diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index db205783d..862f87d68 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -6109,3 +6109,4 @@ Update 176 14/12/23 12:59:55 samtools_split False Tests failed devteam bd850490c Update 176 14/12/23 15:41:55 seqtk False Installed iuc 4b494533146a 4b494533146a 33/33 0/0 FASTA/FASTQ toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_176/install_log.txt Install 1374 18/12/23 09:41:41 geneiobio True Installed iuc fc53fcdbe548 fc53fcdbe548 2/2 2/2 Graph/Display Data toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1374/install_log.txt Install 1376 18/12/23 11:47:34 windowmasker True Installed iuc d90ae4a02efd d90ae4a02efd 11/11 11/11 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1376/install_log.txt +Install 1378 20/12/23 11:41:32 tetoolkit_tetranscripts True Tests failed iuc 8e96d712a2bd 8e96d712a2bd Production Testing 3/3 0/3 RNA-seq toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/install_build_1378/install_log.txt diff --git a/requests/tetoolkit_tetranscripts.yml b/requests/tetoolkit_tetranscripts.yml deleted file mode 100644 index 265908c66..000000000 --- a/requests/tetoolkit_tetranscripts.yml +++ /dev/null @@ -1,8 +0,0 @@ -tools: -- name: tetoolkit_tetranscripts - owner: iuc - revisions: - - 8e96d712a2bd - tool_panel_section_label: RNA-seq - tool_shed_url: toolshed.g2.bx.psu.edu - diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index 48908d47e..18649211a 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -3,10 +3,10 @@ tools: owner: iuc revisions: - c2ef298da409 - - 4efdca267d51 - - 3f3e247c053d - 6e9aea89e388 - 78c75f134c16 + - 3f3e247c053d + - 4efdca267d51 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -36,30 +36,30 @@ tools: - name: annotatemyids owner: iuc revisions: - - 1aae04680c4b - - 133f36c29579 - - 3e1f6f6d557e - fe3ca740a485 - - 4f2967b27e67 - 44018dd6b447 - - b5d8e5475247 + - 4f2967b27e67 + - 1aae04680c4b - f29602ae449e + - 3e1f6f6d557e - cd2480f35935 + - b5d8e5475247 + - 133f36c29579 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - bc88856eddab - e78e25d3b4bd + - bc88856eddab tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: - 7be22100e5e1 - - dc027fa56d55 - 6519ebe25019 + - dc027fa56d55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus @@ -80,8 +80,8 @@ tools: owner: iuc revisions: - 7355bbf5e05f - - fe48aa4ccd5e - 8fd427007e93 + - fe48aa4ccd5e 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 @@ -106,9 +106,9 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: - - 9d1fbff733cf - d9c3016f7283 - 63662ae295d6 + - 9d1fbff733cf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -126,54 +126,54 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - b6b5cd37f2a2 - 9f2455341fac - - 14f588312c56 + - 582fd74dc2a1 - 3bbe70fef6df + - 14f588312c56 + - b6b5cd37f2a2 - 756376aeb1ae - - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: + - 989f7c061f35 - 73428a792541 - - 1691af4a0d17 - 30fb23d4c31c - - 989f7c061f35 - - a230ea445788 - 0ffe5be70caf + - a230ea445788 + - 1691af4a0d17 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 494f0bb4a993 - - e94187d661df - 30f08d74024f - - 563a19373357 + - e94187d661df - 5a5ae61da69c + - 494f0bb4a993 + - 563a19373357 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - d6c7106b7b2e - - f31125bb85ea - - 7abc5f6dd595 - 2bba2ff070d9 - 1bc5a03faf2e + - f31125bb85ea + - 7abc5f6dd595 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - d3af38b9c7e1 + - 520e30695ec3 - fed64e676186 + - 54961e026fe4 - 52af33194019 - - 520e30695ec3 - b3cf4684e9c7 - - 54961e026fe4 + - d3af38b9c7e1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -186,8 +186,8 @@ tools: owner: iuc revisions: - 79261884facd - - 2aea122fbd25 - 07d7991bf205 + - 2aea122fbd25 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -199,10 +199,10 @@ tools: - name: goseq owner: iuc revisions: - - 43798b4caee0 - - 602de62d995b - 8b3e3657034e + - 43798b4caee0 - ef2ad746b589 + - 602de62d995b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -220,16 +220,16 @@ 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: - - c55643c3d813 - 74810db257cc - 98cafcbd2578 + - c55643c3d813 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -247,15 +247,15 @@ tools: - name: maker_map_ids owner: iuc revisions: - - e906fa778440 - 326f9c294b09 + - e906fa778440 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: - - 3c1a01127868 - 370c210d9541 + - 3c1a01127868 - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -288,9 +288,9 @@ tools: owner: crs4 revisions: - eaee459f3d69 - - 8a22554cdde2 - - a17498c603ec - bf68eb663bc3 + - a17498c603ec + - 8a22554cdde2 - d643e3b03500 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -303,8 +303,8 @@ tools: - name: repeat_masker owner: bgruening revisions: - - 3f987772e283 - ba6d2c32f797 + - 3f987772e283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler @@ -323,22 +323,22 @@ tools: - name: snpeff owner: iuc revisions: - - cfcf33df7fc0 - - 268d162b9c49 - - 9473cd297a76 - 8f92c2b26e6d - 5a29ab10dba6 - - 5b80f544c67f + - cfcf33df7fc0 - 68693743661e + - 9473cd297a76 + - 268d162b9c49 + - 5b80f544c67f - 5c7b70713fb5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 09d6806c609e - - 2b3e65a4252f - 5fab4f81391d + - 2b3e65a4252f + - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snptools @@ -363,15 +363,15 @@ tools: - name: tbprofiler owner: iuc revisions: - - 37213cf56392 - - 45083d070fb8 - - ba6f87115e13 - - 200c378d85f3 - 037a11682176 + - 45083d070fb8 - e1a9d6fd258d - - 2c68b0c38785 - 809dfc93d593 - ac8250086ac3 + - ba6f87115e13 + - 37213cf56392 + - 2c68b0c38785 + - 200c378d85f3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index 1d520713f..5158fce7c 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,24 +2,24 @@ tools: - name: abyss owner: iuc revisions: - - 553bfe8bd0b5 - - 8f1b150a2487 - - 7547fcab5d19 - - 0e93176640ac - - fa5259cc561b - 890b794c997d - a929ce596a34 + - 0e93176640ac + - 7547fcab5d19 + - 8f1b150a2487 + - fa5259cc561b - 841084c5fc46 + - 553bfe8bd0b5 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - 067592b6b312 + - ddddce450736 - 94fe43e75ddc - 21e491ad532a - - ddddce450736 - b9e31c5c01c7 + - 067592b6b312 - b2860df42e16 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -33,11 +33,11 @@ tools: - name: bionano_scaffold owner: bgruening revisions: - - 22286dab5aa1 - - faee8629b460 - 5258e18bbe23 - - 3371c5bdc17a + - faee8629b460 + - 22286dab5aa1 - a7f16f24e9a1 + - 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: - - 94170eee0ad8 + - cf13a1e03e5b - 1e62c28ba91d - - 2a5b8b9936bf - - 1440ae06552f - - 5ecdeca79a0d - e824f5d958d0 - - 2dd755c1c6ff - - f18f0b887c31 + - e4bd1e99bacf + - 1440ae06552f + - bb935709506a - 41030a6c03b7 - - 602fb8e63aa7 - 46ae58b1d792 - - bb935709506a + - f18f0b887c31 - 4048d82f0c88 - - cf13a1e03e5b + - 2dd755c1c6ff + - 2a5b8b9936bf + - 94170eee0ad8 + - 5ecdeca79a0d - 0d243f458b53 - - e4bd1e99bacf + - 602fb8e63aa7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - c5b7390290b1 - 5732f959936a - 86f150c8019d + - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -86,8 +86,8 @@ tools: revisions: - 276f5d8712d5 - 1ce9b1d72ec3 - - cb8dfd28c16f - e27815e82dd4 + - cb8dfd28c16f - 8d4f03b5fe9d - 3ee0ef312022 tool_panel_section_label: Assembly @@ -96,8 +96,8 @@ tools: owner: iuc revisions: - 3169a38c2656 - - b2f674562a18 - 01210c4e9144 + - b2f674562a18 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle @@ -106,16 +106,15 @@ tools: - 7348b69e5109 - 06bcf65179fb - 8b330a577046 - - 611219887a48 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 690c2caa367e - - 5127a713de83 - - 3fba9c77550a - 3ef480892a9f + - 3fba9c77550a + - 5127a713de83 + - 690c2caa367e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -127,21 +126,21 @@ tools: - name: hifiasm owner: bgruening revisions: - - 5f625c63b8bc + - 045c7c3d8e59 + - 3f7be05a1597 - f3c89da3af16 + - da9d8bf98802 + - 41cea2aa2dce + - 5f625c63b8bc + - 71740308d412 + - ec9e21e9c71b + - 2061fb3b81b4 - 6505bd37670d - 366a11d316a7 - - 2061fb3b81b4 - 5bec28269d95 - - 41cea2aa2dce + - 0ee0c3089254 - 60024a528cbd - - ec9e21e9c71b - 9ef6920c3089 - - 71740308d412 - - 0ee0c3089254 - - 045c7c3d8e59 - - 3f7be05a1597 - - da9d8bf98802 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -161,37 +160,37 @@ tools: revisions: - de387b2b2803 - a96f3ad4e0d8 - - 14ddfc8ffb93 - 7518ee87b53d + - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - 09c589057ee8 - - f8113c25bc6b - 39edec572bae + - f8113c25bc6b - 9d79beb19ac3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 51c2360aa807 - 29dabd8db6f2 + - 51c2360aa807 - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: + - eb7a370f6588 + - f338e9942b27 - 3ca2d2a9068c - - e731ea24e48d - - fd128c111ab0 - 2ecf5a570907 - 606b09cc9860 - - eb7a370f6588 - - f338e9942b27 + - fd128c111ab0 + - e731ea24e48d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -203,11 +202,11 @@ tools: - name: miniasm owner: iuc revisions: - - a7b889b90140 - - 80d1250bd5fd - 73a3846701e1 - - 8dee0218ac7d - 8b6d0d85252b + - 8dee0218ac7d + - a7b889b90140 + - 80d1250bd5fd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -219,9 +218,9 @@ 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 @@ -235,10 +234,10 @@ tools: revisions: - d256a51a656b - 2b16ba799da9 - - bbe19ef04a74 - - dfb8a4497339 - 8fef980d48b5 + - bbe19ef04a74 - 02831bf9e95f + - dfb8a4497339 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups @@ -252,35 +251,35 @@ tools: - name: quast owner: iuc revisions: + - 6fcbee531de6 - 7594365c546b - 342a1d1fed7b - - 6fcbee531de6 - - 3061c8b029e5 - - ebb0dcdb621a - 59db8ea8c845 + - 3061c8b029e5 - 72472698a2df - - 675488238c96 - 875d0f36d66f + - 675488238c96 + - ebb0dcdb621a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: - - 39bed8de8017 - - cd06929b224b - d865b62f501c + - 39bed8de8017 - aa39b19ca11e - a199cd7ac344 + - cd06929b224b - 78c533842eeb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - - 33b7d8481a76 - - 2b2a352488fa - 3edba9afc9bc + - 2b2a352488fa - f11b994b7eb2 + - 33b7d8481a76 - f8564b2d7f63 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -288,19 +287,19 @@ tools: owner: iuc revisions: - 53c2bc8c2ae3 + - 378e55aeeb25 - ef69617ecb42 - - e122f9101584 - 1d06c8b38e77 - - 378e55aeeb25 + - e122f9101584 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - ba7b0f11e470 + - ab5b7f6b7198 - 9a22227bb6d0 - f77f7a7f3b83 - - ab5b7f6b7198 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -312,70 +311,70 @@ tools: - name: shovill owner: iuc revisions: - - 196a599ec43d - - ad80238462c1 - ee17a294d3a3 - - 83ead2be47b2 - 865119fcb694 + - ad80238462c1 - d9f6a00b6db7 + - 196a599ec43d - f698c7604b3b + - 83ead2be47b2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: + - 5e0825476fb7 - 24e471d13fe9 - 5a0ddb4dc3a4 - - 5e0825476fb7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: + - 7490b213baa9 + - 1bb12736175c - 904bf932cf78 - 051fd2db8a27 - 1fc82fe7ebef - - 7490b213baa9 - - 1bb12736175c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - ad8b536d1caa - - d6e617c4e338 + - 808b3a0a6716 - 34305b013402 - fee85957cebe - - 808b3a0a6716 + - d6e617c4e338 + - ad8b536d1caa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - e5a3b75a271f - - b8002c3f7141 - 21da31ed41a1 - - 8d4b90bf9caf - 6b5a5842531e + - 8d4b90bf9caf + - b8002c3f7141 