81 + - c69f69d7867a + - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher @@ -396,15 +396,15 @@ tools: - name: openms_msfraggeradapter owner: galaxyp revisions: - - e133b5c8878f - 9866e1170611 + - e133b5c8878f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msgfplusadapter owner: galaxyp revisions: - - 2b2a7551a857 - c18d8efa4474 + - 2b2a7551a857 - a407b6790342 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -418,9 +418,9 @@ tools: - name: openms_mztabexporter owner: galaxyp revisions: - - 8098330f6d91 - - bf32e0bcf554 - ee860980edc6 + - bf32e0bcf554 + - 8098330f6d91 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer @@ -433,22 +433,22 @@ tools: - name: openms_openswathassaygenerator owner: galaxyp revisions: - - 2a9ff56cb279 - 8c01da82292c + - 2a9ff56cb279 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - e8f64a7dc470 - 1bf940c18d93 + - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - f861ec9fbe59 - 9f505cd4428f + - f861ec9fbe59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring @@ -468,46 +468,46 @@ tools: - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - - f9ed7e074900 - 05ec9fb05ed1 + - f9ed7e074900 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 6e8cc5ed2a9b - 18826fb8e5db + - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - - 2aebe58de46e - bc63b4d12779 + - 2aebe58de46e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: + - decc397c3b7e - 3d8d4ada5405 - 5ae104d0da6e - - decc397c3b7e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: + - e039cc5c7aed + - dd173849c3d8 - 539a3a4dcc9e - 5182338d5e7c - - dd173849c3d8 - - e039cc5c7aed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 16026cdb1330 - 8a45fd5a608a + - 16026cdb1330 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter @@ -554,14 +554,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - a72c48001f7c - - da885ca16cb2 - 3634c90301af - - 943a34df6047 - - 7fdd9119cc4f - 3ec27b4cee7c - 1beff3ddce58 + - 7fdd9119cc4f - 07ff622ec007 + - a72c48001f7c + - da885ca16cb2 + - 943a34df6047 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -615,10 +615,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - a371252a2cf6 - - 12692567c7f9 - 1a5690a5eedc + - a371252a2cf6 - 265c35540faa + - 12692567c7f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index b47cb35b6..0b008acf8 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - cd5f98911089 - 42201b90e3f4 - 2f1d464ebfd2 - 289b7d6b69a4 - e345aadf914f - 110a346daf36 + - cd5f98911089 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -19,12 +19,12 @@ tools: - name: stacks2_cstacks owner: iuc revisions: + - 0345dbaaa79b + - 8501601a118d - c207119ba5f6 - - fcce77c09289 - 42d9087b4789 - 0cd2df8af811 - - 0345dbaaa79b - - 8501601a118d + - fcce77c09289 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 - 89eb29319bf4 - 33486216eec0 - 405a212b32ab - 04db7fd6b238 + - 421c33b8bf17 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -54,11 +54,11 @@ tools: owner: iuc revisions: - eb784fa07f80 + - 1d839ead7ad3 - fa51dc5e8386 - - f6e91108b7b1 - 7370bb65bad4 - - 1d839ead7ad3 - 7b72fde3d27e + - f6e91108b7b1 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: - - d30e36c48c93 + - a3e86cd9cac7 - 8a55d29c8fcf - - 3d70c2996730 - 1544278c272e + - d30e36c48c93 + - 3d70c2996730 - c9b77ced9a78 - - a3e86cd9cac7 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -87,12 +87,12 @@ tools: - name: stacks2_populations owner: iuc revisions: - - 7b881f5f5ad5 - e2db212d64ad - - b242deb58952 - - 564c33e5c3e3 - a5969aa9347e + - 7b881f5f5ad5 - 887cf585cafc + - b242deb58952 + - 564c33e5c3e3 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: - - e897c74a48bb - - bd5ff77e2036 + - 8cff84759bf6 - 9a171f9a450b - b4bab607eb05 - - 8cff84759bf6 + - e897c74a48bb + - bd5ff77e2036 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: - - 4f65e343ecdf - - 887e0991eb24 - 6dafad990086 + - 887e0991eb24 - adc7a7610d4f - 33f0793edf93 - 5e10f396979e + - 4f65e343ecdf tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -137,12 +137,12 @@ tools: - name: stacks2_shortreads owner: iuc revisions: - - 17d39bf0a63a - - c5d7050e4ad7 - - 43e3eeb2e0ec - - 4e280b27a831 - 97575d01f06b - c287418eb288 + - 43e3eeb2e0ec + - 4e280b27a831 + - c5d7050e4ad7 + - 17d39bf0a63a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,12 +154,12 @@ tools: - name: stacks2_sstacks owner: iuc revisions: - - 9586f08634c0 - - 0b8c84a7fdb5 - - 09b8edb56d80 - - cd034465d4a4 - d9bf483266a1 - a819ec3b362d + - 0b8c84a7fdb5 + - cd034465d4a4 + - 9586f08634c0 + - 09b8edb56d80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -171,11 +171,11 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: + - a4b4bd84f69e - 69842dd5aa48 - - bf0e43ab0416 - 95351dd0fd3f - - a4b4bd84f69e - 2645575d1bf2 + - bf0e43ab0416 - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - 8a35a3bc6752 - - cfb504394ae1 - d033e1ccb386 - d1fda11e602f - - 912f904a6e1e - bb0475c884ff + - 912f904a6e1e + - cfb504394ae1 + - 8a35a3bc6752 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,8 +235,8 @@ tools: - name: stacks_populations owner: iuc revisions: - - 95286af4139b - d1fad35bdb4a + - 95286af4139b - d504d945a655 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -267,8 +267,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 96de7538bf0c - 563af4497055 + - 96de7538bf0c tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index c1606ad36..4a470095c 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 - - 2d4e3aff9dc7 - 31f8063eedea + - 2d4e3aff9dc7 + - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters @@ -56,8 +56,8 @@ 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 @@ -70,9 +70,9 @@ tools: - name: cuffmerge owner: devteam revisions: + - 6a6717a5f421 - 86285ddd4512 - cf747d1bd79a - - 6a6717a5f421 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -109,10 +109,10 @@ tools: - name: describe_samples owner: iuc revisions: - - 0693ccd171c4 + - 8f0181aacb7a - 3b36efd62b3e + - 0693ccd171c4 - e3b16fd7dd08 - - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -124,13 +124,13 @@ tools: - name: deseq2 owner: iuc revisions: - - cd9874cb9019 - - 0696db066a5b - - 9a882d108833 - - 24a09ca67621 - - 6a3a025714d3 - d027d1f4984e - 8fe98f7094de + - 6a3a025714d3 + - 9a882d108833 + - 0696db066a5b + - 24a09ca67621 + - cd9874cb9019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -143,8 +143,8 @@ tools: owner: iuc revisions: - df929f257179 - - b47c006d90c5 - 62adf13b86ea + - b47c006d90c5 - 2872c633f07e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -157,17 +157,17 @@ tools: - name: edger owner: iuc revisions: - - 0cb907a2a810 + - 3d89af8a44f0 + - 555659de7321 - 6e53e565fc6a - 334ce9b1bac5 - - 5bf899c13979 - f2843df56434 - - 3d89af8a44f0 - - a8305cf0c951 - 9bdff28ae1b1 - - 070900306913 + - 5bf899c13979 + - 0cb907a2a810 - df0c8d0a5992 - - 555659de7321 + - 070900306913 + - a8305cf0c951 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -179,8 +179,8 @@ 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 @@ -198,17 +198,17 @@ tools: - name: featurecounts owner: iuc revisions: - - f9d49f5cb597 + - 6f66ae7c5f7a + - ea04b737afa0 - e6a2a912677a + - a56fbe2d6ba7 + - 38b6d12edc68 - 90d16db017d7 + - f9d49f5cb597 - f3a5f075498f - - 7db9d3ea71c9 - - ea04b737afa0 - - 38b6d12edc68 - - a56fbe2d6ba7 - a37612abf7f9 + - 7db9d3ea71c9 - af814359d244 - - 6f66ae7c5f7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -233,8 +233,8 @@ tools: owner: iuc revisions: - f99dd58de04f - - 0f710191a66d - 3c97c841a443 + - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -252,13 +252,13 @@ tools: - name: hisat2 owner: iuc revisions: - - 6c19daec423d - - 26371a1df031 - 6ab42baa56e9 - - f4af63aaf57a - - a86e80d3c09c + - 26371a1df031 - 3fb01a8c902d + - f4af63aaf57a + - 6c19daec423d - d4b55e2beb12 + - a86e80d3c09c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -295,11 +295,11 @@ tools: - name: kallisto_pseudo owner: iuc revisions: + - 5ae5c312d718 + - ce5d418183c5 - 1c75aa5de15e - 01247aaf0a10 - - 5ae5c312d718 - 87c11c05d238 - - ce5d418183c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -311,10 +311,10 @@ tools: - name: kallisto_quant owner: iuc revisions: + - 40985510cd98 - 10c98fab6c5a - - c971db6f0fe5 - 4f9c4e6566e5 - - 40985510cd98 + - c971db6f0fe5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -326,13 +326,13 @@ tools: - name: limma_voom owner: iuc revisions: + - 97e06a4c7c75 - 32511f586472 + - d6f5fa4ee473 - 0921444c832d - - 708348a17fa1 - e827f9aae031 - 58c35179ebf0 - - d6f5fa4ee473 - - 97e06a4c7c75 + - 708348a17fa1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom @@ -393,19 +393,19 @@ tools: - name: rgrnastar owner: iuc revisions: - - c7c55b694974 - - 5ec75f5dae3c - - 7ed2edc1337f - - 4df95e2d7f61 - 4074fc1940e2 - - e132e7d02a3e + - 4df95e2d7f61 - 0a563fd2f22e - - b9e04854e2bb + - c7c55b694974 + - e132e7d02a3e + - 7ed2edc1337f + - 980d2a2e1180 - 3ea5a2a63fa2 - 79de45b5069b - - 980d2a2e1180 + - b9e04854e2bb - 99b17b74a8cd - c772497b2c32 + - 5ec75f5dae3c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -429,13 +429,13 @@ tools: - name: salmon owner: bgruening revisions: - - ebab418107f5 - - 15cd64d7c58b - - cc05793bb896 - 53e9709776a0 - - 49121db48873 - e3d32471da11 + - 49121db48873 - 2c0ca397d302 + - ebab418107f5 + - 15cd64d7c58b + - cc05793bb896 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -447,22 +447,22 @@ tools: - name: seurat owner: iuc revisions: - - c0fd285eb553 - fab6ff46e019 - - 56242ff81c84 - 8c28affc7c48 + - c0fd285eb553 + - 56242ff81c84 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - dd4df992d93d + - 1ebd14235b92 + - 258d696dbd7e - cef79931dda5 - 76d290331481 - - 258d696dbd7e - - 914cfcba0ec8 - - 1ebd14235b92 - ae618321f34a + - 914cfcba0ec8 + - dd4df992d93d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -513,10 +513,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: + - 74217fbfba4d + - bcc5f03f1900 - ba3720d7e68b - d6a479fd4281 - - bcc5f03f1900 - - 74217fbfba4d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -528,10 +528,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 478f36effca1 - - c2b82a94493e - 2fb4ee002432 + - 478f36effca1 - 56162e446004 + - c2b82a94493e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -543,9 +543,9 @@ tools: - name: trinity_analyze_diff_expr owner: iuc revisions: + - 9ff3765e7172 - 3f4094b6a565 - fab23c3b5258 - - 9ff3765e7172 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -557,10 +557,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - be3f26533209 - - 34a018cbee9c - 4687ecf0eb2d + - 34a018cbee9c - 870ac06dff8e + - be3f26533209 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -572,11 +572,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 5192f657f305 - 05ab8d5e04a2 + - c5fbddcac63a - 33406f5a445c - 65e7dea767ea - - c5fbddcac63a + - 5192f657f305 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -588,9 +588,9 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - e406ac71165d - a35cba31d904 - 1fdb25a8384d + - e406ac71165d - 6f0fb35b799c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -603,8 +603,8 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - 964b7efe2639 - c2c039e421af + - 964b7efe2639 - 7c7fbf13aadd - 37a1129c89d2 tool_panel_section_label: RNA-seq @@ -619,9 +619,9 @@ tools: owner: iuc revisions: - eafea3083352 + - 047c22569787 - 24e94d84adc9 - 1d689e4e1caf - - 047c22569787 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -633,10 +633,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: + - 1812dbc5bb7b - 3a4ac03d1266 - - 9871104ea630 - 04bb8bb7c198 - - 1812dbc5bb7b + - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -648,15 +648,15 @@ tools: - name: trinity owner: iuc revisions: - - cee61b3fcf78 - - db1f362cca3e - - c9cfec002f71 - - d2bc35f3d1c5 - 32b86cd8eb50 - - 8f1c3df4dd49 + - d2bc35f3d1c5 + - cee61b3fcf78 - 9fa24d5aac68 - 48636f857c4b + - db1f362cca3e + - c9cfec002f71 - d84caa5a98ad + - 8f1c3df4dd49 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -668,10 +668,10 @@ tools: - name: trinotate owner: iuc revisions: - - 4383070d29ed - 2b093007fab9 - - 9e61bc67866f - 6fd16fad465d + - 4383070d29ed + - 9e61bc67866f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinotate diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index ba833d62f..ad071beec 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -3,7 +3,7 @@ tools: owner: nilesh revisions: - 473382134e56 - - 1a052c827e88 - 080fd5739bb4 + - 1a052c827e88 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/sambam.yml b/staging.gvl.org.au/sambam.yml index d4f4ea96d..98e3f3909 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: - - a53efedba9e7 - 10184eaa85fc - 88eedb4abea0 + - a53efedba9e7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -16,9 +16,9 @@ tools: - name: bamtools_filter owner: devteam revisions: - - 1dfd95ee241e - cb20f99fd45b - 108db6635177 + - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -36,8 +36,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - 9c1c0b947e46 - ef11139d4545 + - 9c1c0b947e46 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -55,9 +55,9 @@ tools: - name: qualimap_bamqc owner: iuc revisions: + - e7fd6754d093 - 5f8e69cc4c6e - 19ece8afbaab - - e7fd6754d093 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -69,8 +69,8 @@ tools: - name: sam2interval owner: devteam revisions: - - 75557c0908a9 - 8c737b8ddc45 + - 75557c0908a9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_bitwise_flag_filter @@ -89,8 +89,8 @@ tools: - name: sam_to_bam owner: devteam revisions: - - 9bd1568619cd - cf1ffd88f895 + - 9bd1568619cd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam @@ -108,18 +108,18 @@ tools: - name: samtool_filter2 owner: devteam revisions: + - dc6ff68ea5e8 - 56c31114ad4a - 649a225999a5 - - dc6ff68ea5e8 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - - 12749212f61b - - 46c6639921f1 - 6856f8a01905 - 9149ad20699a + - 12749212f61b + - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -131,10 +131,10 @@ tools: - name: samtools_calmd owner: devteam revisions: - - c89806670ab9 - - 92ec40abcdcf - 06dc50b7b711 - 33208952b99d + - 92ec40abcdcf + - c89806670ab9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -146,10 +146,10 @@ tools: - name: samtools_fastx owner: iuc revisions: - - 66e23b11feae - b3d99709fe1a - - 720217c23995 - a8d69aee190e + - 66e23b11feae + - 720217c23995 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -164,8 +164,8 @@ tools: - cc61ade70eb8 - fe34990e5ce7 - 22970df7a40e - - db17d5321bad - fefd89ab563c + - db17d5321bad tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -177,8 +177,8 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - 811fc2d75ad4 - 88b8c2916784 + - 811fc2d75ad4 - fa5d3e61e429 - 7def34e6cf4d - 7a6034296ae9 @@ -193,20 +193,20 @@ tools: - name: samtools_merge owner: iuc revisions: - - 36677f429310 - 65a38e8c8e2a - - b40e2d865d52 + - 36677f429310 - 740ce0a18f0d + - b40e2d865d52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: + - 329deb17a9f7 + - fa7ad9b89f4a - 9da0311ab1dd - b61f5d6a7f25 - - fa7ad9b89f4a - 583abf29fc8e - - 329deb17a9f7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -218,8 +218,8 @@ tools: - 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_phase @@ -231,10 +231,10 @@ tools: - name: samtools_reheader owner: devteam revisions: + - 30388d878f81 - bb8cfc6f6e0c - d7b4851d1971 - db000c6007a0 - - 30388d878f81 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -253,8 +253,8 @@ tools: owner: devteam revisions: - b5c88b7b153e - - a4a10c7924d1 - 344fc91e1bfd + - a4a10c7924d1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -268,8 +268,8 @@ tools: revisions: - e613c1ad4c4c - 6c2c1836728b - - cab3f8d35989 - a577ea614bed + - cab3f8d35989 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -283,8 +283,8 @@ tools: revisions: - 5d9ae78f34d3 - b7f7826ef1cd - - bcedabb53ddf - 135c85f4cfaf + - bcedabb53ddf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -297,11 +297,11 @@ tools: owner: devteam revisions: - 1cc79f49b8d5 - - 24c5d43cb545 - 5a08c09b9311 - fed4aa48ba09 - 145f6d74ff5e - 3a0efe14891f + - 24c5d43cb545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats @@ -313,14 +313,14 @@ tools: - name: samtools_view owner: iuc revisions: - - 5826298f6a73 - - 0dbf49c414ae - b01db2684fa5 - - bf328cec6a42 + - c370440f901e + - 350bbc5c2ffd - b72793637686 - 6be888be75f9 - - 350bbc5c2ffd - - c370440f901e + - 0dbf49c414ae + - 5826298f6a73 + - bf328cec6a42 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 a699c4b2c..a21d149bc 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -2,11 +2,11 @@ tools: - name: ena_upload owner: iuc revisions: - - d147d6455873 - - 6f6537780379 - a62c4a11a67d - 480d9e9d156b - - 59bb6d34fca6 - 4aab5ae907b6 + - 59bb6d34fca6 + - 6f6537780379 + - d147d6455873 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 c4adc0611..e70cc5117 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -3,10 +3,10 @@ tools: owner: iuc revisions: - cfc3f5a57dc6 - - 93dd15e13e6a - - 00712416fdaa - 55e35e9203cf - 32e547223c9e + - 93dd15e13e6a + - 00712416fdaa - fb9e030ffae4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -19,12 +19,12 @@ tools: - name: anndata_inspect owner: iuc revisions: - - 038e32885fec - - ee98d611afc6 - - 6f0d0c784f09 - - b9fac48532eb - 688357ad5e61 + - 6f0d0c784f09 + - 038e32885fec - 39e945f0b2c1 + - b9fac48532eb + - ee98d611afc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -36,12 +36,12 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - 43cb7b5a6fe7 - - ed4996a16f7f - 3d748954434b - - 9bd945a03d7b - b85871dd69f9 + - 43cb7b5a6fe7 + - ed4996a16f7f - d4af736e7b83 + - 9bd945a03d7b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -54,9 +54,9 @@ tools: owner: iuc revisions: - a9caad671439 - - 8855361fcfc5 - - cdf4443d5625 - 2c1200fba922 + - cdf4443d5625 + - 8855361fcfc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils @@ -81,15 +81,15 @@ tools: - 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 @@ -101,8 +101,8 @@ tools: - name: raceid_clustering owner: iuc revisions: - - f911a64454fb - 7e014059a88d + - f911a64454fb - 0bff0ee0683a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -122,8 +122,8 @@ tools: owner: iuc revisions: - f3eb2291da05 - - 2b0d3e2f402a - 37a47c4fd84d + - 2b0d3e2f402a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -136,8 +136,8 @@ tools: owner: iuc revisions: - df8e4e54d367 - - 69018f285aa3 - a6821f856a1e + - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspecttrajectory @@ -163,9 +163,9 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: + - b2df381a6004 - 77b91b9bdf52 - aaa5da8e73a9 - - b2df381a6004 - 6acb08931836 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -178,10 +178,10 @@ tools: - name: scanpy_filter owner: iuc revisions: - - a97abb8cd15b - b409c2486353 - 3c86f71498bc - a03ff8633507 + - a97abb8cd15b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -193,9 +193,9 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - 6c145a6868cc - cc0deb593fc8 - 3081ff5c84a3 + - 6c145a6868cc - c5d3684f7c4c - 5e9171dc8244 tool_panel_section_label: Single-cell @@ -224,9 +224,9 @@ tools: - name: scanpy_plot owner: iuc revisions: + - 6adf98e782f3 - dbbe1ea8ecb1 - aa0c474463c2 - - 6adf98e782f3 - 9b0cdb8cf6be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -240,9 +240,9 @@ tools: owner: iuc revisions: - 458e8f43a775 - - f2f6c703da06 - - 215733a383f2 - 73ab2ac53d06 + - 215733a383f2 + - f2f6c703da06 - bf2017df9837 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -255,9 +255,9 @@ tools: - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - fd808de478b1 - 8f333f90d8d6 - b834074a9aff + - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -269,9 +269,9 @@ tools: - name: scater_filter owner: iuc revisions: - - b7ea9f09c02f - - 7a365ec81b52 - 652923ce664f + - 7a365ec81b52 + - b7ea9f09c02f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -297,9 +297,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 46fc6751d746 - - c99ba278dfa9 - 9e5c0bb18d08 + - c99ba278dfa9 + - 46fc6751d746 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index 85601ee65..c80041072 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,9 +32,9 @@ tools: - name: datamash_ops owner: iuc revisions: - - 746e8e4bf929 - - 562f3c677828 - 419027d822d6 + - 562f3c677828 + - 746e8e4bf929 - 4c07ddedc198 - 2f3c6f2dcf39 tool_panel_section_label: Statistics @@ -42,15 +42,15 @@ tools: - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - 8564f6927b87 - e01e8a9a82f4 + - 8564f6927b87 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all @@ -63,8 +63,8 @@ tools: - name: dwt_var_perclass owner: devteam revisions: - - cb422b6f49d2 - 781e68074f84 + - cb422b6f49d2 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - b1eda492f063 - - 840f29aad145 - - 4c4ec859c31a - - aef56d0e7a61 - 7442b94d6a1e + - aef56d0e7a61 + - 4c4ec859c31a + - 840f29aad145 - 9c3e1d3235c8 + - b1eda492f063 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 07843f917990 - - 9fda0b82f419 - 375bbd555f4a - 30d21a6041f6 + - 9fda0b82f419 + - 07843f917990 - d0352e8b4c10 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - cd02bf168d23 - - 8b1b2b91f8d0 - 7ae443e6217d - - 2c58b83c9bad - 4cc980df6265 + - 2c58b83c9bad + - cd02bf168d23 + - 8b1b2b91f8d0 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - 1dd433d2c92c + - 4bbaf77573ef - ad7e0b4291ee + - 1dd433d2c92c + - bb9fc9d46ea4 - e10e776f2109 - - 4bbaf77573ef - 7dd3fb35904f - - bb9fc9d46ea4 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/staging.gvl.org.au/text_manipulation.yml b/staging.gvl.org.au/text_manipulation.yml index eb6a0406d..55b131cfc 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -8,8 +8,8 @@ tools: - name: add_value owner: devteam revisions: - - 023f0a3760b3 - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -29,13 +29,13 @@ tools: owner: devteam revisions: - 6595517c2dd8 - - 6e8d94597139 - - 626658afe4cb - 464b9305180e + - 626658afe4cb + - 6e8d94597139 - 9cd341095afd - - be25c075ed54 - - 02026300aa45 - 13b6f0007d9e + - 02026300aa45 + - be25c075ed54 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -72,8 +72,8 @@ tools: - name: filter_tabular owner: iuc revisions: - - 37cde8134c6a - 34d29339abab + - 37cde8134c6a - 9cc411a62277 - 557ec8d7087d tool_panel_section_label: Text Manipulation @@ -99,29 +99,29 @@ tools: - name: merge_cols owner: devteam revisions: - - dd40b1e9eebe - - ae7843d06f8f - f2aac0c5c60d + - ae7843d06f8f + - dd40b1e9eebe tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - cf34c344508d - - 623f3eb7aa48 - - 1ea4e668bf73 - - 2e8f945f7285 - 3a6b78c39dca - 33d61c89fb8d + - 623f3eb7aa48 + - 2e8f945f7285 - 83069b38aa85 + - cf34c344508d + - 1ea4e668bf73 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - ae8c4b2488e7 - - 503bcd6ebe4b - 399da6b5ec21 + - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -141,18 +141,18 @@ tools: - name: table_compute owner: iuc revisions: - - 3bf5661c0280 - 60ff16842fcd + - 3bf5661c0280 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: - 9ff72e942410 - - a6f147a050a2 - - ddf54b12c295 - f46f0e4f75c4 - d698c222f354 + - a6f147a050a2 + - ddf54b12c295 - 74a8bef53a00 - 0a8c6b61f0f4 tool_panel_section_label: Text Manipulation diff --git a/staging.gvl.org.au/variant_calling.yml b/staging.gvl.org.au/variant_calling.yml index dfed04aa2..80b80064c 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -3,8 +3,8 @@ tools: owner: iuc revisions: - 82fb5e3bb93e - - 0d18a3ba2d1c - 85c57cc9b558 + - 0d18a3ba2d1c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cutesv @@ -16,56 +16,56 @@ tools: - name: freebayes owner: devteam revisions: + - 04fa42777df9 - 57def2d7c093 - 156b60c1530f - ef2c525bd8cd - - 04fa42777df9 - a5937157062f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: + - 435b157bed6d + - 09d6e4693887 - e61c9ac190ad - 791f73caa0c8 - - 09d6e4693887 - - 435b157bed6d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - - e1461b5c52a0 - - 3b4b2121842f + - 03627f24605f - 65432c3abf6c - 074d44697036 - - dfadc322b065 - - 03627f24605f + - 3b4b2121842f + - e1461b5c52a0 - 4805fe3d8fda + - dfadc322b065 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 7dfca164d2e3 - 701d134358ad + - 7dfca164d2e3 - 9cb929f21cfa tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - 426d707dfc47 - f4473557ffc7 - 971e07ca4456 - c27549b9aa1f + - 426d707dfc47 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - cdaab621d454 - dbd9f2db9ed8 + - cdaab621d454 - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -84,11 +84,11 @@ tools: - name: snippy owner: iuc revisions: - - fa016f1eea1a - - d220115f882b - - c9a8ef2aa380 - - 9bccc8404a3c - 5bbf9eada9c2 + - 9bccc8404a3c + - c9a8ef2aa380 + - d220115f882b + - fa016f1eea1a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -130,11 +130,11 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - 40f0591deda0 - - ee4a90760848 - 3b1e7c170b10 - - 32f14a2723ec - e7aff4a85df5 + - 40f0591deda0 + - 32f14a2723ec + - ee4a90760848 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index 1eb393f78..46ec908de 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -2,13 +2,13 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - e075b1be5abb - - b7ea370b8f5d - 8a2e296c07ef - 6a88248893c4 + - b7ea370b8f5d - 265fe0f9ea64 - - 3f62d4939d54 - ebe5fc018e72 + - e075b1be5abb + - 3f62d4939d54 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -20,13 +20,13 @@ tools: - name: bcftools_call owner: iuc revisions: - - 21687e35f066 - - 544cb432072b - b03984136ce4 - 22637b1a55bf - - 0fba2c15b40d - - f0d44631365f + - 21687e35f066 - c37b684e7f4e + - 544cb432072b + - f0d44631365f + - 0fba2c15b40d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -38,14 +38,14 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - 3a7084316a6e - - 01d6b7d6365e - - 0238f68ad641 + - 8627b2b383b4 - bf1f4994f104 + - 0238f68ad641 - 6d35a3780bfd + - 01d6b7d6365e - 8ca3647c90fd - - 8627b2b383b4 - 8408bffd5616 + - 3a7084316a6e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -57,14 +57,14 @@ tools: - name: bcftools_concat owner: iuc revisions: + - 6b6c992d3a14 - 81426b3cf18b - - d144af39073a + - f430a1ec7ee4 - 08296952d12f + - d144af39073a + - 62ca6da715bf - 03e0645395d2 - - 6b6c992d3a14 - 9b5abbf50d23 - - f430a1ec7ee4 - - 62ca6da715bf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_concat @@ -76,13 +76,13 @@ tools: - name: bcftools_consensus owner: iuc revisions: - - 147de996e34f + - d37e313a41be + - 95c6f3f4c77f - e522022137f6 + - 147de996e34f - 1829900b5dcd - d3081540d175 - 2363ef414c9b - - d37e313a41be - - 95c6f3f4c77f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -94,13 +94,13 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - 1137ce8efc1e - - 9b29129fb491 + - b14ff40958cb + - 92c0aff8b53e - 348cd212dbad + - 9b29129fb491 - cacc9970727a + - 1137ce8efc1e - 09f37afb3621 - - 92c0aff8b53e - - b14ff40958cb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -112,11 +112,11 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - ecc9192912b8 - 55c0e906c14c + - de68c11034f6 + - ecc9192912b8 - 4935320a59a8 - 1f2183a23823 - - de68c11034f6 - 367ba501b6eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -129,12 +129,12 @@ tools: - name: bcftools_csq owner: iuc revisions: + - 039ea3f1dea9 + - 7cbf3c66d4ad + - 6c790a091c7c - ae68ceb4cca3 - f01b2c9506b9 - - 6c790a091c7c - 64a8f7dae3ad - - 039ea3f1dea9 - - 7cbf3c66d4ad tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -146,13 +146,13 @@ tools: - name: bcftools_filter owner: iuc revisions: + - 963a3635b2e1 - 277719af4dd7 - - 656a916779fe - 6ea7170a016d - - 963a3635b2e1 - 33bd9301568c - - e7452697afd9 - cdb7b4927742 + - e7452697afd9 + - 656a916779fe tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -164,13 +164,13 @@ tools: - name: bcftools_gtcheck owner: iuc revisions: + - 3eac729e66c9 - 26d97cdd5410 - - b7f0f59baa7e - - a29a2f40b665 - a1213a0b7b66 - - 3eac729e66c9 - - 501bfb078342 - 5a321fab1fe4 + - 501bfb078342 + - b7f0f59baa7e + - a29a2f40b665 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -182,13 +182,13 @@ tools: - name: bcftools_isec owner: iuc revisions: - - d7d1663559e9 - - 63aabc920911 - 5f27e814a119 - - c803c34361e0 - - 81e4014fa809 - 97d19c008d15 - 709dd8291b83 + - c803c34361e0 + - 63aabc920911 + - 81e4014fa809 + - d7d1663559e9 - 768d04526638 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -201,13 +201,13 @@ tools: - name: bcftools_merge owner: iuc revisions: - - 7ba36babba2d - - 2215287d5cc9 - - b1eba148b35b - - b931e65638b8 - af163c712539 - 86296490704e + - 7ba36babba2d + - b1eba148b35b - 85ee7e6c4204 + - b931e65638b8 + - 2215287d5cc9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -219,15 +219,15 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - ce9396ddcb2b - 4e1d23e5c691 + - 37757ffb4c5f + - 03191140c66a - 31ea13dfe5e6 - - 5660b21a0dbd - - f506df85c652 + - ce9396ddcb2b - cf06b44624c7 - - 03191140c66a - - 37757ffb4c5f + - 5660b21a0dbd - 9c711df3258d + - f506df85c652 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -239,12 +239,12 @@ tools: - name: bcftools_norm owner: iuc revisions: + - ebb2e12a6de1 - a404f786a94c - 021693fdadaa - 19905c025d2a - - 48291658fdf6 - - ebb2e12a6de1 - 6deb4d549bc9 + - 48291658fdf6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -256,13 +256,13 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - f7879f1e77f9 - 71c78e0eea52 - 5ad5d4243987 - c450406f722b - - be6b217710af - - 69d8b7567281 + - f7879f1e77f9 - 97e8145d7e30 + - 69d8b7567281 + - be6b217710af tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -274,13 +274,13 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: + - 2514e684f8a3 + - 52f9e4a660e3 - cc7f9a4e186b - - 89720ec3d58e + - 0fe007201caf - 79f7a1acc2cd - d31a2e310a52 - - 52f9e4a660e3 - - 2514e684f8a3 - - 0fe007201caf + - 89720ec3d58e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -292,13 +292,13 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 80e6e399ccd0 - - 75ddd081f608 - - 026a989b7cee + - 0a62420cb9cd - 230e424bde67 - 1411bef27a75 + - 026a989b7cee + - 75ddd081f608 + - 80e6e399ccd0 - 99f4a81a47be - - 0a62420cb9cd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -310,13 +310,13 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - e493702b19eb - - bca7ce81688f + - c01be0ab9806 - 5acfca5a76af + - 5808f77b2bb6 - ba20340426fe - 444e6a756c35 - - 5808f77b2bb6 - - c01be0ab9806 + - bca7ce81688f + - e493702b19eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -329,12 +329,12 @@ tools: owner: iuc revisions: - d52b8947b269 - - 4d236c696844 - - 7fe09ad6a939 - - 