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: + - 2a10645aeadd - 9de69775f512 - - 328aa71f0f3c - f1532cb33c75 - 86f66ab58e14 - - 2a10645aeadd + - 328aa71f0f3c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 1708851f8804 - - 85fb02c43042 - - 6aad515a5270 - e41dcb0e913b + - 6aad515a5270 + - 85fb02c43042 + - 1708851f8804 - 340bc17f49cf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -383,100 +382,100 @@ tools: owner: iuc revisions: - 249f6a28c751 - - b65a43f70b99 - - d159735a6a9f - b3490b036c5a + - b65a43f70b99 - d5fb354f745d + - d159735a6a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: + - dd7ad84f3943 - d2d1df21dfb9 - 9006e5836729 - b7829778729f - - 33368fec3b70 - - dd7ad84f3943 - 7897763d14ec + - 33368fec3b70 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 505a9833ab5d - - 8f631679571f - ced385aa976d - - 189e837009c9 - 6f4c8ad6ea01 + - 189e837009c9 + - 8f631679571f + - 505a9833ab5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - 356afed970b4 + - d40ed4eb0c0e - e59bee4565b3 - 9ded6109434a - 19bdfd1e6fe3 - - d40ed4eb0c0e + - 356afed970b4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 6dd935e4984b - - 80a17897564d - - b23249f81bc4 - ebd801e712bc - 4688ae3b49b5 + - 80a17897564d + - b23249f81bc4 + - 6dd935e4984b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - b64696992ee9 + - cb1e3db43020 - b5e35a2ca4f3 - - 59bd28f6265d - 937ea677d437 - - cb1e3db43020 + - b64696992ee9 + - 59bd28f6265d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - 05bd7504fdb2 - - 6015aa0303f2 - 383bb5ad32e2 - 2628f6790eda + - 6015aa0303f2 - cb4768eeca3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - d10bdad2fd17 - - 9e3e80cc4ad4 - 6e26c9afd301 - e92675014ac9 + - 9e3e80cc4ad4 + - d10bdad2fd17 - 0a3a602cd1e3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 5da9a0e2fb2d - - 920677cd220f - 8d09f8be269e + - 920677cd220f - 08256557922f + - 5da9a0e2fb2d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 0e2b4e3f9ca1 - d81360ea69d8 - - 82398ba86ba7 - - 4a53b89fa703 - 37d88f41c810 + - 4a53b89fa703 + - 0e2b4e3f9ca1 + - 82398ba86ba7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index 8cdb9ee84..4780df845 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -16,16 +16,16 @@ tools: owner: iuc revisions: - ded48b36f3b7 + - 8e8dc9a1e3e5 - 31812e7a1315 - 1f5641a52664 - - 8e8dc9a1e3e5 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 5c8ff92e38a9 - 17fcac7ddf54 + - 5c8ff92e38a9 - 24a7a95867b0 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 35dcfef42..93b7c3d31 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -3,7 +3,7 @@ tools: owner: iuc revisions: - a9c9d768b751 - - 204a131e47db - 159b04e36791 + - 204a131e47db 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 b2a6c3853..10d554a70 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: - - a1a923cd89e8 - e19bebe96cd2 - - a68aa6c1204a - - a8eabd2838f6 - - 589e7e57fd6d - 07e8b80f278c + - a8eabd2838f6 - 87ee588b3d45 - - dde39ba9c031 - - b28e0cfa7ba1 + - a1a923cd89e8 - ce3c7f062223 + - 589e7e57fd6d + - b28e0cfa7ba1 + - dde39ba9c031 - 0a5c785ac6db + - 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 4d4e21d13..26b706796 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 - 54f751e413f4 - e8ac2b53f262 - 62c9df8382c2 - - f921014aba5a tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,13 +23,13 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: + - e25d3acf6e68 + - acf4e47b734c + - 2889433c7ae1 - 0e3cf9594bb7 - - a52d2d93e595 - 6f386c5dc4fb + - a52d2d93e595 - 5edc472ec434 - - 2889433c7ae1 - - acf4e47b734c - - 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 e1bf6c079..8a1d0481a 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -3,12 +3,12 @@ tools: owner: chemteam revisions: - 27ee142314a9 + - 095ad4d096d1 + - f4230f116196 + - 710301bc46fa - da6bd1975a71 - 6ca543ec1bf8 - c8cdde00b105 - - f4230f116196 - - 095ad4d096d1 - - 710301bc46fa tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -87,8 +87,8 @@ tools: - name: enumerate_charges owner: bgruening revisions: - - 67ee76f0e497 - 2a868592ebcb + - 67ee76f0e497 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: fpocket @@ -106,91 +106,91 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 79cfd9ead848 - - 88076940fa94 - - 0fac8e2afc13 - 3b8a9d5ced85 - bfb65cb551d8 + - 79cfd9ead848 + - 0fac8e2afc13 + - 88076940fa94 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - eb6564a60136 - - b46d4b4d995c - 55918daa5651 + - d532b7e5f64b - 715cd0e87781 + - b46d4b4d995c - f5d979cb4b54 - - d532b7e5f64b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - 97872d87ba80 - f26afd1b7104 - - fdf2cc80adb5 - - d2f955aea23a - 5579659312e6 + - d2f955aea23a + - 97872d87ba80 + - fdf2cc80adb5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - 319a28774da9 - bc31d02be922 - d1d0efda35c0 + - 319a28774da9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - ed736e6eee39 - - 2c349b027a01 + - 4da9ee404eab - 070e3ecc3fda + - 2c349b027a01 - cac1886249a2 - - 4da9ee404eab + - ed736e6eee39 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - da8753545526 + - d1f803b5943c - c0c9a5024177 - - 525ca7c8065f - - 807aa4c9293d + - 73008ef1f487 - 2e219a2d9327 + - 525ca7c8065f - f197e34c33a9 - - 73008ef1f487 - - d1f803b5943c + - 807aa4c9293d + - da8753545526 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 1809414a9454 - 27ea4e1a3f95 - 61094e01eff9 - - c4fbab8e03c5 - - 7568ae18908a - 2c8ed1b52bf7 + - 7568ae18908a + - 1809414a9454 + - c4fbab8e03c5 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: - - 79e8ab8f1e81 + - 730ef07b90ae - ba83f0923369 - - ccfbd956a2d3 - d7ec25187599 - - 730ef07b90ae + - ccfbd956a2d3 + - 79e8ab8f1e81 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 9a3a1f698fc6 - 48d6a6eb438b + - 9a3a1f698fc6 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: natural_product_likeness @@ -203,8 +203,8 @@ tools: owner: bgruening revisions: - e6011617c748 - - b59c91adeac1 - 1400d1977e7b + - b59c91adeac1 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: + - 9b48456a96fe - 85fad59f8168 - - bf99565cec1f - d4c67ced6abc - - 9b48456a96fe + - bf99565cec1f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: vmd_hbonds diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index ecea3afd4..3b9a2169f 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -2,8 +2,8 @@ tools: - name: diffbind owner: bgruening revisions: - - 163688bb8f73 - fa56d93f7980 + - 163688bb8f73 - c97a786e8fb5 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -22,18 +22,18 @@ tools: - name: macs21 owner: pjbriggs revisions: - - 4124781932db - 11cf21ee4242 + - 4124781932db tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 owner: iuc revisions: + - 640d3af5d833 + - 86e2413cf3f8 - 424aefbd7777 - - f5d67c722d67 - 495a4173006f - - 86e2413cf3f8 - - 640d3af5d833 + - f5d67c722d67 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -45,16 +45,16 @@ tools: - name: rnachipintegrator owner: pjbriggs revisions: - - 087d9872fb0d - b695071de766 + - 087d9872fb0d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer owner: devteam revisions: - - 5c2cc3b58c7d - - 74c9214cc8e6 - 4a14714649b4 + - 74c9214cc8e6 + - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/staging.gvl.org.au/collection_operations.yml b/staging.gvl.org.au/collection_operations.yml index 862143a00..79bbd2c6f 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -2,16 +2,16 @@ tools: - name: bundle_collections owner: nml revisions: - - cd6da887a5f4 - 705ebd286b57 + - cd6da887a5f4 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: - - 25136a2b0cfe - 33151a38533a - 90981f86000f + - 25136a2b0cfe - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu @@ -26,8 +26,8 @@ tools: owner: bgruening revisions: - baabc30154cd - - 6cbe2f30c2d7 - 0046692724f9 + - 6cbe2f30c2d7 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index 0ee9f610f..4803b92d9 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -9,36 +9,36 @@ tools: owner: iuc revisions: - dad9da48a09a - - f3a19509108a - - 367b1ed91207 - - 0b3c3ad92827 - 6ef0b5664c69 + - 4a6ee918c13a + - 0b3c3ad92827 + - 367b1ed91207 + - f3a19509108a - a3b86937ead6 - - 5e1240a87bcb - e3cbd2287f63 - - 4a6ee918c13a + - 5e1240a87bcb tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - e177a8ea0bf1 - - 33c99804a32f + - 1b5fc03380d4 - 584008e574b2 - 54ccb7e1f49a - - 1b5fc03380d4 - bd46669113b9 + - e177a8ea0bf1 + - e525f9ffb9ac - 501c21cce614 - - 72ed72122deb - a4db66553a61 - - e525f9ffb9ac + - 72ed72122deb + - 33c99804a32f tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 owner: iuc revisions: - - a0d092f27fdf - 11c3eb512633 + - a0d092f27fdf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: compress_file @@ -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: - 186b8d913e6c - - 77b41c89d856 - 8979c288aefb + - 77b41c89d856 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: - - 8e9d604e92f4 - e33c82b63727 + - 8e9d604e92f4 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -91,8 +91,8 @@ tools: - name: gffread owner: devteam revisions: - - 4dea02886337 - 154d00cbbf2d + - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -110,32 +110,32 @@ 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 owner: devteam revisions: - - 0b4e36026794 - 0a7799698fe5 + - 0b4e36026794 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq owner: devteam revisions: - 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name: deeptools_plot_heatmap owner: bgruening revisions: - - a4dfb122e52b + - 25d830337d31 - 512155688d98 - - a7849312d328 - - 010e58e9d822 - e4c7985d4585 - ba6efa77fb79 - c60570fa602f - - 25d830337d31 + - a4dfb122e52b + - 010e58e9d822 + - a7849312d328 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - c899e0ccff8c - - 69264da0ce77 - - 00d869ea03a1 - - 4d678170d29b - - aa200e4f3939 - 38e3f226248b - 443d9a9d6d11 + - 4d678170d29b + - aa200e4f3939 + - 69264da0ce77 + - 00d869ea03a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: + - 6662b1a8d326 - aac8444d6681 - - a2d70c4fd406 - c361b12d207a - - d806504e96d9 - 10301d137111 - - 6662b1a8d326 + - 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 d99f72271..a3e2b1a19 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -2,8 +2,8 @@ tools: - name: obi_annotate owner: iuc revisions: - - f82cefbbcea5 - 3021b9f5809f + - f82cefbbcea5 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_clean @@ -16,15 +16,15 @@ tools: - name: obi_convert owner: iuc revisions: - - 374fd9feb032 - 4d705e3443a7 + - 374fd9feb032 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep owner: iuc revisions: - - e9e49cf06b42 - fe7ec8a3d35e + - e9e49cf06b42 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend @@ -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 @@ -58,14 +58,14 @@ tools: - name: obi_tab owner: iuc revisions: - - 3299c7d5268f - 5f7003111e32 + - 3299c7d5268f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq owner: iuc revisions: - - c0f7b58b4ce4 - ec215ed98831 + - c0f7b58b4ce4 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index 58b655034..c72370b98 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - 63dd26468588 - - dba489bfcd62 - ce385837c160 - 832c20329690 + - 63dd26468588 + - dba489bfcd62 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 85a3f9836..f21e9b48f 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -2,10 +2,10 @@ tools: - name: bwameth owner: iuc revisions: - - d82648ad25a3 - 62f5fab76dfb - - 29bdbc353f20 - 6da3972210ee + - d82648ad25a3 + - 29bdbc353f20 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 8864ab9e8..ec4d06e63 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: - - 8c0175e03cee - - e4691e1589d3 - - de6cebe3c043 + - 5915ea1ec9b1 - 135b80fb1ac2 - - 48f587c13075 - - 8665bcc8b847 - c053d4cad713 - - 5915ea1ec9b1 - - 49370cb85f0f - - 660cffd8d92a + - 44e2cc14f75b + - e4691e1589d3 + - 288f97432497 - 093678460093 + - c4b82dce8335 + - 8665bcc8b847 + - de6cebe3c043 - 4e5056fefd88 - - 288f97432497 + - 660cffd8d92a + - 49370cb85f0f + - 48f587c13075 + - 8c0175e03cee - c5e2e5902201 - - 44e2cc14f75b - - c4b82dce8335 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -35,9 +35,9 @@ tools: - name: fasta_clipping_histogram owner: devteam revisions: - - f666895cbebd - - 8889eb864cef - 9db07fd39f85 + - 8889eb864cef + - f666895cbebd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -56,8 +56,8 @@ tools: - name: fasta_concatenate_by_species owner: devteam revisions: - - 717aee069681 - 25b8736c627a + - 717aee069681 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_extract @@ -69,16 +69,16 @@ tools: - name: fasta_filter_by_length owner: devteam revisions: - - e626b3ff9922 - 8cacfcf96a52 + - e626b3ff9922 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: - - 516b97a23d7e - 859422bcb689 - 9457a20156db + - 516b97a23d7e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -90,8 +90,8 @@ tools: - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - f546e7278f04 - 2904d46167da + - f546e7278f04 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -111,10 +111,10 @@ tools: - name: fasta_stats owner: iuc revisions: - - 9c620a950d3a - - 56022eb50bbd - 0dbb995c7d35 - cd0874854f51 + - 56022eb50bbd + - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -126,9 +126,9 @@ tools: - name: fastp owner: iuc revisions: + - 65b93b623c77 - dbf9c561ef29 - 1d8fe9bc4cb0 - - 65b93b623c77 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -140,36 +140,36 @@ tools: - name: fastq_combiner owner: devteam revisions: - - f1dc2a761c30 - b05e39b9c170 + - f1dc2a761c30 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter owner: devteam revisions: - - 10b75444feae - 81a9090d6df3 + - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer owner: devteam revisions: - - 8611b80a14d6 - 47e5dbc3e790 + - 8611b80a14d6 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: - - 9282652e7234 - 9dfda4e310ed + - 9282652e7234 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer @@ -189,8 +189,8 @@ 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 @@ -210,9 +210,9 @@ tools: - name: fastq_quality_converter owner: devteam revisions: - - 74db4cffab1f - 54053ea6c77e - 045f0e1043f7 + - 74db4cffab1f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -244,10 +244,10 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 529bccd5e4a1 - - d5e9e83cd3d8 - 09070cacefd8 - 567d5b3c52b1 + - d5e9e83cd3d8 + - 529bccd5e4a1 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: - - 4bedca26c133 - - 8abdedf55101 - 0b7ec11b3c7c + - 8abdedf55101 + - 4bedca26c133 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 @@ -288,9 +288,9 @@ tools: - name: fastx_collapser owner: devteam revisions: - - 07497255281e - - 7ce1891db6f5 - 421f0af4ee95 + - 7ce1891db6f5 + - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -302,10 +302,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - b29d37ca9e41 - f984bb114520 - - 3599f5451ee2 + - b29d37ca9e41 - 02f8a17a4ebd + - 3599f5451ee2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -317,10 +317,10 @@ tools: - name: fastx_reverse_complement owner: devteam revisions: - - 6027ef51ef91 - - e246088b6e34 - 177f0621c266 - 0c2907307ba4 + - 6027ef51ef91 + - e246088b6e34 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: + - 377ac2829eac - 61b4cedc8934 - - 73194cdd4f57 - 547e8d00f11c - - 377ac2829eac + - 73194cdd4f57 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: - - 2f804526f5fd - b4c6f054210a + - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: pear @@ -372,15 +372,15 @@ tools: - name: seq_select_by_id owner: peterjc revisions: - - 3b0a14722175 - 8e1a90917fa7 + - 3b0a14722175 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - 4b494533146a - 3da72230c066 + - 4b494533146a 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 @@ -418,10 +418,10 @@ tools: - name: umi_tools_count owner: iuc revisions: - - 24013bf85a6f + - a535cf1e5da4 - e654095ab143 + - 24013bf85a6f - b557acca0b56 - - a535cf1e5da4 - 8250ea3a1501 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -440,12 +440,12 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - f3759eec3018 - - 6a675c3aa610 - - 828dba98cdb4 - 7accf7407811 - - 27ac32a22ad2 + - 828dba98cdb4 - 9fa7803d1c51 + - 27ac32a22ad2 + - 6a675c3aa610 + - f3759eec3018 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 f58375d61..0fe69d880 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -2,10 +2,10 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - ce9cd02d5b88 - - e41385662e5e - 64e9a6afdd0c + - e41385662e5e - 7b4468117008 + - ce9cd02d5b88 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,13 +18,13 @@ tools: - name: fastqc owner: devteam revisions: + - 5ec9f6bceaee + - 2b0c9d9fc6ca + - e7b2202befea - 3d0c7bdf12f5 - 9da02be9c6cc - - 5ec9f6bceaee - ff9530579d1f - f2e8552cf1d0 - - 2b0c9d9fc6ca - - e7b2202befea tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -37,46 +37,46 @@ tools: - name: fastx_nucleotides_distribution owner: devteam revisions: - - b6b54ba71bd8 - - 18a51655db17 - ad116ae3f4d9 + - 18a51655db17 + - b6b54ba71bd8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - cc0fd298cc17 - - 59003d0543cd - 7306ec78632a + - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: + - 1f296803dfa3 - 8880fb74ef56 - a72af9de6bf5 - - 1f296803dfa3 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - 5e33b465d8d5 - - bf675f34b056 + - 1c2db0054039 - 9a913cdee30e - 75c93c70d094 - - f7985e0479b9 - 3d93dd18d9f8 + - f7985e0479b9 - abfd8a6544d7 - - 1c2db0054039 + - bf675f34b056 - b2f1f75d49c4 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: + - 949f01671246 - 084bbd8ba7b8 - cd7e644cae1d - - 949f01671246 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 7e6d121cc..789344242 100644 --- a/staging.gvl.org.au/filter_and_sort.yml +++ b/staging.gvl.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - 3c623e81be77 - dff7df6fcab5 + - 3c623e81be77 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index 1e5deb4fd..a414a7d43 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -9,16 +9,16 @@ tools: - name: gemini_amend owner: iuc revisions: - - be828b79bd4d - 4bd4870ecd33 + - be828b79bd4d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - f2f3bc622a16 - - 8f53b238a360 - 0c8f7322f8fc + - 8f53b238a360 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -31,8 +31,8 @@ tools: - name: gemini_comp_hets owner: iuc revisions: - - 7cf9bc210044 - 62647e2637f6 + - 7cf9bc210044 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_db_info @@ -52,8 +52,8 @@ tools: - name: gemini_dump owner: iuc revisions: - - 40f85b45e472 - 96a2d270bf0f + - 40f85b45e472 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - d46017ddbf94 - 452104bdc655 + - d46017ddbf94 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -79,23 +79,23 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 2550239feed5 - 184aa4e686e2 + - 2550239feed5 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load owner: iuc revisions: - - b2c25142267e - - cf61daf064fe - 45296e47d565 + - cf61daf064fe + - b2c25142267e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 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: - - 6b09debcfc49 - 9199331c3421 + - 6b09debcfc49 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -137,8 +137,8 @@ tools: - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh @@ -151,21 +151,21 @@ tools: - name: gemini_set_somatic owner: iuc revisions: - - ef9991a4a9a7 - e4e2128460e3 + - ef9991a4a9a7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats owner: iuc revisions: - - 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 ba4164156..095be2eba 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -2,22 +2,22 @@ tools: - name: mageck_count owner: iuc revisions: - - e329d44424d7 - 3edbd1ff5602 + - e329d44424d7 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea owner: iuc revisions: - - d46e36492bff - b946929d31c4 + - d46e36492bff tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index 3aab1d013..393f2987d 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,40 +2,40 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - e9df53a75f3c - - 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: - - f5ea3ce9b9b0 - 1790dcf3c32d - - 4317d3cb6cba - - e407b9da183a - - 653e89d73fc4 - 6591f049cf7e - - 734abc7ac21d - - e08a7ad4378b - - aad3885b3216 - - 7068f48d0ef9 - - 4df8de2d0e48 - 9a776b080193 - - c441583adae5 + - 4df8de2d0e48 - 6ea73833cf67 + - 69ebb7f46e45 + - e08a7ad4378b - 83c7d564b128 + - 7068f48d0ef9 + - e407b9da183a + - f5ea3ce9b9b0 - 5e6237d58b0c - - 69ebb7f46e45 + - 4317d3cb6cba + - c441583adae5 + - aad3885b3216 + - 653e89d73fc4 + - 734abc7ac21d tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept @@ -43,8 +43,8 @@ tools: revisions: - 34758ab8aaa4 - 7863f1abcdda - - 75b3b3d0adbf - 9aaa46d45472 + - 75b3b3d0adbf tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index 71ea54d55..6f0271b6d 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -2,14 +2,14 @@ tools: - name: circos owner: iuc revisions: - - 740057a5126d - - ae9994cf526f - 4b519282a05b - a64dc31ab7f2 - - df7356989ac1 - - fd59d783248a - 290a11559985 + - ae9994cf526f + - 740057a5126d + - df7356989ac1 - c4bde687c846 + - fd59d783248a - 7f13dc906cb9 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 - 867ab348287d - 7cf5b1d072b5 + - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -48,31 +48,31 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: + - '566197475670' + - 3b37b1b1c3a7 - 53460afd5115 - ca7cb0eaad62 - - 3b37b1b1c3a7 - - '566197475670' tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - 391a4cc45fea - - 10515715c940 - - da4c086cff5b - 3d059e9c2fba - d3a9e32672ec + - 10515715c940 + - 391a4cc45fea + - da4c086cff5b tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - e3a675da7fd0 - - d0fc8b746d57 - - 5fe1dc76176e - 1acf88921176 + - e3a675da7fd0 - 3b12bf9b4b87 + - 5fe1dc76176e - 299307abd804 + - d0fc8b746d57 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -106,16 +106,16 @@ tools: owner: iuc revisions: - 1cfc579079a6 + - ca2def38369c - 2bb2e07a7a21 - - 17359b808b01 - - 4542035c1075 + - a6e57ff585c0 + - 6cd09d7b5f37 - 667e17248bfe - 836d1aa3e89a - - ca2def38369c + - 4542035c1075 - 112eb40ba6cf - - a6e57ff585c0 + - 17359b808b01 - fd5dbf0f732e - - 6cd09d7b5f37 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -133,8 +133,8 @@ tools: - name: pathview owner: iuc revisions: - - f1691de443a7 - fe154a7af404 + - f1691de443a7 - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -154,8 +154,8 @@ tools: - 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 @@ -180,22 +180,22 @@ tools: - name: pygenometracks owner: iuc revisions: - - a1abfa420d9d - - 2824d77cd8f8 + - 4ac4e7083b7e - 326a3db8d9d1 - - 14e7c35f3d00 - - 59fd173ac850 - 360df4999907 - - 4ac4e7083b7e + - a1abfa420d9d + - 59fd173ac850 - 7dd841a32245 + - 2824d77cd8f8 + - 14e7c35f3d00 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 82523cc33..650427647 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 1a642de6db01 - 14b3f2a4523b + - 1a642de6db01 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -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/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 68646b3c3..02defab36 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,10 +2,10 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 29f66c353bcb - - 921a2da49a0c - 9edf8894a22d + - 29f66c353bcb - ed2cca6b5de4 + - 921a2da49a0c tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads @@ -13,34 +13,34 @@ tools: revisions: - d404277cc87a - 5746d61f0a91 - - 78fb5e286609 - ec4b948dc6f0 + - 78fb5e286609 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 977dc15add20 - - 9e357a8b2ec3 - 4d511437b1e5 - 03dd3c16ae4e + - 9e357a8b2ec3 + - 977dc15add20 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - 0ba4f56a3613 - - 3b5b54ed6392 - 77919cc3618e - 41dbf4d162a2 + - 3b5b54ed6392 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 9939786dd9c9 - b63363075c2e - 5308ca68ef3d - 7babd8a46fe0 + - 9939786dd9c9 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 2eedbcdd0..e46831522 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,9 +2,9 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 0c777d708acc - 3df9f0a4bf34 - 81f0cbca04a7 + - 0c777d708acc tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction @@ -17,15 +17,15 @@ tools: - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - 6ad1d3cfdea1 - e576b73a2e2f + - 6ad1d3cfdea1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization owner: imgteam revisions: - - 70316d792fc9 - 77f7159d775a + - 70316d792fc9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter @@ -38,33 +38,33 @@ tools: - name: bfconvert owner: imgteam revisions: - - f3360fbeda64 - - b07f4839ca77 - 85edbb7a436b + - f3360fbeda64 - 10eed33aa9b2 + - b07f4839ca77 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 6e65fd971e13 - 984358e43242 + - 6e65fd971e13 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - 5bf8eb50b280 - - 664232d2a3f7 - b58447a2eed2 + - 664232d2a3f7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - eb6c08714244 - 0e4dccaafef5 - e917a2424690 + - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -77,25 +77,25 @@ tools: - name: cp_common owner: bgruening revisions: + - 670975e92458 - 6070780813d9 - e7273daa5ae2 - - 670975e92458 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image owner: bgruening revisions: - df3ad3ba5c6f - - ef4aed1d34c4 - cdf8e3c57dae + - 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 @@ -110,16 +110,16 @@ tools: owner: bgruening revisions: - f24c370e5ea4 - - f8fa0f6718a3 - d0178bdcd00e + - f8fa0f6718a3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: + - 3245681b2f6d - 31d195bedf6d - ad271f78a87a - - 3245681b2f6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects @@ -134,8 +134,8 @@ tools: owner: bgruening revisions: - ff1a86a87364 - - c09dcda1143f - 6100a22bf4f2 + - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image @@ -157,49 +157,49 @@ tools: - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 91e03287f285 - - a32c3f810ade - 20dbb1f7ec7b + - a32c3f810ade + - 91e03287f285 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - 8536b1ae0254 - - 5499dc6f8ac1 - b64af54c5c09 + - 5499dc6f8ac1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - e972e07c7845 - - 6f4715b8540a - d3890df07463 + - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: - - e52c75a28c4b - 980aed9e8fd5 + - e52c75a28c4b - 407925835dd9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - d85f11570109 - - acf3aa487283 - 79e10d12d90a + - acf3aa487283 + - d85f11570109 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - 035a58c7f54a - b76841ee5560 - 80b200ae516b + - 035a58c7f54a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -211,17 +211,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: - - 3a3033222f61 - - 48102a685037 - 8083a87d2fdf + - 48102a685037 + - 3a3033222f61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: + - 33f4fa1413fb - 27edbb90ab2b - 4ecf93628f97 - - 33f4fa1413fb tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -233,15 +233,15 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 1fd453cd757b - 972d2c365739 + - 1fd453cd757b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 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 diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index e5875bb9d..2b3033a55 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,88 +2,88 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 78bbd17d0703 - - e319b5b65879 - - d6e72da3ec35 - 17f911830a8c - - a38934e303b9 - - 1069f6db0a0e + - d6e72da3ec35 + - e319b5b65879 - f362150bef41 + - a38934e303b9 + - 78bbd17d0703 - e4ee04da1c19 - 3e4f434a69c6 + - 1069f6db0a0e tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 8f8df367470d - - 9537184d421f - - 72ddd32392cd - - 7fe36019c073 + - 0135f1d487a0 - c88553ec696e + - 9537184d421f - 2b95d5c04908 - - f91cfb73d369 - - 0135f1d487a0 - 1ef5b6e3e09d + - 8f8df367470d + - f91cfb73d369 + - 7fe36019c073 + - 72ddd32392cd tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - d7e79eb3bcb3 + - 2cf4a1cafc16 - ad0dc9f4c9e2 + - d7e79eb3bcb3 - fafb3d685fa9 - - 2cf4a1cafc16 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 69797fa273c3 - - 8c05afb547fa - 43aac8d29685 - - 7f1cfa4c0e32 - - 3d18f8c3c0f6 - - 8d36959b000d - - 28a6f1908fcc - - 94df24c6bc00 - bd2a7d1316b9 - - ee29337f905c - - ee2beb764a7b - 6a1515bb0687 + - 8c05afb547fa + - 8d36959b000d + - ee2beb764a7b + - 94df24c6bc00 - 9eaadf03e0df + - 7f1cfa4c0e32 + - 3d18f8c3c0f6 + - ee29337f905c + - 69797fa273c3 + - 28a6f1908fcc tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 5671e1d3d5ee - 9f978da6528a + - bcaa0d571ce2 + - c092052ed673 + - 364f4ffec275 + - 8858fa037a15 - d37ede8589b2 + - 5671e1d3d5ee + - e3bb03cf207a - 5d6ed46cc101 - - 364f4ffec275 - db536ad45f28 - - bcaa0d571ce2 - - 8858fa037a15 - 0893a1dbb807 - - e3bb03cf207a - cb903c9dc33d - - c092052ed673 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - ed28dd32141c - - e1a015876aa9 + - 38b91a3190cd - 49236b03e4fd - - f95f403841ad - - c5c9f02b6167 - 12d66d0d05ac - - 230b05597996 + - e1a015876aa9 + - c5c9f02b6167 + - 584beffa972b - 3b6a16d82c1b + - ed28dd32141c - 045d6d00f606 - - 38b91a3190cd - - 584beffa972b + - f95f403841ad + - 230b05597996 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 4e5a7d989..6bf3795b2 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: - - 17e3b698dd52 - - b8a457820315 - 0f1724dd59d2 + - b8a457820315 + - 17e3b698dd52 - f198773344e4 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - 374cb875d38a - - 22c2a1ac7ae3 - - a513e3fbb4c5 - ba0c40780ecf - ac092723240d + - 22c2a1ac7ae3 + - 374cb875d38a + - a513e3fbb4c5 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 52ab820f6..3df16de48 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -2,99 +2,99 @@ tools: - name: keras_model_builder owner: bgruening revisions: - - 772e0e89fc68 - 522137aaa9c4 + - 772e0e89fc68 - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - f22a9297440f - 8a794e6d3388 - 4d81e3e2fb63 + - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - 818f9b69d8a0 - - b6ef6d0cb6b7 + - e1317b5502fa - 2af1346e68c9 + - b6ef6d0cb6b7 - f1b9a42d6809 - - e1317b5502fa tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - 947c2eacccb8 - c80db5d6fd8c - - 1588f9076e32 - - 8334dc98c48e - 05143043ca13 + - 947c2eacccb8 + - 8334dc98c48e + - 1588f9076e32 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - 29e4122c90de - - 83228baae3c5 - 25b46af53232 - 9991c4ddde14 - 1552b8cb4a94 + - 83228baae3c5 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 53616c8b0865 + - a07ab242b0b5 + - 060ca94ac049 - 1a53edc4b438 + - 53616c8b0865 - 841a6cc5fc58 - - 060ca94ac049 - - a07ab242b0b5 - f3dfa4bdf87e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: + - 2fc89dcd41c8 + - 91c4e3331208 - 40f4447733b2 + - d4808d5b83da - 927586a18553 - dc4b5fd604a6 - - d4808d5b83da - - 2fc89dcd41c8 - - 91c4e3331208 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 36e8d6d5d01b - - e5a5ad882f1f - 25ab6b4e376e - - 301e07345c93 - c6ae57f774c6 + - 36e8d6d5d01b + - 301e07345c93 + - e5a5ad882f1f - 7626ea9c2e1b tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 0630258dcf35 - - b7c3e9a3b954 - 80852884053f + - 4ed102b922cb - f9639b488779 + - b7c3e9a3b954 + - 0630258dcf35 - 02d2be90dedb - - 4ed102b922cb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - 14180f9c831e - 61634a87efc7 - caeb57858702 + - 14180f9c831e - ec69cbe34b73 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index ee5f6eb9e..4e83b6339 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -2,15 +2,15 @@ tools: - name: bowtie2 owner: devteam revisions: - - 17062a0decb7 - - cd659e8cc5fa - - a6d65b0c67af - f6877ad76b00 + - 749c918495f7 + - cd659e8cc5fa - 03e9b2fbc005 + - 017aba02828d - 3ba8d4563129 + - 17062a0decb7 + - a6d65b0c67af - 937aa69e715f - - 017aba02828d - - 749c918495f7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -22,18 +22,18 @@ 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: - - e188dc7a68e6 + - dfd8b7f78c37 - 64f11cf59c6e - - 3fe632431b68 - 53646aaaafef - - dfd8b7f78c37 + - 3fe632431b68 + - e188dc7a68e6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -45,10 +45,10 @@ tools: - name: lastz owner: devteam revisions: - - 60afcc2c1d05 - 2ff111fac1d7 - 3e1ea2facca6 - e7f19d6a9af8 + - 60afcc2c1d05 - 37b497aa133f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -56,32 +56,32 @@ tools: owner: iuc revisions: - c0c2d0941de8 - - f54f5baedfdd + - be1d967337e4 - 037c6e54df11 - - 77b2770508f6 - - 6b1e195506a3 - - 11a0d50a54e6 - - 09b53c1d4ab1 + - f54f5baedfdd + - 53c0b7a1a0c3 - b3eab4b67562 + - 09b53c1d4ab1 - 3f4d6399997b - - be1d967337e4 - 8c6cd2650d1f - - 53c0b7a1a0c3 + - 11a0d50a54e6 + - 77b2770508f6 + - 6b1e195506a3 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 00fbfac99d39 - - 9ee34ba73ebf + - ec9cbd6b9a49 + - 13022c3d3076 - 1cd2511a396e - - 5ef7ec16b04f - e403d27e8f24 - - 13022c3d3076 + - 9ee34ba73ebf - 79b885ce78d7 + - 00fbfac99d39 + - 5ef7ec16b04f - b8f5f6e87f5c - 178bdbdb6d24 - - ec9cbd6b9a49 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 9b3abcb51..634d4ab5f 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -2,8 +2,8 @@ tools: - name: cat_bins owner: iuc revisions: - - 18676df0cb3a - 0094893f5001 + - 18676df0cb3a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -34,19 +34,19 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 76d3d2b10738 - 5b5a7af9fbb4 - - 7c2100246a2f - 63f86089423e + - 7c2100246a2f + - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 1c35dadbe76f + - 18a502a9d287 - 84fd33a60b35 + - 1c35dadbe76f - 96336c6a2bb7 - - 18a502a9d287 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim @@ -54,24 +54,24 @@ tools: revisions: - f732237754fc - 34e55239e68b - - addaf9d22850 - a9f4a217dcd6 + - addaf9d22850 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 04c15826a0b8 - 8c202e741d68 - 75403243703a - 0776d824d896 + - 04c15826a0b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 43c99742158b - e96bbb9e24ea + - 43c99742158b - 8470de786d47 - 1c9b3bcd4261 tool_panel_section_label: Metagenomic