157ffcdd3fa7 - - 68fec03a63b7 - 12152af85697 + - 68fec03a63b7 + - 157ffcdd3fa7 + - 7fe09ad6a939 - f2482aa4862e + - 4d236c696844 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -346,13 +346,13 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: - - 29ba253e2e05 - - 8dbce095986c - - 8f2fc0ab30fb - cbe39e530cbf + - 8f2fc0ab30fb + - 29ba253e2e05 - 6f8e223f78f3 - 0e5d11004815 - 27e2611639a9 + - 8dbce095986c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -364,13 +364,13 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: + - 9708e3086f32 - a367a15c6de5 - a8630d4fbaf8 - - 9708e3086f32 + - af36eb5418fe - e0a856def0b0 - - 3ff5654b4e7d - 88bb477f45f7 - - af36eb5418fe + - 3ff5654b4e7d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian @@ -382,13 +382,13 @@ tools: - name: bcftools_plugin_missing2ref owner: iuc revisions: - - 4ed46189d6c6 + - 5c9729d54721 - 96d0145c041a + - 4ed46189d6c6 - 03e30f06f15f + - 6ce175385dd9 - 2f4eef1f0d22 - - 5c9729d54721 - 31c096c6b156 - - 6ce175385dd9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -400,13 +400,13 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: - - 46eb13bc2c73 - - 11af7fce71cf - - 40daf124be88 - 2c4941386820 - - 262bba5b90ef - - a1aad8b559c6 - 09f5e45a8212 + - 46eb13bc2c73 + - a1aad8b559c6 + - 262bba5b90ef + - 40daf124be88 + - 11af7fce71cf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -418,14 +418,14 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - f272b8ba0983 - - 12038f59c0f4 - - 4b796b58938b - 743cd1472aeb - 0594ea1417c8 - - 8cb121b6a1d2 + - 4b796b58938b - 6cbb9c47795c - 882b2e649602 + - 8cb121b6a1d2 + - f272b8ba0983 + - 12038f59c0f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -438,12 +438,12 @@ tools: owner: iuc revisions: - cced6715f926 - - 18cf9de1cf73 - - dba06328556a + - 238f78e38a8b - 8c3ff4ef1190 + - dba06328556a - eccb508bb678 - - 238f78e38a8b - adee7e8b746f + - 18cf9de1cf73 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples @@ -455,13 +455,13 @@ tools: - name: bcftools_query owner: iuc revisions: - - e0ad88dec40d - e53501abf992 - - a850902cac64 - - c9935c9e8a24 - 3ce32adc55b2 - - f64e7ca2efd2 - 9f36041495a3 + - f64e7ca2efd2 + - e0ad88dec40d + - c9935c9e8a24 + - a850902cac64 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -473,13 +473,13 @@ tools: - name: bcftools_reheader owner: iuc revisions: + - 79489d5685dd + - b7be725976b6 - 8057cf55fa41 - - d68c43202172 - d43eb39b989e + - d68c43202172 - fd3539749127 - - b7be725976b6 - 4db0695a6fc7 - - 79489d5685dd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -491,13 +491,13 @@ tools: - name: bcftools_roh owner: iuc revisions: - - b0d39ef600a7 - - 78cd8b69da4c - 1ccf0e7fb4f6 - 6a636d58dfc2 + - 5296d26b0373 - 58091e1be01b + - b0d39ef600a7 + - 78cd8b69da4c - bdc67eeb0bc9 - - 5296d26b0373 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -509,13 +509,13 @@ tools: - name: bcftools_stats owner: iuc revisions: - - b641062a2587 - e8af591435d1 - - '388983871932' - - 4d3ce9dc1525 - baa8823f8073 - - b17394940c7a - a2f8dc22d7c0 + - 4d3ce9dc1525 + - b641062a2587 + - b17394940c7a + - '388983871932' tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -527,13 +527,13 @@ tools: - name: bcftools_view owner: iuc revisions: + - e6b5cbbf449b + - 3a233c8eb814 + - 3ca3de4e5291 - 38d75661c235 - - d1f8f55f564d - 59fa8742285e + - d1f8f55f564d - abc3ced31cd1 - - 3ca3de4e5291 - - 3a233c8eb814 - - e6b5cbbf449b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -545,8 +545,8 @@ tools: - name: vcf2tsv owner: devteam revisions: - - e92b3c0f9224 - 285060661b45 + - e92b3c0f9224 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfaddinfo @@ -573,36 +573,36 @@ tools: - name: vcfannotategenotypes owner: devteam revisions: - - 84959112d9a6 - 70bc6ced57f7 + - 84959112d9a6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect owner: devteam revisions: - - aea8e90ad788 - 9edfe5145ba8 + - aea8e90ad788 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbreakcreatemulti owner: devteam revisions: - - 690b1d846263 - 9fd5d91eb91b + - 690b1d846263 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcheck owner: devteam revisions: - - 5e850c85ba32 - aa8e8c96ca06 + - 5e850c85ba32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine owner: devteam revisions: - - 1f0ba67cc85a - 53edb91ed051 + - 1f0ba67cc85a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcommonsamples @@ -615,15 +615,15 @@ tools: - name: vcfdistance owner: devteam revisions: - - 48e458c721b3 - 5822b40f3037 + - 48e458c721b3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter owner: devteam revisions: - - eae7c08ebb6f - fa24bf0598f4 + - eae7c08ebb6f - 6b935ab36d7b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -637,15 +637,15 @@ tools: - name: vcfflatten owner: devteam revisions: - - b24e368ae7b1 - f285aa6bdcfb + - b24e368ae7b1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgeno2haplo owner: devteam revisions: - - b890055e07bd - a3dea556218d + - b890055e07bd tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes @@ -665,22 +665,22 @@ 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: - - d226a7327946 - 17096387c0e6 + - d226a7327946 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample owner: devteam revisions: - - 12b570dd0bc5 - 6257ee3b50d3 + - 12b570dd0bc5 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfselectsamples diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index f6f1fb8dd..24baabc5f 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: + - 3f3e247c053d + - 78c75f134c16 - 6e9aea89e388 - c2ef298da409 - - 3f3e247c053d - 4efdca267d51 - - 78c75f134c16 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -36,38 +36,38 @@ tools: - name: annotatemyids owner: iuc revisions: - - cd2480f35935 - - 1aae04680c4b - - 4f2967b27e67 - - b5d8e5475247 - fe3ca740a485 + - b5d8e5475247 - f29602ae449e - 44018dd6b447 - 133f36c29579 + - 1aae04680c4b + - 4f2967b27e67 - 3e1f6f6d557e + - cd2480f35935 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 - ca6d970d931c - 28433faa6e42 + - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta @@ -79,9 +79,9 @@ tools: - name: barrnap owner: iuc revisions: - - 7355bbf5e05f - 8fd427007e93 - fe48aa4ccd5e + - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -93,8 +93,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 1b9a9409831d - 8bd92f2404dd + - 1b9a9409831d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: cpat @@ -106,8 +106,8 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: - - d9c3016f7283 - 63662ae295d6 + - d9c3016f7283 - 9d1fbff733cf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -127,55 +127,55 @@ tools: owner: iuc revisions: - 3bbe70fef6df - - 756376aeb1ae - - 9f2455341fac - 14f588312c56 - b6b5cd37f2a2 + - 756376aeb1ae - 582fd74dc2a1 + - 9f2455341fac tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: + - 1691af4a0d17 + - 73428a792541 - a230ea445788 + - 30fb23d4c31c - 989f7c061f35 - 0ffe5be70caf - - 73428a792541 - - 1691af4a0d17 - - 30fb23d4c31c tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 30f08d74024f - - e94187d661df + - b69c46064ec7 - 494f0bb4a993 - 5a5ae61da69c + - 30f08d74024f - 563a19373357 - - b69c46064ec7 + - e94187d661df tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: + - d6c7106b7b2e - 7abc5f6dd595 - 1bc5a03faf2e - - f77d7b685bb3 - - 2bba2ff070d9 - - d6c7106b7b2e - f31125bb85ea + - 2bba2ff070d9 + - f77d7b685bb3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - 52af33194019 - - fed64e676186 - - b3cf4684e9c7 - - 54961e026fe4 - d3af38b9c7e1 - 520e30695ec3 + - 54961e026fe4 + - b3cf4684e9c7 + - 52af33194019 + - fed64e676186 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -187,9 +187,9 @@ tools: - name: gff_to_prot owner: iuc revisions: + - 79261884facd - 07d7991bf205 - 2aea122fbd25 - - 79261884facd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -201,8 +201,8 @@ tools: - name: goseq owner: iuc revisions: - - 8b3e3657034e - 602de62d995b + - 8b3e3657034e - 43798b4caee0 - ef2ad746b589 tool_panel_section_label: Annotation @@ -222,16 +222,16 @@ 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 - - c55643c3d813 - 74810db257cc + - c55643c3d813 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -256,9 +256,9 @@ tools: - name: maker owner: iuc revisions: - - 3c1a01127868 - - d46d803ca6cc - 370c210d9541 + - d46d803ca6cc + - 3c1a01127868 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 @@ -289,10 +289,10 @@ tools: - name: prokka owner: crs4 revisions: + - 8a22554cdde2 - bf68eb663bc3 - d643e3b03500 - a17498c603ec - - 8a22554cdde2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -311,8 +311,8 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snap_training @@ -326,12 +326,12 @@ tools: revisions: - 8f92c2b26e6d - cfcf33df7fc0 + - 9473cd297a76 - 68693743661e - - 5b80f544c67f + - 5a29ab10dba6 - 268d162b9c49 - - 9473cd297a76 + - 5b80f544c67f - 5c7b70713fb5 - - 5a29ab10dba6 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift @@ -345,8 +345,8 @@ tools: - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -359,14 +359,14 @@ tools: owner: iuc revisions: - e1a9d6fd258d - - 809dfc93d593 - - 2c68b0c38785 - - 037a11682176 - ac8250086ac3 + - 809dfc93d593 - ba6f87115e13 + - 037a11682176 - 45083d070fb8 - 37213cf56392 - 200c378d85f3 + - 2c68b0c38785 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 218fd6126..265a9cdc6 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,42 +2,42 @@ tools: - name: abyss owner: iuc revisions: - - a929ce596a34 - - 890b794c997d - 7547fcab5d19 + - 890b794c997d + - 841084c5fc46 - 0e93176640ac + - a929ce596a34 + - fa5259cc561b - 553bfe8bd0b5 - 8f1b150a2487 - - fa5259cc561b - - 841084c5fc46 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 067592b6b312 - - b2860df42e16 - - 21e491ad532a - - b9e31c5c01c7 - ddddce450736 + - 21e491ad532a + - b2860df42e16 - 94fe43e75ddc + - b9e31c5c01c7 + - 067592b6b312 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: - 3371c5bdc17a - - faee8629b460 - 5258e18bbe23 - - 22286dab5aa1 + - faee8629b460 - a7f16f24e9a1 + - 22286dab5aa1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -49,29 +49,29 @@ tools: - name: busco owner: iuc revisions: + - bb935709506a - 1e62c28ba91d - 46ae58b1d792 + - 0d243f458b53 + - cf13a1e03e5b + - 2a5b8b9936bf - 602fb8e63aa7 - - 94170eee0ad8 - 4048d82f0c88 - - 2a5b8b9936bf - 5ecdeca79a0d + - 94170eee0ad8 + - e4bd1e99bacf - 41030a6c03b7 - e824f5d958d0 - 2dd755c1c6ff - 1440ae06552f - - bb935709506a - - 0d243f458b53 - - cf13a1e03e5b - - e4bd1e99bacf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - 5732f959936a - - 86f150c8019d - c5b7390290b1 + - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -83,27 +83,27 @@ tools: - name: flye owner: bgruening revisions: - - 8d4f03b5fe9d + - 1ce9b1d72ec3 + - cb8dfd28c16f + - 3ee0ef312022 - e27815e82dd4 + - 8d4f03b5fe9d - 276f5d8712d5 - - 3ee0ef312022 - - cb8dfd28c16f - - 1ce9b1d72ec3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 01210c4e9144 - 3169a38c2656 + - 01210c4e9144 - b2f674562a18 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 8b330a577046 - 06bcf65179fb + - 8b330a577046 - 7348b69e5109 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -111,9 +111,9 @@ tools: owner: bgruening revisions: - 690c2caa367e + - 3ef480892a9f - 3fba9c77550a - 5127a713de83 - - 3ef480892a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -125,21 +125,21 @@ tools: - name: hifiasm owner: bgruening revisions: - - 0ee0c3089254 - - 41cea2aa2dce - - 6505bd37670d + - 045c7c3d8e59 + - 5f625c63b8bc + - f3c89da3af16 - 60024a528cbd - - 71740308d412 - - 5bec28269d95 + - 366a11d316a7 + - 6505bd37670d + - 2061fb3b81b4 - ec9e21e9c71b + - 0ee0c3089254 - da9d8bf98802 - - f3c89da3af16 - - 2061fb3b81b4 - - 9ef6920c3089 - - 5f625c63b8bc - - 366a11d316a7 - - 045c7c3d8e59 + - 41cea2aa2dce - 3f7be05a1597 + - 9ef6920c3089 + - 5bec28269d95 + - 71740308d412 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -157,9 +157,9 @@ tools: - name: megahit owner: iuc revisions: - - de387b2b2803 - - 7518ee87b53d - a96f3ad4e0d8 + - 7518ee87b53d + - de387b2b2803 - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -167,29 +167,29 @@ tools: owner: iuc revisions: - 39edec572bae - - 9d79beb19ac3 - f8113c25bc6b + - 9d79beb19ac3 - 09c589057ee8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: + - 29dabd8db6f2 - eadfd71dde37 - 51c2360aa807 - - 29dabd8db6f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: + - f338e9942b27 - 3ca2d2a9068c - e731ea24e48d - 606b09cc9860 - - 2ecf5a570907 - - fd128c111ab0 - eb7a370f6588 - - f338e9942b27 + - fd128c111ab0 + - 2ecf5a570907 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -201,11 +201,11 @@ tools: - name: miniasm owner: iuc revisions: + - 80d1250bd5fd - 8dee0218ac7d - a7b889b90140 - - 73a3846701e1 - - 80d1250bd5fd - 8b6d0d85252b + - 73a3846701e1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -217,9 +217,9 @@ tools: - name: novoplasty owner: iuc revisions: + - 64a1c751d99b - 15200570e926 - 7c2f5268d01c - - 64a1c751d99b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -231,45 +231,45 @@ tools: - name: pretext_map owner: iuc revisions: - - 8fef980d48b5 - - bbe19ef04a74 - - 2b16ba799da9 - - 511e5e3cd55e - - d256a51a656b - 02831bf9e95f - dfb8a4497339 + - 2b16ba799da9 + - d256a51a656b + - 511e5e3cd55e + - 8fef980d48b5 + - bbe19ef04a74 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: - - ebb0dcdb621a - - 6fcbee531de6 - - 7594365c546b - - 342a1d1fed7b - 875d0f36d66f + - 342a1d1fed7b + - ebb0dcdb621a - 675488238c96 - 3061c8b029e5 - - 72472698a2df + - 6fcbee531de6 + - 7594365c546b - 59db8ea8c845 + - 72472698a2df tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - cd06929b224b - - d865b62f501c - aa39b19ca11e + - cd06929b224b - a199cd7ac344 - 39bed8de8017 + - d865b62f501c - 78c533842eeb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -277,27 +277,27 @@ tools: owner: iuc revisions: - 2b2a352488fa - - 3edba9afc9bc + - 33b7d8481a76 - f11b994b7eb2 - f8564b2d7f63 - - 33b7d8481a76 + - 3edba9afc9bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - ef69617ecb42 - - e122f9101584 - 53c2bc8c2ae3 - - 378e55aeeb25 + - e122f9101584 + - ef69617ecb42 - 1d06c8b38e77 + - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - - ab5b7f6b7198 - 9a22227bb6d0 + - ab5b7f6b7198 - ba7b0f11e470 - f77f7a7f3b83 tool_panel_section_label: Assembly @@ -311,170 +311,169 @@ tools: - name: shovill owner: iuc revisions: - - d9f6a00b6db7 - - 865119fcb694 - - 196a599ec43d - f698c7604b3b - - ee17a294d3a3 + - 196a599ec43d - 83ead2be47b2 + - 865119fcb694 - ad80238462c1 + - ee17a294d3a3 + - d9f6a00b6db7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - 24e471d13fe9 - - 5a0ddb4dc3a4 - 5e0825476fb7 + - 5a0ddb4dc3a4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: + - 904bf932cf78 - 1fc82fe7ebef - 1bb12736175c - - 7490b213baa9 - - 904bf932cf78 - 051fd2db8a27 + - 7490b213baa9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: + - 808b3a0a6716 - ad8b536d1caa - 34305b013402 - - 808b3a0a6716 - - d6e617c4e338 - fee85957cebe + - d6e617c4e338 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 8d4b90bf9caf - - b8002c3f7141 - e5a3b75a271f - 21da31ed41a1 + - b8002c3f7141 + - 8d4b90bf9caf - 6b5a5842531e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 2a10645aeadd - - f1532cb33c75 - 328aa71f0f3c + - 2a10645aeadd - 9de69775f512 - 86f66ab58e14 + - f1532cb33c75 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 85fb02c43042 - 1708851f8804 - - 6aad515a5270 + - 85fb02c43042 - e41dcb0e913b + - 6aad515a5270 - 340bc17f49cf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - b3490b036c5a - - b65a43f70b99 - - d159735a6a9f - d5fb354f745d + - b65a43f70b99 + - b3490b036c5a - 249f6a28c751 + - d159735a6a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - 7897763d14ec - - dd7ad84f3943 - - 33368fec3b70 - d2d1df21dfb9 - 9006e5836729 + - dd7ad84f3943 - b7829778729f + - 33368fec3b70 + - 7897763d14ec tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - ced385aa976d - - 6f4c8ad6ea01 - 505a9833ab5d - - 189e837009c9 + - 6f4c8ad6ea01 - 8f631679571f + - 189e837009c9 + - ced385aa976d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - e59bee4565b3 - - d40ed4eb0c0e - - 356afed970b4 - 19bdfd1e6fe3 + - d40ed4eb0c0e - 9ded6109434a + - 356afed970b4 + - e59bee4565b3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: + - 6dd935e4984b + - 80a17897564d - ebd801e712bc - - b23249f81bc4 - 4688ae3b49b5 - - 80a17897564d - - 6dd935e4984b + - b23249f81bc4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - b5e35a2ca4f3 - 937ea677d437 - cb1e3db43020 - - 59bd28f6265d + - b5e35a2ca4f3 - b64696992ee9 + - 59bd28f6265d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: + - cb4768eeca3b - 05bd7504fdb2 - - 6015aa0303f2 - 383bb5ad32e2 - - cb4768eeca3b + - 6015aa0303f2 - 2628f6790eda tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - e92675014ac9 - 8f9f06995f98 + - e92675014ac9 - 6e26c9afd301 - - d10bdad2fd17 - - 9e3e80cc4ad4 - 0a3a602cd1e3 + - 9e3e80cc4ad4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - 920677cd220f - - 5da9a0e2fb2d - 08256557922f + - 5da9a0e2fb2d - 8d09f8be269e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 4a53b89fa703 - - 37d88f41c810 - 82398ba86ba7 + - 37d88f41c810 + - 4a53b89fa703 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index f8b23878a..9ba37af21 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,17 +2,17 @@ tools: - name: integron_finder owner: iuc revisions: - - 1ae00120dd24 - 4768f7f8e93f + - 1ae00120dd24 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - 8e8dc9a1e3e5 - - 31812e7a1315 - - 1f5641a52664 - ded48b36f3b7 + - 1f5641a52664 + - 31812e7a1315 + - 8e8dc9a1e3e5 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index 35dcfef42..70adf3e9d 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -2,8 +2,8 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - a9c9d768b751 - 204a131e47db - 159b04e36791 + - a9c9d768b751 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 6a4f5ede9..6a51bdf32 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: - - 0a5c785ac6db - b28e0cfa7ba1 - - 589e7e57fd6d - - dde39ba9c031 - - e19bebe96cd2 - - 87ee588b3d45 - - 07e8b80f278c - a1a923cd89e8 - - a68aa6c1204a + - 589e7e57fd6d - a8eabd2838f6 - ce3c7f062223 + - a68aa6c1204a + - 87ee588b3d45 + - e19bebe96cd2 + - dde39ba9c031 + - 0a5c785ac6db + - 07e8b80f278c 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 00690fc84..2f8127629 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,23 +8,23 @@ tools: - name: diamond owner: bgruening revisions: - - 62c9df8382c2 - e8ac2b53f262 - - f921014aba5a - 54f751e413f4 + - f921014aba5a + - 62c9df8382c2 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: + - 6f386c5dc4fb + - acf4e47b734c - 2889433c7ae1 - - e25d3acf6e68 - - d999e774072a - - 5edc472ec434 - 0e3cf9594bb7 - - acf4e47b734c + - d999e774072a + - e25d3acf6e68 - a52d2d93e595 - - 6f386c5dc4fb + - 5edc472ec434 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index 0a0d6fcee..7754df683 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -2,13 +2,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: + - 095ad4d096d1 - 6ca543ec1bf8 - c8cdde00b105 - - 710301bc46fa - da6bd1975a71 - - 095ad4d096d1 - 27ee142314a9 - f4230f116196 + - 710301bc46fa tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -80,15 +80,15 @@ 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: enumerate_charges owner: bgruening revisions: - - 2a868592ebcb - 67ee76f0e497 + - 2a868592ebcb tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -106,21 +106,21 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 88076940fa94 - - 0fac8e2afc13 - - bfb65cb551d8 - 3b8a9d5ced85 + - bfb65cb551d8 + - 0fac8e2afc13 + - 88076940fa94 - 79cfd9ead848 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: + - d532b7e5f64b + - 55918daa5651 - f5d979cb4b54 - 715cd0e87781 - - d532b7e5f64b - b46d4b4d995c - - 55918daa5651 - eb6564a60136 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -128,69 +128,69 @@ tools: owner: chemteam revisions: - d2f955aea23a - - f26afd1b7104 - - fdf2cc80adb5 - 5579659312e6 + - fdf2cc80adb5 + - f26afd1b7104 - dae135dfd519 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - 319a28774da9 - - d1d0efda35c0 - bc31d02be922 + - d1d0efda35c0 + - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - ed736e6eee39 - - cac1886249a2 - 4da9ee404eab - - 2c349b027a01 - 070e3ecc3fda + - ed736e6eee39 + - 2c349b027a01 + - cac1886249a2 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - d1f803b5943c - 73008ef1f487 - - f197e34c33a9 - 525ca7c8065f + - d1f803b5943c + - c0c9a5024177 - 2e219a2d9327 - - 807aa4c9293d - da8753545526 - - c0c9a5024177 + - f197e34c33a9 + - 807aa4c9293d tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 1809414a9454 - c4fbab8e03c5 - - 7568ae18908a - 2c8ed1b52bf7 - 27ea4e1a3f95 - 61094e01eff9 + - 1809414a9454 + - 7568ae18908a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: - - ba83f0923369 - d7ec25187599 - 730ef07b90ae - - ccfbd956a2d3 - 79e8ab8f1e81 + - ccfbd956a2d3 + - ba83f0923369 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 48d6a6eb438b - 9a3a1f698fc6 + - 48d6a6eb438b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: natural_product_likeness @@ -203,8 +203,8 @@ tools: owner: bgruening revisions: - e6011617c748 - - e2c36f62e22f - b59c91adeac1 + - e2c36f62e22f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_svg_depiction @@ -234,10 +234,10 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 85fad59f8168 - bf99565cec1f - - d4c67ced6abc - 9b48456a96fe + - d4c67ced6abc + - 85fad59f8168 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 97754ead5..a9358ee21 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,9 +2,9 @@ tools: - name: diffbind owner: bgruening revisions: - - c97a786e8fb5 - - fa56d93f7980 - 163688bb8f73 + - fa56d93f7980 + - c97a786e8fb5 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -16,18 +16,18 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 11cf21ee4242 - 4124781932db + - 11cf21ee4242 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: + - 640d3af5d833 + - 495a4173006f + - 86e2413cf3f8 - 424aefbd7777 - f5d67c722d67 - - 86e2413cf3f8 - - 495a4173006f - - 640d3af5d833 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index e56ba4ce1..a97c186cd 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -9,10 +9,10 @@ tools: - name: collapse_collections owner: nml revisions: - - 33151a38533a - - 90981f86000f - - 25136a2b0cfe - 830961c48e42 + - 25136a2b0cfe + - 90981f86000f + - 33151a38533a tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -25,15 +25,15 @@ tools: - name: split_file_to_collection owner: bgruening revisions: + - 6cbe2f30c2d7 - 0046692724f9 - baabc30154cd - - 6cbe2f30c2d7 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 57f0914ddb7b - 38eec75fbe9b + - 57f0914ddb7b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index f000c92a2..0d8580879 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -9,29 +9,29 @@ tools: owner: iuc revisions: - dad9da48a09a - - 0b3c3ad92827 - - 4a6ee918c13a - e3cbd2287f63 + - f3a19509108a - 6ef0b5664c69 - - a3b86937ead6 - 5e1240a87bcb + - 0b3c3ad92827 - 367b1ed91207 - - f3a19509108a + - 4a6ee918c13a + - a3b86937ead6 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - e177a8ea0bf1 + - bd46669113b9 - 33c99804a32f - - a4db66553a61 - - 501c21cce614 + - 1b5fc03380d4 - 72ed72122deb + - a4db66553a61 + - e525f9ffb9ac - 584008e574b2 + - 501c21cce614 - 54ccb7e1f49a - - e525f9ffb9ac - - bd46669113b9 - - 1b5fc03380d4 + - e177a8ea0bf1 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -56,8 +56,8 @@ tools: - name: fastq_to_fasta owner: devteam revisions: - - 8979c288aefb - 77b41c89d856 + - 8979c288aefb - 186b8d913e6c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -104,8 +104,8 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - f5c632894818 - 8190f6083c0d + - f5c632894818 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta @@ -125,10 +125,10 @@ tools: owner: galaxyp revisions: - 19e45916daf9 - - 63769c4217a7 - - b9b385097f13 - 26c6706bfb07 + - 63769c4217a7 - 92ac8e086317 + - b9b385097f13 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index 5aed6751d..2f5720491 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,22 +2,22 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - a1ca9bccc7f2 - - 29451af70c52 - - 5f6d123679f4 - - de72ba3ed6f2 - c929a006727f + - 5f6d123679f4 - 268e91e540ee - e821645ef8fc + - de72ba3ed6f2 + - 29451af70c52 + - a1ca9bccc7f2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 5d11599b8a7d - - 0e49b109abc2 - - 2d2cf5c1ea8a - 0e143b4c3987 + - 2d2cf5c1ea8a + - 0e49b109abc2 + - 5d11599b8a7d - 12af64f93288 - bb1e4f63e0e6 - 7a7fd0f5f15d @@ -27,58 +27,58 @@ tools: owner: bgruening revisions: - c06951d10364 - - 81b1e3e1fc6c - - dc059492a995 + - 7c1beb6d6eca - 1d848bc4585f + - 81b1e3e1fc6c - 195e98217334 - - 7c1beb6d6eca + - dc059492a995 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - 71aa86af6762 - - 26e7304d6737 - - bfff7454b59a + - a67ac707496a + - 93eb012d9eed - 3d211717a775 + - bfff7454b59a - 07418a30ed01 - - 93eb012d9eed - - a67ac707496a + - 26e7304d6737 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: + - dd0b7398bb96 + - 2bc10a9ca58b - 26983857c91a - 5be24eba848d - - b8858746dc1f - - dd0b7398bb96 - - 56d5b797ce84 - 29fcfd36e90a - - 2bc10a9ca58b + - 56d5b797ce84 + - b8858746dc1f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - c3e012dfe21f - - 7e6bcd2e5128 + - ee3a1b0f45f1 - 7ef978dc1b8a + - 9384cd033f30 + - 7e6bcd2e5128 - 72bfafe3330b + - c3e012dfe21f - e6d0bff01239 - - 9384cd033f30 - - ee3a1b0f45f1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - d9a637e83828 + - fb9cf9c97ec4 - b73e213add0c - - 167788df3b46 + - d9a637e83828 - 514fa53b5efb - 9470f29702f8 - - fb9cf9c97ec4 + - 167788df3b46 - a60c359ec43c - fd1275e01605 tool_panel_section_label: DeepTools @@ -86,121 +86,121 @@ tools: - name: deeptools_correct_gc_bias owner: bgruening revisions: + - c34d11ea4ba6 - ca0616bb2cdf + - a02cfa31e9cb + - 2c37ce318bc3 - e479c7ca5570 - - c34d11ea4ba6 - 5bffaa8354a1 - 86febdcc4283 - - 2c37ce318bc3 - - a02cfa31e9cb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 69a8621ca2f0 - - 78f405266706 - - 1fcb7adc39b8 - 004aea905d4d - - 2d466b530754 - 192ef85c0b0b + - 78f405266706 - 01fb6a7654e6 + - 1fcb7adc39b8 + - 69a8621ca2f0 + - 2d466b530754 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 459cfa861f0b - d9ce4897dbb2 - - db940c262830 - d580d6acd1df + - db940c262830 + - 459cfa861f0b - 3c9f0c486cca - - 9ecba5e225a6 - 137c4beed34b + - 9ecba5e225a6 - 2f9e4843f480 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - fd408d755394 + - fbe773640707 - bd7db9e2f2cb + - fd408d755394 - 2c66e43f1c86 - - fbe773640707 + - 32e451def88c - f264afa9fa6f - bad3ca889618 - - 32e451def88c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 4e12ea27f788 - - 7e361d147872 - - 7fda5607e777 - 3b9d990a0a0e - - 9368fbc49c8b + - 7fda5607e777 - 56bce3c82278 + - 7e361d147872 + - 4e12ea27f788 + - 9368fbc49c8b - 231994413f89 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - 4431f39ede55 - ce4ce3316f74 - - c03c3384cd81 - - d9114ef1c8a5 + - 94ca68515826 + - 4431f39ede55 - b1779366c8e9 + - c03c3384cd81 - e65d16fb2724 - - 94ca68515826 + - d9114ef1c8a5 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 793665fff0f8 - - 23f7c5f1fdaf - b88ebb3672a1 - - 4ed32329e0ed + - 23f7c5f1fdaf + - 793665fff0f8 + - d57251071381 - 2da482e408b8 - f8fc4e5aff9d - - d57251071381 + - 4ed32329e0ed tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - e4c7985d4585 + - 25d830337d31 - ba6efa77fb79 + - c60570fa602f - a4dfb122e52b - 010e58e9d822 - - 25d830337d31 - - 512155688d98 - - c60570fa602f - a7849312d328 + - 512155688d98 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - 4d678170d29b - - c899e0ccff8c + - 00d869ea03a1 - 69264da0ce77 - - 443d9a9d6d11 + - c899e0ccff8c - aa200e4f3939 - 38e3f226248b - - 00d869ea03a1 + - 443d9a9d6d11 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - c361b12d207a - 10301d137111 + - a2d70c4fd406 + - d806504e96d9 - 6662b1a8d326 - aac8444d6681 - - d806504e96d9 - - a2d70c4fd406 + - c361b12d207a 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 128085fbe..d3712dc89 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -9,8 +9,8 @@ tools: - name: obi_clean owner: iuc revisions: - - 12baadec7809 - 7d16de45c021 + - 12baadec7809 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -37,8 +37,8 @@ tools: - name: obi_ngsfilter owner: iuc revisions: - - 76e69de726b2 - 3bf57dadf7cd + - 76e69de726b2 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort @@ -58,8 +58,8 @@ tools: - name: obi_tab owner: iuc revisions: - - 5f7003111e32 - 3299c7d5268f + - 5f7003111e32 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index 9e65a9209..90da8fd01 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -3,8 +3,8 @@ tools: owner: devteam revisions: - ce385837c160 - - 832c20329690 - - dba489bfcd62 - 63dd26468588 + - dba489bfcd62 + - 832c20329690 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 c8668c907..9e5b4b27f 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -2,10 +2,10 @@ tools: - name: bwameth owner: iuc revisions: - - d82648ad25a3 - 6da3972210ee - - 62f5fab76dfb - 29bdbc353f20 + - d82648ad25a3 + - 62f5fab76dfb tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index 1a9a552a0..1fbdeb1cf 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,30 +8,30 @@ tools: - name: cutadapt owner: lparsons revisions: - - c053d4cad713 - - 48f587c13075 - - de6cebe3c043 + - c4b82dce8335 + - 093678460093 + - 44e2cc14f75b - 8c0175e03cee + - 660cffd8d92a - 8665bcc8b847 - - c5e2e5902201 + - 4e5056fefd88 - e4691e1589d3 + - de6cebe3c043 + - c5e2e5902201 + - 288f97432497 + - 135b80fb1ac2 + - c053d4cad713 - 49370cb85f0f - - 093678460093 - - 660cffd8d92a - 5915ea1ec9b1 - - 135b80fb1ac2 - - 4e5056fefd88 - - 44e2cc14f75b - - c4b82dce8335 - - 288f97432497 + - 48f587c13075 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: + - f666895cbebd - 8889eb864cef - 9db07fd39f85 - - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length @@ -56,48 +56,48 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 516b97a23d7e - 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: - - 2904d46167da - f546e7278f04 + - 2904d46167da tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: - f773e98b26cf - - f81d4362b6c1 - ec0b5076173a + - f81d4362b6c1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: + - cd0874854f51 - 0dbb995c7d35 - - 56022eb50bbd - 9c620a950d3a - - cd0874854f51 + - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - dbf9c561ef29 - 65b93b623c77 + - dbf9c561ef29 - 1d8fe9bc4cb0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner owner: devteam revisions: - - b05e39b9c170 - f1dc2a761c30 + - b05e39b9c170 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -110,29 +110,29 @@ tools: - name: fastq_groomer owner: devteam revisions: - - 47e5dbc3e790 - 8611b80a14d6 + - 47e5dbc3e790 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation 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 owner: devteam revisions: - - 9dfda4e310ed - 9282652e7234 + - 9dfda4e310ed tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer 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 @@ -145,16 +145,16 @@ tools: - name: fastq_paired_end_joiner owner: devteam revisions: - - 09a2199cd356 - c885369b207b + - 09a2199cd356 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: - - e39cc71d3ed6 - - 35e38452bb3f - 249c8393f2d4 + - 35e38452bb3f + - e39cc71d3ed6 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -168,15 +168,15 @@ tools: - name: fastq_stats owner: devteam revisions: - - b1cea1b2fcd0 - f0e7deab6518 + - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer owner: devteam revisions: - - 33794bdb7fe0 - b63b2bfb3ea3 + - 33794bdb7fe0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta @@ -189,61 +189,61 @@ tools: owner: devteam revisions: - d5e9e83cd3d8 - - 09070cacefd8 - - 529bccd5e4a1 - 567d5b3c52b1 + - 529bccd5e4a1 + - 09070cacefd8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - - 0b7ec11b3c7c - 8abdedf55101 + - 0b7ec11b3c7c - 4bedca26c133 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper owner: devteam revisions: + - 90858c306551 - cb1e251cac37 - 736b8f6ee456 - bdf1ce174e39 - - 90858c306551 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: - - 07497255281e - - 421f0af4ee95 - 7ce1891db6f5 + - 421f0af4ee95 + - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - - f984bb114520 - 02f8a17a4ebd - - 3599f5451ee2 - b29d37ca9e41 + - f984bb114520 + - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - 6027ef51ef91 + - 0c2907307ba4 - e246088b6e34 - 177f0621c266 - - 0c2907307ba4 + - 6027ef51ef91 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - 377ac2829eac - - 61b4cedc8934 - - 547e8d00f11c - 73194cdd4f57 + - 547e8d00f11c + - 61b4cedc8934 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -262,8 +262,8 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 8e1a90917fa7 - 3b0a14722175 + - 8e1a90917fa7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -276,8 +276,8 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - 51b771646466 - dfa082f84068 + - 51b771646466 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -290,11 +290,11 @@ tools: - name: umi_tools_count owner: iuc revisions: + - 24013bf85a6f + - e654095ab143 - 8250ea3a1501 - a535cf1e5da4 - - 24013bf85a6f - b557acca0b56 - - e654095ab143 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup @@ -306,11 +306,11 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 6a675c3aa610 - - 828dba98cdb4 - - 27ac32a22ad2 - 9fa7803d1c51 - - f3759eec3018 - 7accf7407811 + - 828dba98cdb4 + - 6a675c3aa610 + - f3759eec3018 + - 27ac32a22ad2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastq_quality_control.yml b/usegalaxy.org.au/fastq_quality_control.yml index ab432b1d0..1f9ecd1e4 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -3,28 +3,28 @@ tools: owner: devteam revisions: - e41385662e5e + - 64e9a6afdd0c - ce9cd02d5b88 - 7b4468117008 - - 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: - - f2e8552cf1d0 - - 3d0c7bdf12f5 - - 9da02be9c6cc - - ff9530579d1f - 5ec9f6bceaee + - ff9530579d1f - e7b2202befea - 2b0c9d9fc6ca + - 3d0c7bdf12f5 + - 9da02be9c6cc + - f2e8552cf1d0 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -53,30 +53,30 @@ tools: - 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 - - bf675f34b056 - - c1a4b5f3b432 - abfd8a6544d7 - 75c93c70d094 + - 3d93dd18d9f8 + - c1a4b5f3b432 - 5e33b465d8d5 + - b2f1f75d49c4 - 1c2db0054039 + - bf675f34b056 - 9a913cdee30e - - 3d93dd18d9f8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 949f01671246 - cd7e644cae1d + - 949f01671246 - 084bbd8ba7b8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index 85c239a05..d934ded82 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs @@ -15,8 +15,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: - - 83a19df00eab - 85ef5f5a0562 - 141612f8c3e3 + - 83a19df00eab tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index 502f37a89..15ffefd3d 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -2,8 +2,8 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 3630a6e624d4 - 142d95ab942e + - 3630a6e624d4 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend @@ -16,9 +16,9 @@ tools: - name: gemini_annotate owner: iuc revisions: + - f2f3bc622a16 - 0c8f7322f8fc - 8f53b238a360 - - f2f3bc622a16 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -38,8 +38,8 @@ tools: - name: gemini_db_info owner: iuc revisions: - - 7d75673f4d6f - 4c5f4e9b1931 + - 7d75673f4d6f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo @@ -86,9 +86,9 @@ tools: - name: gemini_load owner: iuc revisions: + - cf61daf064fe - 45296e47d565 - b2c25142267e - - cf61daf064fe tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -101,15 +101,15 @@ tools: - 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: - - 6b09debcfc49 - 9199331c3421 + - 6b09debcfc49 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -122,9 +122,9 @@ tools: - name: gemini_query owner: iuc revisions: - - 666f60a9331a - - 840fb4850be3 - da74170c55c7 + - 840fb4850be3 + - 666f60a9331a tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -151,8 +151,8 @@ tools: - name: gemini_set_somatic owner: iuc revisions: - - e4e2128460e3 - ef9991a4a9a7 + - e4e2128460e3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats @@ -165,7 +165,7 @@ tools: - name: gemini_windower owner: iuc revisions: - - 8f04952b8882 - 0c58ba91d018 + - 8f04952b8882 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 0fe27413f..095be2eba 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -9,8 +9,8 @@ tools: - name: mageck_gsea owner: iuc revisions: - - d46e36492bff - b946929d31c4 + - d46e36492bff tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle @@ -30,7 +30,7 @@ tools: - name: mageck_test owner: iuc revisions: - - 688a8eccea71 - 9b4f4533c9ee + - 688a8eccea71 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index 687be192c..094a7a615 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,48 +2,48 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - e9df53a75f3c - - c1b437242fee - - 983bf725dfc2 - b39347891609 + - 983bf725dfc2 + - c1b437242fee + - e9df53a75f3c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download owner: iuc revisions: - - 28587613264f - e063168e0a81 - 1c58de56d587 + - 28587613264f tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 83c7d564b128 - - 734abc7ac21d - - c441583adae5 - - 69ebb7f46e45 - - 6ea73833cf67 - - 1790dcf3c32d + - 4317d3cb6cba + - e08a7ad4378b - 7068f48d0ef9 - - aad3885b3216 - - 9a776b080193 - - 5e6237d58b0c + - 6ea73833cf67 + - 4df8de2d0e48 - e407b9da183a + - 83c7d564b128 + - c441583adae5 - f5ea3ce9b9b0 - - e08a7ad4378b + - 734abc7ac21d + - 5e6237d58b0c - 653e89d73fc4 - - 4317d3cb6cba - - 4df8de2d0e48 + - aad3885b3216 - 6591f049cf7e + - 9a776b080193 + - 1790dcf3c32d + - 69ebb7f46e45 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: + - 75b3b3d0adbf - 7863f1abcdda - 9aaa46d45472 - - 75b3b3d0adbf - 34758ab8aaa4 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 d9d10fea6..3eb22f9c6 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: - - a64dc31ab7f2 + - c4bde687c846 + - 740057a5126d - fd59d783248a - - 7f13dc906cb9 - - ae9994cf526f - 290a11559985 - - c4bde687c846 + - 7f13dc906cb9 - 4b519282a05b - df7356989ac1 - - 740057a5126d + - ae9994cf526f + - a64dc31ab7f2 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,9 +28,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: + - 867ab348287d - 7cf5b1d072b5 - f95284aa2946 - - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -42,31 +42,31 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - ca7cb0eaad62 - 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: - - 10515715c940 - - 3d059e9c2fba + - 391a4cc45fea - da4c086cff5b + - 3d059e9c2fba + - 10515715c940 - d3a9e32672ec - - 391a4cc45fea tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 3b12bf9b4b87 - - d0fc8b746d57 - 1acf88921176 - 5fe1dc76176e + - 3b12bf9b4b87 - e3a675da7fd0 - 299307abd804 + - d0fc8b746d57 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -98,17 +98,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 1cfc579079a6 - - a6e57ff585c0 - - 4542035c1075 - 6cd09d7b5f37 - - 836d1aa3e89a + - 667e17248bfe + - 4542035c1075 + - fd5dbf0f732e - 2bb2e07a7a21 + - a6e57ff585c0 - 112eb40ba6cf - - ca2def38369c - - fd5dbf0f732e + - 836d1aa3e89a + - 1cfc579079a6 - 17359b808b01 - - 667e17248bfe + - ca2def38369c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -140,15 +140,15 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: - - 62e3a4e8c54c - 85da91bbdbfb + - 62e3a4e8c54c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot owner: bgruening revisions: - - 7b21a9b5922f - 9958188c6195 + - 7b21a9b5922f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_regression_performance_plots @@ -174,22 +174,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - 7dd841a32245 - - 2824d77cd8f8 + - 14e7c35f3d00 - 360df4999907 - a1abfa420d9d - - 4ac4e7083b7e + - 2824d77cd8f8 + - 7dd841a32245 - 326a3db8d9d1 - - 14e7c35f3d00 - 59fd173ac850 + - 4ac4e7083b7e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 44608d0193ed - 73b8cb5bddcd - 83c573f2e73c + - 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 565534d9b..3a82427d9 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 14b3f2a4523b - 1a642de6db01 + - 14b3f2a4523b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph @@ -82,8 +82,8 @@ tools: - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 9a2f72d7dbd2 - 94697510d55f + - 9a2f72d7dbd2 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index 82f3cf3fd..315f3ddde 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,45 +2,45 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 9edf8894a22d - 29f66c353bcb - - ed2cca6b5de4 - 921a2da49a0c + - 9edf8894a22d + - ed2cca6b5de4 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - ec4b948dc6f0 - - 78fb5e286609 - - 5746d61f0a91 - d404277cc87a + - 5746d61f0a91 + - 78fb5e286609 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 9e357a8b2ec3 - - 03dd3c16ae4e - 977dc15add20 - 4d511437b1e5 + - 03dd3c16ae4e + - 9e357a8b2ec3 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - 77919cc3618e - - 3b5b54ed6392 - 0ba4f56a3613 + - 3b5b54ed6392 - 41dbf4d162a2 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - b63363075c2e + - 9939786dd9c9 - 7babd8a46fe0 - 5308ca68ef3d - - 9939786dd9c9 + - b63363075c2e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index f271e5b3e..f5f3a1eb3 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,9 +2,9 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 81f0cbca04a7 - - 0c777d708acc - 3df9f0a4bf34 + - 0c777d708acc + - 81f0cbca04a7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction @@ -24,23 +24,23 @@ tools: - name: 2d_histogram_equalization owner: imgteam revisions: - - 77f7159d775a - 70316d792fc9 + - 77f7159d775a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - f70b215d155c - dba87c4b32d3 + - f70b215d155c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - - b07f4839ca77 - 85edbb7a436b - f3360fbeda64 + - b07f4839ca77 - 10eed33aa9b2 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -54,80 +54,80 @@ tools: - name: count_objects owner: imgteam revisions: - - 664232d2a3f7 - - 5bf8eb50b280 - b58447a2eed2 + - 5bf8eb50b280 + - 664232d2a3f7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - 0e4dccaafef5 - eb6c08714244 + - 0e4dccaafef5 - e917a2424690 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - bad171ed1e96 - e8f822eeb9fd + - bad171ed1e96 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: + - 670975e92458 - e7273daa5ae2 - 6070780813d9 - - 670975e92458 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - cdf8e3c57dae - - ef4aed1d34c4 - df3ad3ba5c6f + - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: - 6a7da2e5f696 - - 5d28ac336861 - 2484086dee41 + - 5d28ac336861 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - f2ed92b011a9 - - 11f177b1a59e - bace5a93a97c + - 11f177b1a59e + - f2ed92b011a9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - f24c370e5ea4 - f8fa0f6718a3 - d0178bdcd00e + - f24c370e5ea4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - 3245681b2f6d - - 31d195bedf6d - ad271f78a87a + - 31d195bedf6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - - 993faa34333b - - b6eec6087271 - 87d4d92d7487 + - b6eec6087271 + - 993faa34333b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math @@ -141,17 +141,17 @@ tools: - name: cp_mask_image owner: bgruening revisions: - - b178453ea8d1 - 667a513e67e4 - 3a05117669cf + - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - a1a961c46d4b - 2564f461de62 - ac5bea85a391 + - a1a961c46d4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied @@ -165,41 +165,41 @@ tools: - name: cp_measure_image_intensity owner: bgruening revisions: + - 8536b1ae0254 - 5499dc6f8ac1 - b64af54c5c09 - - 8536b1ae0254 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - 6f4715b8540a - e972e07c7845 + - 6f4715b8540a - d3890df07463 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - e52c75a28c4b - 407925835dd9 + - e52c75a28c4b - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - d85f11570109 - 79e10d12d90a + - d85f11570109 - acf3aa487283 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - 035a58c7f54a - 80b200ae516b - b76841ee5560 + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -212,17 +212,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 48102a685037 - - 8083a87d2fdf - 3a3033222f61 + - 8083a87d2fdf + - 48102a685037 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 @@ -234,8 +234,8 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 972d2c365739 - 1fd453cd757b + - 972d2c365739 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index 08338d2b7..440504fea 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,29 +2,29 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 3e4f434a69c6 - - 78bbd17d0703 - - f362150bef41 - e319b5b65879 + - e4ee04da1c19 + - 1069f6db0a0e - a38934e303b9 - d6e72da3ec35 - - e4ee04da1c19 + - f362150bef41 + - 3e4f434a69c6 - 17f911830a8c - - 1069f6db0a0e + - 78bbd17d0703 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - f91cfb73d369 - - 72ddd32392cd - - 7fe36019c073 - - c88553ec696e - 8f8df367470d - 9537184d421f - - 1ef5b6e3e09d - 0135f1d487a0 + - 72ddd32392cd - 2b95d5c04908 + - 7fe36019c073 + - f91cfb73d369 + - 1ef5b6e3e09d + - c88553ec696e tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked @@ -32,58 +32,58 @@ tools: revisions: - fafb3d685fa9 - ad0dc9f4c9e2 - - 2cf4a1cafc16 - d7e79eb3bcb3 + - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 8c05afb547fa - - 7f1cfa4c0e32 - ee29337f905c + - 3d18f8c3c0f6 - 8d36959b000d - - ee2beb764a7b - - 43aac8d29685 - - bd2a7d1316b9 - - 69797fa273c3 - 9eaadf03e0df - 94df24c6bc00 - - 6a1515bb0687 - - 