Analysis @@ -79,68 +79,68 @@ tools: - name: dada2_mergepairs owner: iuc revisions: - - 306a40d4bb8f - - 1d75bd0595e2 - 84743da21318 - 5c865a382933 + - 306a40d4bb8f + - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - ac72310b038a - - 78faebd0879c - 555ccac8a4c5 - 8daf4564ccda + - 78faebd0879c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - f947b4bb5107 - - a58e4a43f49c - 7b8cb2b02978 + - a58e4a43f49c + - f947b4bb5107 - d60df8727f59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: + - 7136e9ab70db - 04144473e59e - 1bc3657cd694 - - 7136e9ab70db - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - d943081510da - 9058d8943303 - 19299bb1c6af + - d943081510da - 0a1224c4b781 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - e005e659ae21 - c7e73acfa3eb + - e005e659ae21 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: - 6501b5b33988 - - dbf1798c0dcc - c4db8c4de66f + - dbf1798c0dcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 15dbb444df71 - fa35f1106d3e + - 15dbb444df71 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level @@ -161,23 +161,23 @@ tools: owner: iuc revisions: - 6aad8ca3918b - - bd7a9c6efb10 - e66ab198ec15 + - bd7a9c6efb10 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: - - c6676a890f50 - d77397f09da1 + - c6676a890f50 - b084117133af tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - 7f208f1eb64f - 9704f1a3b32d + - 7f208f1eb64f - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -191,50 +191,50 @@ tools: owner: iuc revisions: - c409a495841f - - 31c6d107e7a5 - 79706f10d680 + - 31c6d107e7a5 - e88b731dad59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 172920f67a84 - - 094ad9c068af - d24841f5c3d2 - - 71ea608ddfa3 + - 094ad9c068af + - 172920f67a84 - 714d5a28cc5c + - 71ea608ddfa3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: + - a4d7148ccee4 + - a293a742194f - 12fb63b5f63f - 4137b492233e - - a293a742194f - - a4d7148ccee4 - d7e9a3c41657 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: + - e2c71b852aba + - 75bedfb2078b - cf87759761eb - - 64bc7acc22a9 - 97f7bb0851e7 + - 64bc7acc22a9 - 6fcb8ac37a3e - - e2c71b852aba - - 75bedfb2078b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - 4033827c76b8 - - c82508e76ad1 + - 080ea153677c - 5e5a999ffaa9 - 2d35528d2141 - - 080ea153677c + - c82508e76ad1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann @@ -308,16 +308,16 @@ tools: - name: kraken2 owner: iuc revisions: - - 4a9da2b6c2e3 - 328c607150ff - e674066930b2 + - 4a9da2b6c2e3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax owner: devteam revisions: - - 50bd98b3ae5a - f03c7ba8d8bc + - 50bd98b3ae5a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -329,15 +329,15 @@ tools: - name: kraken_filter owner: devteam revisions: - - 5bee9adae474 - 3d6570bffdb1 + - 5bee9adae474 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 1902d3de4a4f - 6c09bed3444f + - 1902d3de4a4f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -389,17 +389,17 @@ tools: revisions: - 0270541aaf46 - 4fd3b5d8706b - - 27250f92a01a - 2cff76cf35c6 - e073891b2afc + - 27250f92a01a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - 76bc4efa1aeb - 708abf08a626 - eb50e7eca3dc + - 76bc4efa1aeb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -465,20 +465,20 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - ebb74774457e - fdbd63e92b01 + - ebb74774457e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - b89b0765695d - - 6dee4abadccb - - a16313517e55 - - a92a632c4d9b - 1a6cdf55390f - - ff8f55893e7d + - a92a632c4d9b + - a16313517e55 - 2131d7dca455 + - 6dee4abadccb + - ff8f55893e7d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -569,8 +569,8 @@ 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 @@ -602,11 +602,11 @@ tools: revisions: - 141afacabcfa - 4b9a8031ab74 - - aeaa20b96ef2 - 2fd4d4c9c5c2 - - 4d83eccf5f81 - - 3b22de20bd4b - be818ae858e4 + - 3b22de20bd4b + - 4d83eccf5f81 + - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -637,7 +637,7 @@ tools: owner: iuc revisions: - b3c7199d8786 - - 576963db5f1b - 9495df9dd6ef + - 576963db5f1b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index 3a4bc2787..2ec77e04a 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: - - 63b74bfc8052 - f4d7d5755f01 + - 63b74bfc8052 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 72be09dfd803 - 2344ed181ae6 + - 72be09dfd803 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 e22b7df28..ab08d4758 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: - - 6ae5a7b5a0a2 - - 9eeb13a92d79 - - 2263989660f5 + - 48c13389050d - cd07731e4434 + - bdfbaf0c10aa + - 6ae5a7b5a0a2 - 9baa871cb1d1 + - 94b8c6013083 + - 9eeb13a92d79 - 80f03df2e2ce + - a74dbfee5a86 - 9422c5a87ee2 - - 48c13389050d - - 94b8c6013083 + - 2263989660f5 - 8b67dd48fec1 - - a74dbfee5a86 - - bdfbaf0c10aa tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - f14193ec1f50 - - be78f13134e2 - - f0af8936ed41 + - bc3831dd65c1 - aaa0d6a8b808 - - c18157c68134 - 3ff17bad4006 + - fc2e49f91e52 + - c18157c68134 + - f0af8936ed41 - d7ce0ec78e51 - 2e093badc689 - '764845535798' - - bc3831dd65c1 - - 5abf2c2249aa - - 4a60927aaca5 - - fc2e49f91e52 + - f14193ec1f50 + - be78f13134e2 - d390fe1567dc + - 4a60927aaca5 + - 5abf2c2249aa 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: - - b768cc4cca40 - e483be1014b6 + - b768cc4cca40 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -64,19 +64,19 @@ tools: - name: mafft owner: rnateam revisions: - - 15974dd17515 - c5908940967d - a65296ffb4a0 - - f0d493f8f84f - - f1a5908ea2cb - 6f28e90db932 + - f1a5908ea2cb + - 15974dd17515 + - f0d493f8f84f tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: - - b3acbb3a6af0 - fbca557a4847 + - b3acbb3a6af0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff @@ -89,22 +89,22 @@ tools: - name: mummer_mummer owner: iuc revisions: - - bcd65de9725b - 48823c9635a4 + - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - 4fc0cb2ac8ae - ebe3b0f84de9 + - 4fc0cb2ac8ae tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - 636b049e6141 - e18267f90096 + - 636b049e6141 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords diff --git a/staging.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index 65c98eb57..fc6563b0b 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,35 +8,35 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: - - cb34f00cc10f + - 0e9e7fcdd543 - 72b5e9dda577 + - cb34f00cc10f - fc8804320156 - - 0e9e7fcdd543 - - 79e9a869f40e - a7228a7ea146 + - 79e9a869f40e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: + - fa11aa8103b2 - db25ec99c3ea - d6cddc06aeae - - fa11aa8103b2 - 18505fe2bdb1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: - - 19f3b583a9b3 - 2bf63b38ee9b - - 43815fa60f3a - - edf6d4003fad + - eb746fa6f514 + - cc36773a3681 - 0f5f4a208660 + - 43815fa60f3a - ec699520444c - - eb746fa6f514 + - edf6d4003fad - 222669c4afb6 - - cc36773a3681 + - 19f3b583a9b3 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -55,10 +55,10 @@ tools: - name: nanoplot owner: iuc revisions: - - a3c4fe6f49ab - - edbb6c5028f5 - 645159bcee2d + - edbb6c5028f5 - 0f1c34698076 + - a3c4fe6f49ab tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign @@ -72,17 +72,17 @@ tools: - name: nanopolish_methylation owner: bgruening revisions: - - a8d4be409446 - be95355fef8d + - a8d4be409446 - 90a922f32523 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 @@ -96,9 +96,9 @@ tools: - name: porechop owner: iuc revisions: + - 5f76b20953e5 - 93d623d9979c - 543cbeef3949 - - 5f76b20953e5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events @@ -117,8 +117,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - 47936349f3e9 - 5a82eb9e1b89 + - 47936349f3e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -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 46a3bb4c8..9803c2e11 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -21,8 +21,8 @@ tools: - name: bcftools_plugin_frameshifts owner: iuc revisions: - - 58341ad4fb42 - 96d2000977ab + - 58341ad4fb42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -52,17 +52,17 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - adfd6bf710bd - 3e73c97f025d + - adfd6bf710bd - d74850cf4e42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: + - 83da94c0e4a6 - 1586b111d2a3 - 9dd107db92c2 - - 83da94c0e4a6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -74,16 +74,16 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: + - ed1518ce2237 - 2f27f3b86827 - edacc4bcd3cb - - ed1518ce2237 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -101,16 +101,16 @@ tools: - 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 owner: bgruening revisions: - - 4a08b7b76b78 - 5a0d0bee4f8d + - 4a08b7b76b78 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath @@ -123,15 +123,15 @@ tools: - name: data_manager_fetch_busco owner: iuc revisions: - - 15b97817550a - 2b4526fdf7fb + - 15b97817550a tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - 4d3eff1bc421 - b1bc53e9bbc5 + - 4d3eff1bc421 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -143,16 +143,16 @@ 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: - - b4b2b284230a - 27a6a256cd23 - 172815da3d41 + - b4b2b284230a - 5bcf0e24f42c tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -165,8 +165,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d74c740bdb25 - d210e1f185bd + - d74c740bdb25 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -178,16 +178,16 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - fea85c467896 - - 87febc68b45b - 19bbd19b74b3 + - 87febc68b45b + - fea85c467896 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan owner: iuc revisions: - - 0df47f8552f6 - 7776cb18fdf8 + - 0df47f8552f6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_kallisto_index_builder @@ -211,8 +211,8 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 5fe20c915fa6 - 9c43baa60906 + - 5fe20c915fa6 - 4ba60cb14cb0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -225,18 +225,18 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - aec831b54a5b - 9d09724f2bf1 - 0db22932bc39 + - aec831b54a5b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - 6e24e79d3d69 - - 29c738066906 - df30a2f1db55 - ed7a967cb11b + - 29c738066906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sam_fasta_index_builder @@ -250,8 +250,8 @@ tools: - name: data_manager_snpeff owner: iuc revisions: - - def511e8e005 - d107d20dc6bd + - def511e8e005 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -263,17 +263,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - d63c1442407f - c520a52b5174 + - d63c1442407f - 64deddb6a8ec tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 625fd9476402 - - 9946bc39c834 - 94a50db37d1a + - 9946bc39c834 + - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1024,15 +1024,15 @@ tools: - name: rdock_rbcavity owner: bgruening revisions: - - 744a777e9f90 - 7e5c2e4bc227 + - 744a777e9f90 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rdock_rbdock owner: bgruening revisions: - - e4b7d1507a75 - a22969b08177 + - e4b7d1507a75 - c362398df83b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index bf9d57350..84546f802 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -33,103 +33,103 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - d033ffc1c161 - - 6a457678efcb - - c78f3d7dd1db + - a6619171428e + - b89cac5156ec + - f04a1264e2a2 + - 8834daeb9892 + - 