3d18f8c3c0f6 + - bd2a7d1316b9 - 28a6f1908fcc + - 69797fa273c3 + - 8c05afb547fa + - ee2beb764a7b + - 43aac8d29685 + - 6a1515bb0687 + - 7f1cfa4c0e32 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 5671e1d3d5ee + - 0893a1dbb807 + - e3bb03cf207a - db536ad45f28 + - bcaa0d571ce2 + - c092052ed673 + - cb903c9dc33d + - 5671e1d3d5ee + - 5d6ed46cc101 - 9f978da6528a + - 364f4ffec275 - 8858fa037a15 - - c092052ed673 - d37ede8589b2 - - 364f4ffec275 - - bcaa0d571ce2 - - 5d6ed46cc101 - - cb903c9dc33d - - 0893a1dbb807 - - e3bb03cf207a tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: + - ed28dd32141c - f95f403841ad - - 230b05597996 - 49236b03e4fd - - ed28dd32141c - - 12d66d0d05ac - e1a015876aa9 + - 230b05597996 - 045d6d00f606 - - 3b6a16d82c1b - 38b91a3190cd + - 3b6a16d82c1b - c5c9f02b6167 - 584beffa972b + - 12d66d0d05ac tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/join_subtract_and_group.yml b/usegalaxy.org.au/join_subtract_and_group.yml index db95dd412..ec3febcd7 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: - - b8a457820315 - 17e3b698dd52 - - 0f1724dd59d2 - 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 - - ba0c40780ecf - - a513e3fbb4c5 - 22c2a1ac7ae3 - 374cb875d38a + - a513e3fbb4c5 + - ba0c40780ecf tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index f3ac7019e..aa72129b0 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -2,99 +2,99 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 522137aaa9c4 - 66d7efc06000 - 772e0e89fc68 + - 522137aaa9c4 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - f22a9297440f - 4d81e3e2fb63 - 8a794e6d3388 + - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - b6ef6d0cb6b7 - - e1317b5502fa - 818f9b69d8a0 - - 2af1346e68c9 + - e1317b5502fa - f1b9a42d6809 + - b6ef6d0cb6b7 + - 2af1346e68c9 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: + - 1588f9076e32 + - 05143043ca13 - 947c2eacccb8 - 8334dc98c48e - - 1588f9076e32 - c80db5d6fd8c - - 05143043ca13 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - - 29e4122c90de + - 83228baae3c5 - 1552b8cb4a94 - 25b46af53232 - - 83228baae3c5 - 9991c4ddde14 + - 29e4122c90de tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - 53616c8b0865 + - a07ab242b0b5 - 060ca94ac049 - 1a53edc4b438 - - 841a6cc5fc58 - f3dfa4bdf87e - - a07ab242b0b5 + - 841a6cc5fc58 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - 927586a18553 - - 40f4447733b2 - 91c4e3331208 - - 2fc89dcd41c8 - d4808d5b83da - dc4b5fd604a6 + - 40f4447733b2 + - 2fc89dcd41c8 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - c6ae57f774c6 + - 25ab6b4e376e - 7626ea9c2e1b + - c6ae57f774c6 + - e5a5ad882f1f - 301e07345c93 - 36e8d6d5d01b - - e5a5ad882f1f - - 25ab6b4e376e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - f9639b488779 - - 4ed102b922cb - - 02d2be90dedb - 80852884053f + - 4ed102b922cb + - f9639b488779 - 0630258dcf35 - b7c3e9a3b954 + - 02d2be90dedb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - caeb57858702 - - ec69cbe34b73 - 14180f9c831e - 61634a87efc7 + - ec69cbe34b73 + - caeb57858702 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index bf627e0a8..73976cb4d 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,14 +2,14 @@ tools: - name: bowtie2 owner: devteam revisions: - - 017aba02828d - - 03e9b2fbc005 - - f6877ad76b00 - 937aa69e715f - cd659e8cc5fa + - f6877ad76b00 - 3ba8d4563129 - - a6d65b0c67af - 749c918495f7 + - 03e9b2fbc005 + - 017aba02828d + - a6d65b0c67af - 17062a0decb7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -22,16 +22,16 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - b4a22d90cce9 - bfaa0d22c2e4 + - b4a22d90cce9 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - - 53646aaaafef - - 64f11cf59c6e - 3fe632431b68 + - 64f11cf59c6e + - 53646aaaafef - e188dc7a68e6 - dfd8b7f78c37 tool_panel_section_label: Mapping @@ -47,40 +47,40 @@ tools: revisions: - e7f19d6a9af8 - 37b497aa133f - - 3e1ea2facca6 - - 2ff111fac1d7 - 60afcc2c1d05 + - 2ff111fac1d7 + - 3e1ea2facca6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 8c6cd2650d1f - - 53c0b7a1a0c3 + - be1d967337e4 - 77b2770508f6 - 037c6e54df11 - - b3eab4b67562 - - c0c2d0941de8 - 09b53c1d4ab1 - 11a0d50a54e6 + - 53c0b7a1a0c3 + - 8c6cd2650d1f + - c0c2d0941de8 - f54f5baedfdd - 3f4d6399997b - - be1d967337e4 - 6b1e195506a3 + - b3eab4b67562 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 00fbfac99d39 - - 178bdbdb6d24 - - 1cd2511a396e - 13022c3d3076 - - 79b885ce78d7 - - 9ee34ba73ebf + - 00fbfac99d39 - ec9cbd6b9a49 - b8f5f6e87f5c - 5ef7ec16b04f + - 1cd2511a396e + - 79b885ce78d7 + - 178bdbdb6d24 + - 9ee34ba73ebf - e403d27e8f24 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index 35413c9bd..cb3635494 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -2,15 +2,15 @@ tools: - name: cat_bins owner: iuc revisions: - - 0094893f5001 - 18676df0cb3a + - 0094893f5001 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_summarise owner: iuc revisions: - - 388e6678fa98 - 7f1aaa1932d8 + - 388e6678fa98 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: combine_metaphlan2_humann2 @@ -22,46 +22,46 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 7c2100246a2f - - 76d3d2b10738 - 63f86089423e + - 76d3d2b10738 - 5b5a7af9fbb4 + - 7c2100246a2f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 84fd33a60b35 - - 18a502a9d287 - 96336c6a2bb7 + - 84fd33a60b35 - 1c35dadbe76f + - 18a502a9d287 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: + - f732237754fc - addaf9d22850 - 34e55239e68b - a9f4a217dcd6 - - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - 8c202e741d68 + - 75403243703a - 04c15826a0b8 - 0776d824d896 - - 75403243703a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 8470de786d47 - - 43c99742158b - e96bbb9e24ea - 1c9b3bcd4261 + - 43c99742158b + - 8470de786d47 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs @@ -76,35 +76,35 @@ tools: - name: dada2_plotcomplexity owner: iuc revisions: - - ac72310b038a - - 78faebd0879c - 555ccac8a4c5 + - ac72310b038a - 8daf4564ccda + - 78faebd0879c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - f947b4bb5107 + - d60df8727f59 - a58e4a43f49c - 7b8cb2b02978 - - d60df8727f59 + - f947b4bb5107 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: + - 7136e9ab70db + - 1bc3657cd694 - 7f3b59dee073 - 04144473e59e - - 1bc3657cd694 - - 7136e9ab70db tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 0a1224c4b781 - d943081510da + - 0a1224c4b781 - 19299bb1c6af - 9058d8943303 tool_panel_section_label: Metagenomic Analysis @@ -119,9 +119,9 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - c4db8c4de66f - - dbf1798c0dcc - 6501b5b33988 + - dbf1798c0dcc + - c4db8c4de66f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -134,9 +134,9 @@ tools: - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 6c84982ee6f7 - 6d364c65c946 - 654548ae1357 + - 6c84982ee6f7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -148,25 +148,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - bd7a9c6efb10 - 6aad8ca3918b - e66ab198ec15 + - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - d77397f09da1 - b084117133af - c6676a890f50 + - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - 9704f1a3b32d - - cad93abecac9 - 7f208f1eb64f + - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -179,48 +179,48 @@ tools: owner: iuc revisions: - c409a495841f + - 31c6d107e7a5 - 79706f10d680 - e88b731dad59 - - 31c6d107e7a5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 172920f67a84 + - 71ea608ddfa3 - 714d5a28cc5c - - d24841f5c3d2 + - 172920f67a84 - 094ad9c068af - - 71ea608ddfa3 + - d24841f5c3d2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - 4137b492233e - d7e9a3c41657 - a293a742194f - a4d7148ccee4 - 12fb63b5f63f + - 4137b492233e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: - - e2c71b852aba + - 6fcb8ac37a3e - cf87759761eb - 97f7bb0851e7 - - 6fcb8ac37a3e - - 75bedfb2078b - 64bc7acc22a9 + - e2c71b852aba + - 75bedfb2078b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - - 080ea153677c - - 5e5a999ffaa9 - 4033827c76b8 + - 5e5a999ffaa9 + - 080ea153677c - c82508e76ad1 - 2d35528d2141 tool_panel_section_label: Metagenomic Analysis @@ -229,9 +229,9 @@ tools: owner: iuc revisions: - 2cd76b089570 - - fc6c328c292f - 6b7622dda516 - 95bf7479d53c + - fc6c328c292f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: jellyfish @@ -291,16 +291,16 @@ tools: - name: kraken2 owner: iuc revisions: - - 328c607150ff - - 4a9da2b6c2e3 - e674066930b2 + - 4a9da2b6c2e3 + - 328c607150ff tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax owner: devteam revisions: - - 50bd98b3ae5a - f03c7ba8d8bc + - 50bd98b3ae5a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -370,19 +370,19 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - 2cff76cf35c6 - - 0270541aaf46 - 4fd3b5d8706b - e073891b2afc - 27250f92a01a + - 0270541aaf46 + - 2cff76cf35c6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - 76bc4efa1aeb - - eb50e7eca3dc - 708abf08a626 + - eb50e7eca3dc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -448,19 +448,19 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - ebb74774457e - fdbd63e92b01 + - ebb74774457e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: + - 6dee4abadccb - ff8f55893e7d - - b89b0765695d - 2131d7dca455 - - 1a6cdf55390f - a16313517e55 - - 6dee4abadccb + - b89b0765695d + - 1a6cdf55390f - a92a632c4d9b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -533,8 +533,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 9168545e09df - 0ba7dfaa941d + - 9168545e09df tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -571,11 +571,11 @@ tools: - name: staramr owner: nml revisions: - - 4d83eccf5f81 - 3b22de20bd4b - - 4b9a8031ab74 - aeaa20b96ef2 + - 4d83eccf5f81 - be818ae858e4 + - 4b9a8031ab74 - 2fd4d4c9c5c2 - 141afacabcfa tool_panel_section_label: Metagenomic Analysis @@ -583,8 +583,8 @@ tools: - name: vsearch owner: iuc revisions: - - 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 8a8ade97a..63a07202b 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: - - 12e856482d26 - de3cfb122105 + - 12e856482d26 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -405,8 +405,8 @@ tools: - name: mothur_make_contigs owner: iuc revisions: - - ab12df91b47f - 4e9136c2c4c3 + - ab12df91b47f tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_make_design @@ -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/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 434617314..9f6f631b7 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,37 +2,37 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - a74dbfee5a86 - - 6ae5a7b5a0a2 - - 94b8c6013083 - - 9baa871cb1d1 + - 2263989660f5 - 48c13389050d + - bdfbaf0c10aa - cd07731e4434 + - 6ae5a7b5a0a2 + - 9eeb13a92d79 - 9422c5a87ee2 - - 8b67dd48fec1 + - 9baa871cb1d1 + - a74dbfee5a86 + - 94b8c6013083 - 80f03df2e2ce - - bdfbaf0c10aa - - 9eeb13a92d79 - - 2263989660f5 + - 8b67dd48fec1 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: + - 5abf2c2249aa + - '764845535798' - f14193ec1f50 - fc2e49f91e52 - - f0af8936ed41 - aaa0d6a8b808 - - '764845535798' - - d390fe1567dc - - d7ce0ec78e51 + - 2e093badc689 - c18157c68134 - - 3ff17bad4006 - bc3831dd65c1 - - be78f13134e2 - - 2e093badc689 - 4a60927aaca5 - - 5abf2c2249aa + - be78f13134e2 + - d7ce0ec78e51 + - f0af8936ed41 + - 3ff17bad4006 + - d390fe1567dc tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -44,15 +44,15 @@ tools: - name: chromeister owner: iuc revisions: - - b768cc4cca40 - e483be1014b6 + - b768cc4cca40 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw owner: devteam revisions: - - d6694932c5e0 - 5b097fde95dd + - d6694932c5e0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -64,40 +64,40 @@ tools: - name: mafft owner: rnateam revisions: - - f0d493f8f84f - 15974dd17515 - - 6f28e90db932 - - c5908940967d - f1a5908ea2cb - a65296ffb4a0 + - 6f28e90db932 + - f0d493f8f84f + - c5908940967d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - fbca557a4847 - b3acbb3a6af0 + - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - 60698466facd - c9685bc0407c + - 60698466facd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - bcd65de9725b - 48823c9635a4 + - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - 4fc0cb2ac8ae - ebe3b0f84de9 + - 4fc0cb2ac8ae tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index 6ea74f125..cb65aa2fb 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -2,33 +2,33 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - 79e9a869f40e - 0e9e7fcdd543 - - 72b5e9dda577 - - fc8804320156 - cb34f00cc10f + - fc8804320156 - a7228a7ea146 + - 79e9a869f40e + - 72b5e9dda577 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - 18505fe2bdb1 - fa11aa8103b2 - - d6cddc06aeae + - 18505fe2bdb1 - db25ec99c3ea + - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: - - edf6d4003fad - 222669c4afb6 - - eb746fa6f514 - - 19f3b583a9b3 - - 2bf63b38ee9b - - 0f5f4a208660 - ec699520444c + - 0f5f4a208660 + - 2bf63b38ee9b + - edf6d4003fad + - 19f3b583a9b3 + - eb746fa6f514 - cc36773a3681 - 43815fa60f3a tool_panel_section_label: Nanopore @@ -50,9 +50,9 @@ tools: owner: iuc revisions: - edbb6c5028f5 + - 645159bcee2d - a3c4fe6f49ab - 0f1c34698076 - - 645159bcee2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign @@ -66,17 +66,17 @@ tools: - name: nanopolish_methylation owner: bgruening revisions: - - a8d4be409446 - - 90a922f32523 - be95355fef8d + - 90a922f32523 + - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 449e9aeded2d - 4857d5bcce52 - d376944466bf + - 449e9aeded2d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants @@ -90,16 +90,16 @@ tools: - name: porechop owner: iuc revisions: - - 93d623d9979c - 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 @@ -111,8 +111,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - 5a82eb9e1b89 - 47936349f3e9 + - 5a82eb9e1b89 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -175,8 +175,8 @@ tools: - name: poretools_yield_plot owner: iuc revisions: - - ca22d8497db5 - 64a83664b814 + - ca22d8497db5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: pycoqc diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index 543db9236..16117c449 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -21,16 +21,16 @@ tools: owner: iuc revisions: - d74850cf4e42 - - 3e73c97f025d - adfd6bf710bd + - 3e73c97f025d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 1586b111d2a3 - - 83da94c0e4a6 - 9dd107db92c2 + - 83da94c0e4a6 + - 1586b111d2a3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -42,8 +42,8 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 19b6a2f0dbe2 - 2f27f3b86827 + - 19b6a2f0dbe2 - ed1518ce2237 - e4b4837f06f5 tool_panel_section_label: None @@ -64,16 +64,16 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 74af283d8ebd - 472dabcb03bf + - 74af283d8ebd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_dada2 owner: iuc revisions: + - 38ccd4589990 - 48a42ca61006 - 5711fc06a63e - - 38ccd4589990 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -100,8 +100,8 @@ tools: - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - 4d3eff1bc421 - b1bc53e9bbc5 + - 4d3eff1bc421 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -120,10 +120,10 @@ tools: - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 52b6a4d98009 - - 172815da3d41 - - b4b2b284230a - 27a6a256cd23 + - b4b2b284230a + - 172815da3d41 + - 52b6a4d98009 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -148,16 +148,16 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 87febc68b45b - 19bbd19b74b3 - fea85c467896 + - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 7776cb18fdf8 - 0df47f8552f6 + - 7776cb18fdf8 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder @@ -181,10 +181,10 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 4ba60cb14cb0 - 9c43baa60906 - 0cb27ea69dc1 - 5fe20c915fa6 + - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -213,8 +213,8 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - 1865e693d8b2 - ad90c2da4f38 + - 1865e693d8b2 - 3e4d45aca422 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -234,17 +234,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: + - 64deddb6a8ec - d63c1442407f - c520a52b5174 - - 64deddb6a8ec tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 9946bc39c834 - - 625fd9476402 - 94a50db37d1a + - 625fd9476402 + - 9946bc39c834 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index 1ed97269c..ce12103ff 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 @@ -33,54 +33,54 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 81e66674859e - - a6619171428e + - 3f59ebfbfe3d + - d033ffc1c161 - 3b8b5bde0bd9 + - c78f3d7dd1db + - 6a457678efcb + - '841557158611' + - 81e66674859e + - 107d3ba7024a + - f73435dc282b + - b89cac5156ec - cce7b18495e4 - 26de3a7b1cb9 - - f04a1264e2a2 - - b89cac5156ec - - 107d3ba7024a + - 5a7c56a5cc08 - d7c7ef3353fe - - c78f3d7dd1db + - a6619171428e - 8834daeb9892 - - 3f59ebfbfe3d - - d033ffc1c161 - - f73435dc282b - - 5a7c56a5cc08 - - 6a457678efcb - - '841557158611' + - f04a1264e2a2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - 7a2092844346 - - 6223845127ea - - 3b96e92e8ec3 + - 6283babe736e - 88c4aa435ded - - 659517798cc4 - 5b777002c2de - - 6a726db04d4b - - df47d4845b62 - - a185b079b095 - 02b8758214b0 - - 4755f52427c4 - - b0af57c1a968 - - e75442c7f4da - - 6283babe736e - 5fcd1ece3a6e + - a185b079b095 + - 3b96e92e8ec3 - aa8cc71438cf + - df47d4845b62 + - b0af57c1a968 + - e75442c7f4da + - 659517798cc4 + - 4755f52427c4 + - 6a726db04d4b + - 6223845127ea tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - c1d53e95327f + - f97743d52b87 - d1c340a5664b - b8476e82ac20 - 9b892d7f82cc - - f97743d52b87 + - c1d53e95327f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade @@ -88,32 +88,32 @@ tools: revisions: - 128ba8da994f - 9e10ba792be2 - - feb40665d7cd - daddf188c13f + - feb40665d7cd tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - 9d61d3fa046c - - 2f1019071464 - - ca0d8cf80567 - - 03ed9524dcd1 + - a2099fb98cdb + - 2fa9d4f1b48f - 7bb8726be37c - - ca337cce3888 - - 81804a978fc0 - - 14ae456b8cc5 - - 36912871ccdc - - abf6dbe8c9d7 - - b7e297c2ede6 - - 5f8727ff21e7 - 83a69484cb87 + - b6abccb1f25b - 42a174224817 - - a2099fb98cdb - - 2fa9d4f1b48f + - 9d61d3fa046c + - 36912871ccdc + - ca337cce3888 + - 03ed9524dcd1 + - b7e297c2ede6 + - 2f1019071464 - 437e28791761 + - 81804a978fc0 + - ca0d8cf80567 + - 14ae456b8cc5 - 3a43c3982401 - - b6abccb1f25b + - 5f8727ff21e7 + - abf6dbe8c9d7 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -126,22 +126,22 @@ tools: - name: raxml owner: iuc revisions: - - ea30d3089354 + - 29ff6a849eac - ba29b5e2a4be + - a4b71be30c3c + - ea30d3089354 - 73a469f7dc96 - b1e68bbe4cef - - 29ff6a849eac - - a4b71be30c3c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 91887494eb97 + - e88a7de55d6e - f1ccc8a6eb05 - 809e42326fc2 - - dbe2b2204555 - - e88a7de55d6e - 15ac71df11a0 + - 91887494eb97 + - dbe2b2204555 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/picard.yml b/usegalaxy.org.au/picard.yml index 40fd2556b..4060af1cc 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,13 +2,13 @@ tools: - name: picard owner: devteam revisions: - - a1f0b3f4b781 + - fc288950c3b7 + - 881d7645d1bf + - 1aac2a13842a - b502c227b5e6 + - a1f0b3f4b781 - 7d34178f2812 - - 1aac2a13842a - - f9242e01365a - f6ced08779c4 - - fc288950c3b7 - - 881d7645d1bf + - f9242e01365a tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomic_ai.yml b/usegalaxy.org.au/proteomic_ai.yml index a369d24c4..9459551d1 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -2,14 +2,14 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: + - 5b85006245f3 - ca90d17ff51b - - 3bd420ec162d - - 7fbec959cf2b - - c0e71cb2bd1b - a58f7eb0df2c - - d00e15139065 - - eb085b3dbaf8 - - 5b85006245f3 + - c0e71cb2bd1b - e4a053d67e24 + - eb085b3dbaf8 + - 7fbec959cf2b + - 3bd420ec162d + - d00e15139065 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 401d3cbcf..e2cf8dabb 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -13,46 +13,46 @@ tools: - name: cardinal_combine owner: galaxyp revisions: - - e988563cc6e5 - - e215f71d7983 - 525f201b86c1 - - b41107d8fe89 + - e215f71d7983 + - e988563cc6e5 - bf06d196e23d + - b41107d8fe89 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - bb6397b94018 - - 4fbffddde8cd - 8da3511c9467 + - 4fbffddde8cd + - bb6397b94018 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - - a8157342d9a3 - - 528fb09022be - b8c79e70516d + - a8157342d9a3 - f23d67e28cc8 + - 528fb09022be tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - 25b83cbd596a - - 80600735685d - - a69865da6f80 - 59e85306eae5 + - a69865da6f80 - a95a82eb4d50 + - 80600735685d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - 611d80c0e29d - - ed9ed1e6cca2 - e0669b1854b1 + - ed9ed1e6cca2 - 798da6bdff3d - f1897eb07081 tool_panel_section_label: Proteomics @@ -60,8 +60,8 @@ tools: - name: cardinal_quality_report owner: galaxyp revisions: - - 5a35e3a8d013 - a7fb9b395ddf + - 5a35e3a8d013 - 74b61bf5bc4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -69,18 +69,18 @@ tools: owner: galaxyp revisions: - 82f6c2f4332d - - df2187f9013b - cc430977c8ff + - df2187f9013b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 043f9c91f686 + - d2483487e077 - 1693b2126f30 - - c5aa9fca18c6 - 10566783d718 - - d2483487e077 + - 043f9c91f686 + - c5aa9fca18c6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -98,9 +98,9 @@ tools: - name: diann owner: galaxyp revisions: + - 9fa3dbf06f17 - ae4dc0c041f9 - bf0728e000cd - - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -147,16 +147,16 @@ 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 @@ -170,15 +170,15 @@ tools: owner: galaxyp revisions: - e42225f8a659 - - f522c08e900c - - 37d669de2828 - - 7f432d87c82c - - 1f39c833f65f - - 837224ad1694 - 8934bc76bb52 - 97a7f34fcb6a - 2133b0be850a - 4d17fcdeb8ff + - 7f432d87c82c + - 837224ad1694 + - f522c08e900c + - 1f39c833f65f + - 37d669de2828 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db @@ -193,10 +193,10 @@ tools: - name: metaquantome_expand owner: galaxyp revisions: - - 1974224d63c2 - 352b37c66d97 - 990b4560ead7 - 4187b6df1a40 + - 1974224d63c2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter @@ -204,35 +204,35 @@ tools: revisions: - deaf035bbe9f - 99450519d727 - - a1daafbf5233 - 4f359549383c + - a1daafbf5233 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - 40ca115438d2 - - c1343e3389ca - c7745841de24 + - c1343e3389ca - e79958768a2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - d2eac53666f0 - - d46d64e7964d - b648e45fd3cf - da986f83631b + - d46d64e7964d + - d2eac53666f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 9bf325045235 - 944b43462104 - eb811f3018ea - 1199751329b0 + - 9bf325045235 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -250,8 +250,8 @@ tools: - name: msstats owner: galaxyp revisions: - - 8212e342e482 - 28434abe6c5c + - 8212e342e482 - 593839e1f2c3 - b7034eff0db1 tool_panel_section_label: Proteomics @@ -267,48 +267,48 @@ tools: owner: galaxyp revisions: - 4e77b8f12cd3 - - 8960fb791701 - 01dbaf6a57e0 + - 8960fb791701 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 25529df60a81 - 370141bc0da3 + - 25529df60a81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 518b1730cf2a - f7fef900f5b2 - - c9eff69a7c62 - 9cdf15d3cfc8 + - c9eff69a7c62 + - 518b1730cf2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - 5e948629bc73 - dff6c756eee5 + - 5e948629bc73 - ca88bd28f116 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 41859bbdc16e - 890025d6e426 + - 41859bbdc16e - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: - - 9b7977080f6d - - 6634cad7d797 - 5ad0b5bf1deb + - 6634cad7d797 + - 9b7977080f6d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter @@ -322,16 +322,16 @@ tools: - name: openms_fileinfo owner: galaxyp revisions: - - 5ad830edc021 - - febd569ad26f - 52ba9695e752 + - febd569ad26f + - 5ad830edc021 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - 39e8fde08881 - 92352a475eed + - 39e8fde08881 - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -339,58 +339,58 @@ tools: owner: galaxyp revisions: - 0efbc235f314 - - 9e26f5c770f8 - d413dc49d650 + - 9e26f5c770f8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 8a04ed1c1d1b - - 3720e349ba2a - c28f13cab67a + - 3720e349ba2a + - 8a04ed1c1d1b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - c55dddc5844a - - 382cde407f81 - - ca799a7246e7 - c427a8628cbe + - ca799a7246e7 + - 382cde407f81 + - c55dddc5844a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - 8ddb7bab1138 - b5d0905419da - 39caaa778d2e + - 8ddb7bab1138 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 8d4db262964c + - 1c5f31b8d632 - f817513840a9 + - 8d4db262964c - 18f93351f8b6 - - 1c5f31b8d632 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: - - c69f69d7867a - - 111c3a00136d - 5d9f175dff81 + - 111c3a00136d + - c69f69d7867a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - be74a8cd7d66 - 0e52c85f3b15 - 476b5e296979 + - be74a8cd7d66 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter @@ -403,8 +403,8 @@ tools: - name: openms_msgfplusadapter owner: galaxyp revisions: - - 2b2a7551a857 - c18d8efa4474 + - 2b2a7551a857 - a407b6790342 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -418,16 +418,16 @@ tools: - name: openms_mztabexporter owner: galaxyp revisions: - - ee860980edc6 - 8098330f6d91 + - ee860980edc6 - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer owner: galaxyp revisions: - - a2a6e9551046 - 0ced5bc9f4dd + - a2a6e9551046 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator @@ -447,8 +447,8 @@ tools: - name: openms_openswathdecoygenerator owner: galaxyp revisions: - - 9f505cd4428f - f861ec9fbe59 + - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring @@ -461,8 +461,8 @@ tools: - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 8b814eafce2c - 89254095cbf6 + - 8b814eafce2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher @@ -497,8 +497,8 @@ tools: - name: openms_peptideindexer owner: galaxyp revisions: - - 539a3a4dcc9e - dd173849c3d8 + - 539a3a4dcc9e - e039cc5c7aed - 5182338d5e7c tool_panel_section_label: Proteomics @@ -532,9 +532,9 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: - - fb52e95a370c - - c8b225c69a7f - 7f6a1f27553e + - c8b225c69a7f + - fb52e95a370c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer @@ -554,14 +554,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - 7fdd9119cc4f - - 07ff622ec007 + - 3634c90301af + - a72c48001f7c + - 3ec27b4cee7c - da885ca16cb2 - 1beff3ddce58 - - 3634c90301af - 943a34df6047 - - 3ec27b4cee7c - - a72c48001f7c + - 07ff622ec007 + - 7fdd9119cc4f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -615,9 +615,9 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 12692567c7f9 - 1a5690a5eedc - a371252a2cf6 + - 12692567c7f9 - 265c35540faa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index d82daae39..0c7912043 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,132 +2,132 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: + - 42201b90e3f4 + - cd5f98911089 - 2f1d464ebfd2 + - e345aadf914f - 110a346daf36 - 289b7d6b69a4 - - cd5f98911089 - - 42201b90e3f4 - - e345aadf914f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks owner: iuc revisions: - - c207119ba5f6 + - 0345dbaaa79b + - 8501601a118d - fcce77c09289 + - c207119ba5f6 - 0cd2df8af811 - - 8501601a118d - 42d9087b4789 - - 0345dbaaa79b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: + - 89eb29319bf4 - 04db7fd6b238 + - ad5ab22ffe24 + - 421c33b8bf17 - 405a212b32ab - 33486216eec0 - - 421c33b8bf17 - - ad5ab22ffe24 - - 89eb29319bf4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - eb784fa07f80 - 7370bb65bad4 - - 1d839ead7ad3 - - 7b72fde3d27e - fa51dc5e8386 + - 7b72fde3d27e + - 1d839ead7ad3 - f6e91108b7b1 + - eb784fa07f80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter owner: iuc revisions: - - c9b77ced9a78 - - a3e86cd9cac7 - - d30e36c48c93 - 8a55d29c8fcf - 1544278c272e + - d30e36c48c93 + - a3e86cd9cac7 + - c9b77ced9a78 - 3d70c2996730 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: - - 887cf585cafc - a5969aa9347e - 564c33e5c3e3 - b242deb58952 - - 7b881f5f5ad5 - e2db212d64ad + - 887cf585cafc + - 7b881f5f5ad5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - e897c74a48bb - 8cff84759bf6 - - b4bab607eb05 - bd5ff77e2036 + - b4bab607eb05 - 9a171f9a450b + - e897c74a48bb tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: + - 6dafad990086 + - 33f0793edf93 + - adc7a7610d4f - 4f65e343ecdf - 5e10f396979e - - 33f0793edf93 - - 6dafad990086 - 887e0991eb24 - - adc7a7610d4f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - 43e3eeb2e0ec - c287418eb288 + - 4e280b27a831 + - 43e3eeb2e0ec - 97575d01f06b - 17d39bf0a63a - - 4e280b27a831 - c5d7050e4ad7 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: + - 9586f08634c0 + - 0b8c84a7fdb5 - cd034465d4a4 - 09b8edb56d80 - - d9bf483266a1 - a819ec3b362d - - 9586f08634c0 - - 0b8c84a7fdb5 + - d9bf483266a1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - - 69842dd5aa48 + - a4b4bd84f69e - 2645575d1bf2 - - a9c34a289493 - bf0e43ab0416 - - a4b4bd84f69e + - a9c34a289493 + - 69842dd5aa48 - 95351dd0fd3f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: + - 912f904a6e1e + - bb0475c884ff - cfb504394ae1 - d033e1ccb386 - - 912f904a6e1e - d1fda11e602f - 8a35a3bc6752 - - bb0475c884ff tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -163,8 +163,8 @@ tools: - name: stacks_populations owner: iuc revisions: - - d1fad35bdb4a - d504d945a655 + - d1fad35bdb4a - 95286af4139b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -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 989174142..a734ed27e 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -2,8 +2,8 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - 31f8063eedea - cf01dd6c6b1f + - 31f8063eedea - 2d4e3aff9dc7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -11,15 +11,15 @@ tools: owner: iuc revisions: - 32e542c2a773 - - 125d20cb23d7 - 703a2cb3fb38 + - 125d20cb23d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 3d61a698e5e1 - 01ccd366690d + - 3d61a698e5e1 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: - - dbb6ee3179bc - aab6cf87b40a + - dbb6ee3179bc tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: circexplorer @@ -50,23 +50,23 @@ tools: - name: cuffcompare owner: devteam revisions: - - e66b9b5b8580 - f648e5180e40 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: - - e04dbae2abe0 - d080005cffe1 + - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - 86285ddd4512 - - 6a6717a5f421 - cf747d1bd79a + - 6a6717a5f421 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -98,46 +98,46 @@ tools: owner: iuc revisions: - 0693ccd171c4 - - 3b36efd62b3e - e3b16fd7dd08 + - 3b36efd62b3e - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - 6a3a025714d3 + - 9a882d108833 + - 8fe98f7094de - 0696db066a5b - - d027d1f4984e - cd9874cb9019 - - 9a882d108833 - 24a09ca67621 - - 8fe98f7094de + - 6a3a025714d3 + - d027d1f4984e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - 2872c633f07e + - df929f257179 - 62adf13b86ea + - 2872c633f07e - b47c006d90c5 - - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 9bdff28ae1b1 - - 5bf899c13979 - - 0cb907a2a810 - - 334ce9b1bac5 + - 6e53e565fc6a - a8305cf0c951 - 3d89af8a44f0 - - f2843df56434 - - 6e53e565fc6a - df0c8d0a5992 - - 070900306913 - 555659de7321 + - 070900306913 + - 334ce9b1bac5 + - f2843df56434 + - 0cb907a2a810 + - 9bdff28ae1b1 + - 5bf899c13979 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -156,16 +156,16 @@ tools: - name: featurecounts owner: iuc revisions: + - ea04b737afa0 + - e6a2a912677a - 7db9d3ea71c9 - - a37612abf7f9 - - af814359d244 - 38b6d12edc68 - - 90d16db017d7 - 6f66ae7c5f7a - - f9d49f5cb597 + - af814359d244 - a56fbe2d6ba7 - - ea04b737afa0 - - e6a2a912677a + - f9d49f5cb597 + - a37612abf7f9 + - 90d16db017d7 - f3a5f075498f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -184,9 +184,9 @@ tools: - name: gffcompare owner: iuc revisions: + - 3c97c841a443 - f99dd58de04f - 0f710191a66d - - 3c97c841a443 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -198,13 +198,13 @@ tools: - name: hisat2 owner: iuc revisions: + - d4b55e2beb12 + - a86e80d3c09c - 6ab42baa56e9 - - 26371a1df031 + - 3fb01a8c902d - f4af63aaf57a - - a86e80d3c09c - - d4b55e2beb12 - 6c19daec423d - - 3fb01a8c902d + - 26371a1df031 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -224,31 +224,31 @@ tools: owner: iuc revisions: - 87c11c05d238 - - 5ae5c312d718 - - 01247aaf0a10 - ce5d418183c5 - 1c75aa5de15e + - 01247aaf0a10 + - 5ae5c312d718 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - 40985510cd98 + - 4f9c4e6566e5 - 10c98fab6c5a - c971db6f0fe5 - - 4f9c4e6566e5 + - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 32511f586472 - 58c35179ebf0 + - e827f9aae031 - 97e06a4c7c75 + - 32511f586472 + - d6f5fa4ee473 - 708348a17fa1 - - e827f9aae031 - 0921444c832d - - d6f5fa4ee473 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -260,8 +260,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - a8d24f4b6d95 - dbbe92348c7a + - a8d24f4b6d95 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_quantifier @@ -297,19 +297,19 @@ tools: - name: rgrnastar owner: iuc revisions: - - 980d2a2e1180 - 5ec75f5dae3c - - 4df95e2d7f61 - - 0a563fd2f22e - 79de45b5069b - - c772497b2c32 - - b9e04854e2bb - - 99b17b74a8cd - - e132e7d02a3e - 4074fc1940e2 + - e132e7d02a3e + - 7ed2edc1337f - 3ea5a2a63fa2 - c7c55b694974 - - 7ed2edc1337f + - 0a563fd2f22e + - c772497b2c32 + - 99b17b74a8cd + - b9e04854e2bb + - 980d2a2e1180 + - 4df95e2d7f61 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -321,34 +321,34 @@ tools: - name: salmon owner: bgruening revisions: + - ebab418107f5 - 49121db48873 - - e3d32471da11 - 2c0ca397d302 - - ebab418107f5 - - cc05793bb896 - 15cd64d7c58b + - cc05793bb896 + - e3d32471da11 - 53e9709776a0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: + - c0fd285eb553 + - 56242ff81c84 - fab6ff46e019 - 8c28affc7c48 - - 56242ff81c84 - - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - cef79931dda5 - - 76d290331481 - - 1ebd14235b92 - - 258d696dbd7e - - ae618321f34a - 914cfcba0ec8 + - 258d696dbd7e + - 1ebd14235b92 + - cef79931dda5 - dd4df992d93d + - ae618321f34a + - 76d290331481 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -378,53 +378,53 @@ tools: - name: transdecoder owner: iuc revisions: - - c6334cb383ff - ffd1300599a1 - - d0d4cef4f967 - 0db979fead3a + - c6334cb383ff + - d0d4cef4f967 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: - - c2b82a94493e - 478f36effca1 - 2fb4ee002432 + - c2b82a94493e - 56162e446004 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: - - 3f4094b6a565 - - fab23c3b5258 - 9ff3765e7172 + - fab23c3b5258 + - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - 870ac06dff8e - - be3f26533209 - - 34a018cbee9c - 4687ecf0eb2d + - 34a018cbee9c + - be3f26533209 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - 33406f5a445c - 05ab8d5e04a2 - 5192f657f305 + - 33406f5a445c - 65e7dea767ea - c5fbddcac63a tool_panel_section_label: RNA-seq @@ -432,18 +432,18 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d - e406ac71165d - - 6f0fb35b799c + - 1fdb25a8384d - a35cba31d904 + - 6f0fb35b799c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - - 964b7efe2639 - 7c7fbf13aadd - c2c039e421af + - 964b7efe2639 - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -451,32 +451,32 @@ tools: owner: iuc revisions: - 1d689e4e1caf - - 047c22569787 - eafea3083352 - 24e94d84adc9 + - 047c22569787 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: - - 1812dbc5bb7b - - 9871104ea630 - 04bb8bb7c198 + - 9871104ea630 - 3a4ac03d1266 + - 1812dbc5bb7b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity owner: iuc revisions: - - db1f362cca3e - - 9fa24d5aac68 - - d84caa5a98ad - 32b86cd8eb50 - 8f1c3df4dd49 - - d2bc35f3d1c5 - 48636f857c4b - - c9cfec002f71 - cee61b3fcf78 + - d84caa5a98ad + - 9fa24d5aac68 + - db1f362cca3e + - c9cfec002f71 + - 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 ee91e8906..dfa03fca7 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: - - 1a052c827e88 - - 473382134e56 - 080fd5739bb4 + - 473382134e56 + - 1a052c827e88 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 1831d75c7..f2b33beb6 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,17 +2,17 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 10184eaa85fc - - 88eedb4abea0 - a53efedba9e7 + - 88eedb4abea0 + - 10184eaa85fc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - - 1dfd95ee241e - - cb20f99fd45b - 108db6635177 + - cb20f99fd45b + - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamutil_diff @@ -42,9 +42,9 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - e7fd6754d093 - 19ece8afbaab - 5f8e69cc4c6e + - e7fd6754d093 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -88,81 +88,81 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - 649a225999a5 - 56c31114ad4a + - 649a225999a5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: + - 12749212f61b + - 46c6639921f1 - 9149ad20699a - 6856f8a01905 - - 46c6639921f1 - - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - 06dc50b7b711 - - 33208952b99d - c89806670ab9 + - 33208952b99d + - 06dc50b7b711 - 92ec40abcdcf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx owner: iuc revisions: - - 66e23b11feae - - b3d99709fe1a - a8d69aee190e - 720217c23995 + - b3d99709fe1a + - 66e23b11feae tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - db17d5321bad - - fefd89ab563c - - 22970df7a40e - fe34990e5ce7 + - 22970df7a40e + - db17d5321bad - cc61ade70eb8 + - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - fa5d3e61e429 - 7def34e6cf4d + - 88b8c2916784 - 7a6034296ae9 - 811fc2d75ad4 - - 88b8c2916784 + - fa5d3e61e429 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - b40e2d865d52 + - 740ce0a18f0d - 36677f429310 - 65a38e8c8e2a - - 740ce0a18f0d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - 329deb17a9f7 - - 8da515fbc1bf - 583abf29fc8e + - 329deb17a9f7 - 9da0311ab1dd + - 8da515fbc1bf - b61f5d6a7f25 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase owner: devteam revisions: - - b5c3b1856370 - 1e5880498f52 + - b5c3b1856370 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -170,8 +170,8 @@ tools: revisions: - db000c6007a0 - d7b4851d1971 - - bb8cfc6f6e0c - 30388d878f81 + - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -183,50 +183,50 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - 344fc91e1bfd - a4a10c7924d1 - b5c88b7b153e + - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - 6c2c1836728b - - cab3f8d35989 - e613c1ad4c4c + - cab3f8d35989 + - 6c2c1836728b - a577ea614bed tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: + - b7f7826ef1cd - bcedabb53ddf - 5d9ae78f34d3 - - b7f7826ef1cd - 135c85f4cfaf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: + - 3a0efe14891f - 1cc79f49b8d5 - - fed4aa48ba09 + - 24c5d43cb545 - 5a08c09b9311 - 145f6d74ff5e - - 24c5d43cb545 - - 3a0efe14891f + - fed4aa48ba09 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: + - b01db2684fa5 - b72793637686 - - 350bbc5c2ffd - - bf328cec6a42 - - c370440f901e - 0dbf49c414ae - - 6be888be75f9 - - b01db2684fa5 - 5826298f6a73 + - bf328cec6a42 + - 6be888be75f9 + - c370440f901e + - 350bbc5c2ffd 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 8cd23d825..ba938068c 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -2,11 +2,11 @@ tools: - name: ena_upload owner: iuc revisions: + - a62c4a11a67d + - 4aab5ae907b6 + - 6f6537780379 - 480d9e9d156b - d147d6455873 - - a62c4a11a67d - 59bb6d34fca6 - - 6f6537780379 - - 4aab5ae907b6 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 5f73ad3b2..ae786f729 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -3,42 +3,42 @@ tools: owner: iuc revisions: - 32e547223c9e - - 00712416fdaa - - 93dd15e13e6a - 55e35e9203cf - - fb9e030ffae4 - cfc3f5a57dc6 + - 00712416fdaa + - fb9e030ffae4 + - 93dd15e13e6a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - ee98d611afc6 + - 038e32885fec - 6f0d0c784f09 - b9fac48532eb - - 038e32885fec - - 39e945f0b2c1 - 688357ad5e61 + - 39e945f0b2c1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - 3d748954434b - - 9bd945a03d7b - 43cb7b5a6fe7 - d4af736e7b83 - - ed4996a16f7f - b85871dd69f9 + - ed4996a16f7f + - 9bd945a03d7b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: dropletutils owner: iuc revisions: - - a9caad671439 + - 2c1200fba922 - 8855361fcfc5 + - a9caad671439 - cdf4443d5625 - - 2c1200fba922 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -50,8 +50,8 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 7ffaa0968da3 - 282819d09a4f + - 7ffaa0968da3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution @@ -64,8 +64,8 @@ tools: - name: music_inspect_eset owner: bgruening revisions: - - 8c64a2da3869 - 7705cc75ac18 + - 8c64a2da3869 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -77,8 +77,8 @@ tools: - name: raceid_clustering owner: iuc revisions: - - f911a64454fb - 0bff0ee0683a + - f911a64454fb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -91,101 +91,101 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - df8e4e54d367 - a6821f856a1e + - df8e4e54d367 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory owner: iuc revisions: - - c92d0f9338c5 - 2af7c5086a96 + - c92d0f9338c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - 6acb08931836 - - 77b91b9bdf52 - b2df381a6004 + - 6acb08931836 - aaa5da8e73a9 + - 77b91b9bdf52 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - - b409c2486353 - a03ff8633507 - - a97abb8cd15b + - b409c2486353 - 3c86f71498bc + - a97abb8cd15b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - c5d3684f7c4c + - 5e9171dc8244 - 6bd82ed14acd - 3081ff5c84a3 - - 5e9171dc8244 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - ab55fe8030b6 - - 94c19fb1281c - 3bcd5445cd7a + - ab55fe8030b6 - a407e7f8bdc1 + - 94c19fb1281c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - dbbe1ea8ecb1 + - aa0c474463c2 - 6adf98e782f3 - 9b0cdb8cf6be - - aa0c474463c2 + - dbbe1ea8ecb1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - f2f6c703da06 - - 73ab2ac53d06 - - bf2017df9837 - 215733a383f2 + - 73ab2ac53d06 + - f2f6c703da06 - 458e8f43a775 + - bf2017df9837 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: + - 652923ce664f - 7a365ec81b52 - b7ea9f09c02f - - 652923ce664f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter owner: iuc revisions: - ef4c80837bc5 - - 2e41b35b5bdd - 81e5bdff4853 + - 2e41b35b5bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca owner: iuc revisions: - 46fc6751d746 - - 9e5c0bb18d08 - c99ba278dfa9 + - 9e5c0bb18d08 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index bb10907a8..f502a65a1 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,32 +32,32 @@ tools: - name: datamash_ops owner: iuc revisions: - - 419027d822d6 - - 2f3c6f2dcf39 - 562f3c677828 + - 419027d822d6 - 4c07ddedc198 - 746e8e4bf929 + - 2f3c6f2dcf39 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all 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: - - 506ae7b0d85d - 0b89b03ad760 + - 506ae7b0d85d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass @@ -71,8 +71,8 @@ tools: owner: devteam revisions: - 6c29c7e347e8 - - 7a15159140d1 - cb1c59d69557 + - 7a15159140d1 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -114,21 +114,21 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - aef56d0e7a61 + - b1eda492f063 + - 7442b94d6a1e - 840f29aad145 + - aef56d0e7a61 - 4c4ec859c31a - - b1eda492f063 - 9c3e1d3235c8 - - 7442b94d6a1e tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - d0352e8b4c10 - - 375bbd555f4a - 9fda0b82f419 - 30d21a6041f6 + - 375bbd555f4a - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu @@ -136,10 +136,10 @@ tools: owner: bgruening revisions: - 4cc980df6265 - - 2c58b83c9bad + - cd02bf168d23 - 7ae443e6217d - 8b1b2b91f8d0 - - cd02bf168d23 + - 2c58b83c9bad tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering @@ -148,8 +148,8 @@ tools: - ad7e0b4291ee - 4bbaf77573ef - e10e776f2109 - - 7dd3fb35904f - bb9fc9d46ea4 + - 7dd3fb35904f - 1dd433d2c92c tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index 641301b3b..c4a88d98d 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -8,8 +8,8 @@ tools: - name: add_value owner: devteam revisions: - - 023f0a3760b3 - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -28,13 +28,13 @@ tools: - name: column_maker owner: devteam revisions: - - 02026300aa45 + - 464b9305180e + - 6595517c2dd8 + - 13b6f0007d9e - 6e8d94597139 - be25c075ed54 - - 6595517c2dd8 - 9cd341095afd - - 464b9305180e - - 13b6f0007d9e + - 02026300aa45 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -71,10 +71,10 @@ tools: - name: filter_tabular owner: iuc revisions: - - 9cc411a62277 - - 34d29339abab - 557ec8d7087d - 37cde8134c6a + - 9cc411a62277 + - 34d29339abab tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -98,28 +98,28 @@ 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 + - 33d61c89fb8d + - 1ea4e668bf73 - 623f3eb7aa48 + - 83069b38aa85 - 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d220115f882b + - fa016f1eea1a - 5bbf9eada9c2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu @@ -122,19 +122,19 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - e7aff4a85df5 - - 32f14a2723ec - 3b1e7c170b10 - - ee4a90760848 + - 32f14a2723ec - 40f0591deda0 + - e7aff4a85df5 + - ee4a90760848 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - 4934c0ac6197 - - adc0645b945c - 02d81b994ef5 + - adc0645b945c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_somatic diff --git a/usegalaxy.org.au/vcfbcf.yml b/usegalaxy.org.au/vcfbcf.yml index e7d7912da..87fd7fe8b 100644 --- a/usegalaxy.org.au/vcfbcf.yml +++ b/usegalaxy.org.au/vcfbcf.yml @@ -2,50 +2,50 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - e075b1be5abb - 8a2e296c07ef - - b7ea370b8f5d - - 265fe0f9ea64 - 6a88248893c4 - - ebe5fc018e72 + - 265fe0f9ea64 - 3f62d4939d54 + - 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