81e66674859e + - 26de3a7b1cb9 + - f73435dc282b - 3f59ebfbfe3d - - 5a7c56a5cc08 - d7c7ef3353fe + - 5a7c56a5cc08 + - 107d3ba7024a - cce7b18495e4 + - 6a457678efcb - 3b8b5bde0bd9 - - f73435dc282b - - 81e66674859e - - 26de3a7b1cb9 - - 8834daeb9892 - - b89cac5156ec + - d033ffc1c161 + - c78f3d7dd1db - '841557158611' - - 107d3ba7024a - - a6619171428e - - f04a1264e2a2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - 02b8758214b0 - - 6a726db04d4b - - 4755f52427c4 - - aa8cc71438cf - - 3b96e92e8ec3 + - e75442c7f4da + - b0af57c1a968 - 6283babe736e - 6223845127ea - - 659517798cc4 - - 5fcd1ece3a6e - - e75442c7f4da + - 3b96e92e8ec3 + - aa8cc71438cf - df47d4845b62 + - 88c4aa435ded + - 4755f52427c4 - 7a2092844346 + - 659517798cc4 + - 5fcd1ece3a6e - a185b079b095 + - 6a726db04d4b - 5b777002c2de - - b0af57c1a968 - - 88c4aa435ded tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - 9b892d7f82cc - - f97743d52b87 + - d1c340a5664b - 524d31add34a + - f97743d52b87 - b8476e82ac20 - - d1c340a5664b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - daddf188c13f - - 9e10ba792be2 - - feb40665d7cd - 128ba8da994f + - feb40665d7cd + - 9e10ba792be2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - 5f8727ff21e7 - - 2f1019071464 - abf6dbe8c9d7 - - ca337cce3888 + - 83a69484cb87 - 2fa9d4f1b48f - - ca0d8cf80567 - - 03ed9524dcd1 - - b6abccb1f25b - - 42a174224817 - - b7e297c2ede6 - - 36912871ccdc - - a2099fb98cdb - - 14ae456b8cc5 - - 9d61d3fa046c - 3a43c3982401 - - 83a69484cb87 - - 81804a978fc0 - 7bb8726be37c + - a2099fb98cdb - 437e28791761 + - 81804a978fc0 + - 42a174224817 + - 03ed9524dcd1 + - 36912871ccdc + - ca337cce3888 + - ca0d8cf80567 + - 9d61d3fa046c + - 2f1019071464 + - b7e297c2ede6 + - 5f8727ff21e7 + - 14ae456b8cc5 + - b6abccb1f25b tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 7157a5b34a68 - 2bf47d57ebb5 + - 7157a5b34a68 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: raxml owner: iuc revisions: - - a4b71be30c3c - 29ff6a849eac - - 73a469f7dc96 + - a4b71be30c3c - b1e68bbe4cef + - 73a469f7dc96 - ba29b5e2a4be - ea30d3089354 tool_panel_section_label: Phylogenetics @@ -137,11 +137,11 @@ tools: - name: roary owner: iuc revisions: - - e88a7de55d6e - 809e42326fc2 - f1ccc8a6eb05 - - dbe2b2204555 - 15ac71df11a0 + - dbe2b2204555 - 91887494eb97 + - e88a7de55d6e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/picard.yml b/staging.gvl.org.au/picard.yml index 222994a76..243ce65a6 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -2,13 +2,13 @@ tools: - name: picard owner: devteam revisions: + - 881d7645d1bf + - 1aac2a13842a + - 7d34178f2812 - a1f0b3f4b781 - - f6ced08779c4 - f9242e01365a - b502c227b5e6 - - 1aac2a13842a - - 881d7645d1bf + - f6ced08779c4 - fc288950c3b7 - - 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 b25222fb5..c776de9b3 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: + - e4a053d67e24 - 7fbec959cf2b - - 5b85006245f3 + - ca90d17ff51b + - eb085b3dbaf8 - a58f7eb0df2c + - 5b85006245f3 - 3bd420ec162d - - eb085b3dbaf8 - - ca90d17ff51b - - d00e15139065 - - e4a053d67e24 - c0e71cb2bd1b + - d00e15139065 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 95bb960c8..1443cdc63 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: - - b18329a8ac14 - - 277dc652246e - - ece627528a78 - b574b84afc4d - f28ad96b76dc + - ece627528a78 + - 277dc652246e + - b18329a8ac14 - 0a18ac48ac53 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - 525f201b86c1 - - bf06d196e23d - - b41107d8fe89 - e988563cc6e5 - e215f71d7983 + - b41107d8fe89 + - bf06d196e23d + - 525f201b86c1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - 8da3511c9467 - - 4fbffddde8cd - bb6397b94018 + - 4fbffddde8cd + - 8da3511c9467 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: + - b8c79e70516d - a8157342d9a3 - - 528fb09022be - f23d67e28cc8 - - b8c79e70516d + - 528fb09022be tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 80600735685d - 59e85306eae5 - a69865da6f80 - - 25b83cbd596a + - 80600735685d - a95a82eb4d50 + - 25b83cbd596a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 611d80c0e29d - - f1897eb07081 - 798da6bdff3d - - e0669b1854b1 - ed9ed1e6cca2 + - f1897eb07081 + - e0669b1854b1 + - 611d80c0e29d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - 74b61bf5bc4b - - 5a35e3a8d013 - a7fb9b395ddf + - 5a35e3a8d013 + - 74b61bf5bc4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: + - 82f6c2f4332d - cc430977c8ff - df2187f9013b - - 82f6c2f4332d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - 043f9c91f686 - - 1693b2126f30 + - 10566783d718 - c5aa9fca18c6 - d2483487e077 - - 10566783d718 + - 1693b2126f30 + - 043f9c91f686 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 - bf0728e000cd - ae4dc0c041f9 - - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -119,16 +119,16 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: + - 1c5cbf8f79ce - 4081e4faa4ab - 0fa397f4f40b - - 1c5cbf8f79ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib owner: galaxyp revisions: - - 36880dfd9fa7 - fb192dd6658a + - 36880dfd9fa7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut @@ -147,16 +147,16 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: - - 160538a890a6 - - d286ff4600dd - e66f552a3c47 + - d286ff4600dd + - 160538a890a6 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 @@ -169,70 +169,70 @@ tools: - name: maxquant owner: galaxyp revisions: - - 37d669de2828 + - 2133b0be850a + - 4d17fcdeb8ff - 97a7f34fcb6a + - 37d669de2828 + - 837224ad1694 + - e42225f8a659 - f522c08e900c + - 8934bc76bb52 - 7f432d87c82c - 1f39c833f65f - - 2133b0be850a - - 8934bc76bb52 - - e42225f8a659 - - 837224ad1694 - - 4d17fcdeb8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: + - 0ed07016d668 + - '860429737408' - 85b8866f06d7 - a72ac2c7cc5b - - '860429737408' - - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: + - 1974224d63c2 - 352b37c66d97 - 4187b6df1a40 - 990b4560ead7 - - 1974224d63c2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 4f359549383c - 99450519d727 - a1daafbf5233 - deaf035bbe9f + - 4f359549383c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: + - 40ca115438d2 - c7745841de24 - - c1343e3389ca - e79958768a2c - - 40ca115438d2 + - c1343e3389ca tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - d46d64e7964d - - d2eac53666f0 - b648e45fd3cf + - d46d64e7964d - da986f83631b + - d2eac53666f0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 9bf325045235 - - 1199751329b0 - eb811f3018ea + - 1199751329b0 - 944b43462104 + - 9bf325045235 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus @@ -250,10 +250,10 @@ tools: - name: msstats owner: galaxyp revisions: - - 28434abe6c5c - - b7034eff0db1 - 8212e342e482 - 593839e1f2c3 + - 28434abe6c5c + - b7034eff0db1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -266,49 +266,49 @@ tools: - name: openms_consensusid owner: galaxyp revisions: + - 01dbaf6a57e0 - 4e77b8f12cd3 - 8960fb791701 - - 01dbaf6a57e0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 370141bc0da3 - 25529df60a81 + - 370141bc0da3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 9cdf15d3cfc8 + - 518b1730cf2a - f7fef900f5b2 + - 9cdf15d3cfc8 - c9eff69a7c62 - - 518b1730cf2a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - dff6c756eee5 - ca88bd28f116 + - dff6c756eee5 - 5e948629bc73 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 41859bbdc16e - 658494a2cb00 + - 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 @@ -323,49 +323,49 @@ tools: owner: galaxyp revisions: - 5ad830edc021 - - febd569ad26f - 52ba9695e752 + - febd569ad26f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - 92352a475eed - 39e8fde08881 + - 92352a475eed - 27cba4c5fc42 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: - - 9e26f5c770f8 - - d413dc49d650 - 0efbc235f314 + - d413dc49d650 + - 9e26f5c770f8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - 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 - - c55dddc5844a - c427a8628cbe tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: + - b5d0905419da - 39caaa778d2e - 8ddb7bab1138 - - b5d0905419da tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger @@ -373,38 +373,38 @@ tools: revisions: - 1c5f31b8d632 - 18f93351f8b6 - - 8d4db262964c - f817513840a9 + - 8d4db262964c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: + - 111c3a00136d - c69f69d7867a - 5d9f175dff81 - - 111c3a00136d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 0e52c85f3b15 - - 476b5e296979 - be74a8cd7d66 + - 476b5e296979 + - 0e52c85f3b15 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - a407b6790342 - c18d8efa4474 + - a407b6790342 - 2b2a7551a857 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -418,44 +418,44 @@ tools: - name: openms_mztabexporter owner: galaxyp revisions: + - ee860980edc6 - bf32e0bcf554 - 8098330f6d91 - - ee860980edc6 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 owner: galaxyp revisions: - - 8c01da82292c - 2a9ff56cb279 + - 8c01da82292c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - - 1bf940c18d93 - e8f64a7dc470 + - 1bf940c18d93 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - 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 owner: galaxyp revisions: - - d4396637b9f5 - 0bddef8d144e + - d4396637b9f5 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter @@ -475,8 +475,8 @@ tools: - 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 @@ -498,9 +498,9 @@ tools: owner: galaxyp revisions: - 5182338d5e7c + - dd173849c3d8 - e039cc5c7aed - 539a3a4dcc9e - - dd173849c3d8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier @@ -532,16 +532,16 @@ tools: - name: openms_xtandemadapter owner: galaxyp revisions: - - c8b225c69a7f - 7f6a1f27553e - fb52e95a370c + - c8b225c69a7f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - 073a2965e3b2 - a6282baa8c6f + - 073a2965e3b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptide_genomic_coordinate @@ -554,14 +554,14 @@ tools: - name: peptideshaker owner: galaxyp revisions: - - a72c48001f7c - - 07ff622ec007 - 3634c90301af - - 3ec27b4cee7c - - da885ca16cb2 - - 7fdd9119cc4f - 1beff3ddce58 + - a72c48001f7c + - 7fdd9119cc4f + - 3ec27b4cee7c + - 07ff622ec007 - 943a34df6047 + - da885ca16cb2 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: - - a371252a2cf6 - 1a5690a5eedc - 12692567c7f9 + - a371252a2cf6 - 265c35540faa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index 0fb65b913..5104329d1 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: - - 110a346daf36 - - 289b7d6b69a4 - - 42201b90e3f4 - 2f1d464ebfd2 + - 289b7d6b69a4 - e345aadf914f + - 110a346daf36 - cd5f98911089 + - 42201b90e3f4 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: - - fcce77c09289 + - 0cd2df8af811 - 42d9087b4789 - c207119ba5f6 - 8501601a118d - - 0cd2df8af811 - 0345dbaaa79b + - fcce77c09289 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -37,11 +37,11 @@ tools: owner: iuc revisions: - 89eb29319bf4 + - 04db7fd6b238 + - ad5ab22ffe24 - 33486216eec0 - 405a212b32ab - - ad5ab22ffe24 - 421c33b8bf17 - - 04db7fd6b238 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -53,12 +53,12 @@ tools: - name: stacks2_gstacks owner: iuc revisions: - - eb784fa07f80 + - 1d839ead7ad3 - fa51dc5e8386 - 7370bb65bad4 - 7b72fde3d27e - f6e91108b7b1 - - 1d839ead7ad3 + - eb784fa07f80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -71,10 +71,10 @@ tools: owner: iuc revisions: - c9b77ced9a78 - - a3e86cd9cac7 - - 8a55d29c8fcf - d30e36c48c93 + - 8a55d29c8fcf - 3d70c2996730 + - a3e86cd9cac7 - 1544278c272e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -87,12 +87,12 @@ tools: - name: stacks2_populations owner: iuc revisions: - - 564c33e5c3e3 - - 887cf585cafc - - 7b881f5f5ad5 - b242deb58952 + - 887cf585cafc + - 564c33e5c3e3 - e2db212d64ad - a5969aa9347e + - 7b881f5f5ad5 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -104,11 +104,11 @@ tools: - name: stacks2_procrad owner: iuc revisions: - - e897c74a48bb - - b4bab607eb05 + - 8cff84759bf6 - 9a171f9a450b - bd5ff77e2036 - - 8cff84759bf6 + - b4bab607eb05 + - e897c74a48bb 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: - - 5e10f396979e - - 33f0793edf93 - - 4f65e343ecdf - adc7a7610d4f + - 4f65e343ecdf - 887e0991eb24 + - 33f0793edf93 - 6dafad990086 + - 5e10f396979e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -137,12 +137,12 @@ tools: - name: stacks2_shortreads owner: iuc revisions: - - 97575d01f06b - - c287418eb288 - - 17d39bf0a63a - 43e3eeb2e0ec + - 17d39bf0a63a - 4e280b27a831 + - c287418eb288 - c5d7050e4ad7 + - 97575d01f06b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,12 +154,12 @@ tools: - name: stacks2_sstacks owner: iuc revisions: - - a819ec3b362d - - cd034465d4a4 - 09b8edb56d80 - 0b8c84a7fdb5 - d9bf483266a1 + - a819ec3b362d - 9586f08634c0 + - cd034465d4a4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -171,12 +171,12 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: - - a4b4bd84f69e + - 69842dd5aa48 - 2645575d1bf2 - - bf0e43ab0416 - - a9c34a289493 - 95351dd0fd3f - - 69842dd5aa48 + - a4b4bd84f69e + - a9c34a289493 + - bf0e43ab0416 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: + - 912f904a6e1e - d033e1ccb386 - - d1fda11e602f - - 8a35a3bc6752 - cfb504394ae1 - - 912f904a6e1e - bb0475c884ff + - d1fda11e602f + - 8a35a3bc6752 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -235,9 +235,9 @@ tools: - name: stacks_populations owner: iuc revisions: + - d504d945a655 - d1fad35bdb4a - 95286af4139b - - d504d945a655 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index 04ca1e099..723394329 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,24 +2,24 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: - - cf01dd6c6b1f - 31f8063eedea - 2d4e3aff9dc7 + - cf01dd6c6b1f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: + - 125d20cb23d7 - 32e542c2a773 - 703a2cb3fb38 - - 125d20cb23d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 01ccd366690d - 3d61a698e5e1 + - 01ccd366690d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -56,8 +56,8 @@ 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 @@ -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 @@ -84,8 +84,8 @@ tools: - name: cuffnorm owner: devteam revisions: - - 6cbfede05833 - 9a854107dbb2 + - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant @@ -110,9 +110,9 @@ tools: owner: iuc revisions: - e3b16fd7dd08 - - 8f0181aacb7a - - 0693ccd171c4 - 3b36efd62b3e + - 0693ccd171c4 + - 8f0181aacb7a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -125,12 +125,12 @@ tools: owner: iuc revisions: - 9a882d108833 - - 24a09ca67621 - - d027d1f4984e + - cd9874cb9019 - 8fe98f7094de - - 0696db066a5b - 6a3a025714d3 - - cd9874cb9019 + - d027d1f4984e + - 24a09ca67621 + - 0696db066a5b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -142,10 +142,10 @@ tools: - name: dexseq owner: iuc revisions: - - 62adf13b86ea - b47c006d90c5 - - 2872c633f07e - df929f257179 + - 62adf13b86ea + - 2872c633f07e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -158,16 +158,16 @@ tools: owner: iuc revisions: - 555659de7321 - - f2843df56434 - - a8305cf0c951 - 3d89af8a44f0 - 5bf899c13979 + - f2843df56434 + - 334ce9b1bac5 - 9bdff28ae1b1 - 6e53e565fc6a - - 0cb907a2a810 - - 334ce9b1bac5 - 070900306913 - df0c8d0a5992 + - a8305cf0c951 + - 0cb907a2a810 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: - - ea04b737afa0 - - 90d16db017d7 + - af814359d244 + - 6f66ae7c5f7a - e6a2a912677a - - a37612abf7f9 - - 38b6d12edc68 - 7db9d3ea71c9 + - ea04b737afa0 + - 90d16db017d7 - a56fbe2d6ba7 - - f3a5f075498f - f9d49f5cb597 - - 6f66ae7c5f7a - - af814359d244 + - 38b6d12edc68 + - a37612abf7f9 + - f3a5f075498f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: featurecounts @@ -232,9 +232,9 @@ tools: - name: gffcompare owner: iuc revisions: - - 0f710191a66d - 3c97c841a443 - f99dd58de04f + - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare @@ -254,11 +254,11 @@ tools: revisions: - 26371a1df031 - d4b55e2beb12 + - 6c19daec423d - a86e80d3c09c - - 3fb01a8c902d - - 6ab42baa56e9 - f4af63aaf57a - - 6c19daec423d + - 6ab42baa56e9 + - 3fb01a8c902d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: hisat2 @@ -276,8 +276,8 @@ tools: - name: htseq_count owner: lparsons revisions: - - 67b0b160903a - 916cb26bd9d3 + - 67b0b160903a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count @@ -298,8 +298,8 @@ tools: - 87c11c05d238 - ce5d418183c5 - 5ae5c312d718 - - 1c75aa5de15e - 01247aaf0a10 + - 1c75aa5de15e 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: - - 10c98fab6c5a + - 4f9c4e6566e5 - 40985510cd98 - c971db6f0fe5 - - 4f9c4e6566e5 + - 10c98fab6c5a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant @@ -327,10 +327,10 @@ tools: owner: iuc revisions: - 708348a17fa1 + - 0921444c832d - e827f9aae031 - - d6f5fa4ee473 - 58c35179ebf0 - - 0921444c832d + - d6f5fa4ee473 - 97e06a4c7c75 - 32511f586472 tool_panel_section_label: RNA-seq @@ -393,19 +393,19 @@ tools: - name: rgrnastar owner: iuc revisions: - - 5ec75f5dae3c - - 7ed2edc1337f - - c772497b2c32 - 0a563fd2f22e - - c7c55b694974 - - 980d2a2e1180 - - b9e04854e2bb - - 79de45b5069b + - 7ed2edc1337f - e132e7d02a3e - - 3ea5a2a63fa2 - 4df95e2d7f61 - - 4074fc1940e2 + - 5ec75f5dae3c + - 79de45b5069b + - 980d2a2e1180 + - 3ea5a2a63fa2 + - b9e04854e2bb - 99b17b74a8cd + - c7c55b694974 + - c772497b2c32 + - 4074fc1940e2 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: - - 2c0ca397d302 - - 15cd64d7c58b - - cc05793bb896 - - ebab418107f5 - e3d32471da11 - - 53e9709776a0 + - ebab418107f5 + - cc05793bb896 - 49121db48873 + - 53e9709776a0 + - 15cd64d7c58b + - 2c0ca397d302 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: - - 8c28affc7c48 - c0fd285eb553 - - 56242ff81c84 + - 8c28affc7c48 - fab6ff46e019 + - 56242ff81c84 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: + - dd4df992d93d - ae618321f34a - 1ebd14235b92 - - 914cfcba0ec8 - - cef79931dda5 - 258d696dbd7e - - dd4df992d93d + - cef79931dda5 - 76d290331481 + - 914cfcba0ec8 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -492,10 +492,10 @@ tools: - name: transdecoder owner: iuc revisions: - - c6334cb383ff - d0d4cef4f967 - - 0db979fead3a + - c6334cb383ff - ffd1300599a1 + - 0db979fead3a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -507,10 +507,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - 74217fbfba4d - - d6a479fd4281 - bcc5f03f1900 + - 74217fbfba4d - ba3720d7e68b + - d6a479fd4281 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -522,10 +522,10 @@ tools: - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - c2b82a94493e - 2fb4ee002432 - - 478f36effca1 - 56162e446004 + - c2b82a94493e + - 478f36effca1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -538,8 +538,8 @@ tools: owner: iuc revisions: - 3f4094b6a565 - - fab23c3b5258 - 9ff3765e7172 + - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr @@ -551,9 +551,9 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 4687ecf0eb2d - 34a018cbee9c - 870ac06dff8e + - 4687ecf0eb2d - be3f26533209 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -566,11 +566,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: + - 05ab8d5e04a2 - 65e7dea767ea - c5fbddcac63a - - 5192f657f305 - - 05ab8d5e04a2 - 33406f5a445c + - 5192f657f305 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -582,9 +582,9 @@ tools: - name: trinity_filter_low_expr_transcripts owner: iuc revisions: + - 6f0fb35b799c - e406ac71165d - a35cba31d904 - - 6f0fb35b799c - 1fdb25a8384d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -597,10 +597,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - 37a1129c89d2 - - 964b7efe2639 - 7c7fbf13aadd + - 964b7efe2639 - c2c039e421af + - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -612,10 +612,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 047c22569787 - 24e94d84adc9 - - 1d689e4e1caf - eafea3083352 + - 1d689e4e1caf + - 047c22569787 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -627,10 +627,10 @@ tools: - name: trinity_samples_qccheck owner: iuc revisions: - - 3a4ac03d1266 - - 9871104ea630 - 1812dbc5bb7b - 04bb8bb7c198 + - 3a4ac03d1266 + - 9871104ea630 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -642,15 +642,15 @@ tools: - name: trinity owner: iuc revisions: - - 48636f857c4b - - c9cfec002f71 - - 9fa24d5aac68 - 32b86cd8eb50 - - db1f362cca3e - - d84caa5a98ad + - 8f1c3df4dd49 - cee61b3fcf78 + - 9fa24d5aac68 + - c9cfec002f71 - d2bc35f3d1c5 - - 8f1c3df4dd49 + - db1f362cca3e + - d84caa5a98ad + - 48636f857c4b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -662,9 +662,9 @@ tools: - name: trinotate owner: iuc revisions: + - 2b093007fab9 - 9e61bc67866f - 4383070d29ed - - 2b093007fab9 - 6fd16fad465d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index ee91e8906..ad071beec 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: - - 1a052c827e88 - 473382134e56 - 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 d77709915..372d16ae3 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -2,9 +2,9 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 10184eaa85fc - 88eedb4abea0 - a53efedba9e7 + - 10184eaa85fc 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: - - ef11139d4545 - 9c1c0b947e46 + - ef11139d4545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -55,8 +55,8 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - e7fd6754d093 - 19ece8afbaab + - e7fd6754d093 - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -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 @@ -116,10 +116,10 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 6856f8a01905 - - 46c6639921f1 - 9149ad20699a + - 6856f8a01905 - 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: - - 33208952b99d - c89806670ab9 - 06dc50b7b711 - 92ec40abcdcf + - 33208952b99d 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: - - a8d69aee190e - - 720217c23995 - b3d99709fe1a - 66e23b11feae + - a8d69aee190e + - 720217c23995 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -161,11 +161,11 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - fefd89ab563c - 22970df7a40e - - db17d5321bad + - fefd89ab563c - fe34990e5ce7 - cc61ade70eb8 + - db17d5321bad tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -177,10 +177,10 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - 811fc2d75ad4 - 88b8c2916784 - 7a6034296ae9 - fa5d3e61e429 + - 811fc2d75ad4 - 7def34e6cf4d tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -193,20 +193,20 @@ tools: - name: samtools_merge owner: iuc revisions: - - 65a38e8c8e2a + - b40e2d865d52 - 36677f429310 + - 65a38e8c8e2a - 740ce0a18f0d - - b40e2d865d52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - fa7ad9b89f4a - - 9da0311ab1dd + - 329deb17a9f7 - b61f5d6a7f25 - 583abf29fc8e - - 329deb17a9f7 + - fa7ad9b89f4a + - 9da0311ab1dd 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 @@ -232,9 +232,9 @@ tools: owner: devteam revisions: - db000c6007a0 + - 30388d878f81 - d7b4851d1971 - bb8cfc6f6e0c - - 30388d878f81 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -252,9 +252,9 @@ tools: - name: samtools_slice_bam owner: devteam revisions: + - b5c88b7b153e - a4a10c7924d1 - 344fc91e1bfd - - b5c88b7b153e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -266,10 +266,10 @@ tools: - name: samtools_sort owner: devteam revisions: - - e613c1ad4c4c - 6c2c1836728b - cab3f8d35989 - a577ea614bed + - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -281,10 +281,10 @@ tools: - name: samtools_split owner: devteam revisions: + - b7f7826ef1cd - 135c85f4cfaf - - bcedabb53ddf - 5d9ae78f34d3 - - b7f7826ef1cd + - bcedabb53ddf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -296,12 +296,12 @@ tools: - name: samtools_stats owner: devteam revisions: - - fed4aa48ba09 - - 5a08c09b9311 - - 24c5d43cb545 + - 1cc79f49b8d5 - 3a0efe14891f - 145f6d74ff5e - - 1cc79f49b8d5 + - 5a08c09b9311 + - 24c5d43cb545 + - fed4aa48ba09 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: - - b01db2684fa5 + - 5826298f6a73 - 350bbc5c2ffd + - c370440f901e - 6be888be75f9 - - bf328cec6a42 - - 0dbf49c414ae + - b01db2684fa5 - b72793637686 - - c370440f901e - - 5826298f6a73 + - 0dbf49c414ae + - 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 431e9b4e3..375444f7b 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: + - 59bb6d34fca6 + - 4aab5ae907b6 - 480d9e9d156b - 6f6537780379 - - 59bb6d34fca6 - a62c4a11a67d - d147d6455873 - - 4aab5ae907b6 tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/single_cell.yml b/staging.gvl.org.au/single_cell.yml index 7625ed051..fb5eeafcd 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -2,12 +2,12 @@ tools: - name: anndata_import owner: iuc revisions: - - 93dd15e13e6a - - cfc3f5a57dc6 - 55e35e9203cf - - 32e547223c9e - 00712416fdaa - fb9e030ffae4 + - 93dd15e13e6a + - 32e547223c9e + - cfc3f5a57dc6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -19,11 +19,11 @@ tools: - name: anndata_inspect owner: iuc revisions: - - b9fac48532eb - - ee98d611afc6 - 39e945f0b2c1 - - 038e32885fec + - ee98d611afc6 - 688357ad5e61 + - b9fac48532eb + - 038e32885fec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -35,12 +35,12 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - d4af736e7b83 - b85871dd69f9 - - ed4996a16f7f - 3d748954434b - - 43cb7b5a6fe7 - 9bd945a03d7b + - 43cb7b5a6fe7 + - d4af736e7b83 + - ed4996a16f7f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -52,9 +52,9 @@ tools: - name: dropletutils owner: iuc revisions: - - 2c1200fba922 - 8855361fcfc5 - cdf4443d5625 + - 2c1200fba922 - a9caad671439 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -80,8 +80,8 @@ tools: - name: music_deconvolution owner: bgruening revisions: - - 56371b5a2da9 - 2ba99a52bd44 + - 56371b5a2da9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset @@ -134,8 +134,8 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - 69018f285aa3 - a6821f856a1e + - 69018f285aa3 - df8e4e54d367 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -162,9 +162,9 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: + - b2df381a6004 - 6acb08931836 - 77b91b9bdf52 - - b2df381a6004 - aaa5da8e73a9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -177,9 +177,9 @@ tools: - name: scanpy_filter owner: iuc revisions: - - 3c86f71498bc - b409c2486353 - a97abb8cd15b + - 3c86f71498bc - a03ff8633507 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -194,9 +194,9 @@ tools: revisions: - 5e9171dc8244 - c5d3684f7c4c - - 6c145a6868cc - 3081ff5c84a3 - cc0deb593fc8 + - 6c145a6868cc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -208,8 +208,8 @@ tools: - name: scanpy_normalize owner: iuc revisions: - - ab55fe8030b6 - 94c19fb1281c + - ab55fe8030b6 - a407e7f8bdc1 - 3bcd5445cd7a tool_panel_section_label: Single-cell @@ -223,10 +223,10 @@ tools: - name: scanpy_plot owner: iuc revisions: - - dbbe1ea8ecb1 - - 9b0cdb8cf6be - - 6adf98e782f3 - aa0c474463c2 + - 6adf98e782f3 + - 9b0cdb8cf6be + - dbbe1ea8ecb1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -239,10 +239,10 @@ tools: owner: iuc revisions: - 458e8f43a775 - - 73ab2ac53d06 - f2f6c703da06 - 215733a383f2 - bf2017df9837 + - 73ab2ac53d06 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -254,9 +254,9 @@ tools: - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - b834074a9aff - - fd808de478b1 - 8f333f90d8d6 + - fd808de478b1 + - b834074a9aff tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -269,8 +269,8 @@ tools: owner: iuc revisions: - 7a365ec81b52 - - b7ea9f09c02f - 652923ce664f + - b7ea9f09c02f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter @@ -282,8 +282,8 @@ tools: - name: scater_plot_dist_scatter owner: iuc revisions: - - 81e5bdff4853 - 2e41b35b5bdd + - 81e5bdff4853 - ef4c80837bc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index b17178f50..af2e42744 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,47 +32,47 @@ tools: - name: datamash_ops owner: iuc revisions: + - 562f3c677828 - 746e8e4bf929 - 2f3c6f2dcf39 - 4c07ddedc198 - 419027d822d6 - - 562f3c677828 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all owner: devteam revisions: - - 8564f6927b87 - e01e8a9a82f4 + - 8564f6927b87 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_ivc_all owner: devteam revisions: - - 0b89b03ad760 - 506ae7b0d85d + - 0b89b03ad760 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass owner: devteam revisions: - - cb422b6f49d2 - 781e68074f84 + - cb422b6f49d2 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - 6c29c7e347e8 - - 7a15159140d1 - cb1c59d69557 + - 7a15159140d1 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 7442b94d6a1e - - aef56d0e7a61 - - b1eda492f063 - 9c3e1d3235c8 - - 4c4ec859c31a + - b1eda492f063 + - 7442b94d6a1e - 840f29aad145 + - 4c4ec859c31a + - aef56d0e7a61 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 9fda0b82f419 - - 07843f917990 - d0352e8b4c10 - - 375bbd555f4a + - 07843f917990 - 30d21a6041f6 + - 375bbd555f4a + - 9fda0b82f419 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - 8b1b2b91f8d0 - - 4cc980df6265 - - cd02bf168d23 - 7ae443e6217d + - 4cc980df6265 - 2c58b83c9bad + - cd02bf168d23 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - e10e776f2109 - - 4bbaf77573ef + - 7dd3fb35904f - bb9fc9d46ea4 - ad7e0b4291ee + - 4bbaf77573ef - 1dd433d2c92c - - 7dd3fb35904f tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/staging.gvl.org.au/text_manipulation.yml b/staging.gvl.org.au/text_manipulation.yml index cfef64466..1e976a46e 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -21,21 +21,21 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - 6c6d26ff01ff - f18f67056946 + - 6c6d26ff01ff tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: - - 02026300aa45 + - 6595517c2dd8 - 6e8d94597139 - - 9cd341095afd - - 13b6f0007d9e - be25c075ed54 - 626658afe4cb + - 9cd341095afd + - 02026300aa45 + - 13b6f0007d9e - 464b9305180e - - 6595517c2dd8 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -47,8 +47,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 3a4694d4354f - 6f54dc6b37da + - 3a4694d4354f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -72,10 +72,10 @@ tools: - name: filter_tabular owner: iuc revisions: - - 34d29339abab - - 557ec8d7087d - 9cc411a62277 + - 557ec8d7087d - 37cde8134c6a + - 34d29339abab tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -100,28 +100,28 @@ tools: owner: devteam revisions: - ae7843d06f8f - - dd40b1e9eebe - f2aac0c5c60d + - dd40b1e9eebe tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 2e8f945f7285 - 33d61c89fb8d - - 623f3eb7aa48 - - 1ea4e668bf73 - 3a6b78c39dca - 83069b38aa85 + - 623f3eb7aa48 + - 2e8f945f7285 - cf34c344508d + - 1ea4e668bf73 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - ae8c4b2488e7 - - 399da6b5ec21 - 503bcd6ebe4b + - 399da6b5ec21 + - ae8c4b2488e7 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: replace_column_by_key_value_file @@ -133,9 +133,9 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: + - b722161a845a - f768f6183386 - bce29ec10b78 - - b722161a845a tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -149,11 +149,11 @@ tools: owner: bgruening revisions: - 9ff72e942410 + - d698c222f354 - ddf54b12c295 - a6f147a050a2 - - 74a8bef53a00 - - 0a8c6b61f0f4 - f46f0e4f75c4 - - d698c222f354 + - 0a8c6b61f0f4 + - 74a8bef53a00 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/variant_calling.yml b/staging.gvl.org.au/variant_calling.yml index 40309f344..dc520dc7d 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -2,9 +2,9 @@ tools: - name: breseq owner: iuc revisions: - - 0d18a3ba2d1c - 85c57cc9b558 - 82fb5e3bb93e + - 0d18a3ba2d1c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: cutesv @@ -17,56 +17,56 @@ tools: owner: devteam revisions: - 57def2d7c093 + - a5937157062f - 04fa42777df9 - 156b60c1530f - - a5937157062f - ef2c525bd8cd tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - e61c9ac190ad - 09d6e4693887 - - 791f73caa0c8 - 435b157bed6d + - e61c9ac190ad + - 791f73caa0c8 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - e1461b5c52a0 + - 65432c3abf6c - 4805fe3d8fda - - 3b4b2121842f - - 074d44697036 - dfadc322b065 - 03627f24605f - - 65432c3abf6c + - 3b4b2121842f + - 074d44697036 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - - 701d134358ad - - 7dfca164d2e3 - 9cb929f21cfa + - 7dfca164d2e3 + - 701d134358ad tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: + - f4473557ffc7 - 426d707dfc47 - - 971e07ca4456 - c27549b9aa1f - - f4473557ffc7 + - 971e07ca4456 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_viterbi owner: iuc revisions: - - aa35ee7f3ab2 - - cdaab621d454 - dbd9f2db9ed8 + - cdaab621d454 + - aa35ee7f3ab2 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -84,11 +84,11 @@ tools: - name: snippy owner: iuc revisions: - - 9bccc8404a3c - - 5bbf9eada9c2 - - fa016f1eea1a - - d220115f882b - c9a8ef2aa380 + - d220115f882b + - fa016f1eea1a + - 5bbf9eada9c2 + - 9bccc8404a3c tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -130,9 +130,9 @@ tools: - name: tb_variant_filter owner: iuc revisions: - - 32f14a2723ec - ee4a90760848 - 40f0591deda0 + - 32f14a2723ec - 3b1e7c170b10 - e7aff4a85df5 tool_panel_section_label: Variant Calling @@ -140,8 +140,8 @@ tools: - name: tbvcfreport owner: iuc revisions: - - adc0645b945c - 02d81b994ef5 + - adc0645b945c - 4934c0ac6197 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index 507825900..cf136816d 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -3,12 +3,12 @@ tools: owner: iuc revisions: - e075b1be5abb - - 6a88248893c4 - 3f62d4939d54 - ebe5fc018e72 - - b7ea370b8f5d - 265fe0f9ea64 - 8a2e296c07ef + - b7ea370b8f5d + - 6a88248893c4 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: - - f0d44631365f - - 544cb432072b - - b03984136ce4 - - 22637b1a55bf - - 21687e35f066 - 0fba2c15b40d + - 21687e35f066 + - 544cb432072b - c37b684e7f4e + - 22637b1a55bf + - f0d44631365f + - b03984136ce4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -38,14 +38,14 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - 8ca3647c90fd - - 3a7084316a6e - 8408bffd5616 - 0238f68ad641 - - 8627b2b383b4 - - 6d35a3780bfd - bf1f4994f104 + - 8627b2b383b4 - 01d6b7d6365e + - 3a7084316a6e + - 6d35a3780bfd + - 8ca3647c90fd 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: - - 9b5abbf50d23 - - 6b6c992d3a14 - - 81426b3cf18b - 62ca6da715bf - - f430a1ec7ee4 - 03e0645395d2 - - d144af39073a + - 6b6c992d3a14 - 08296952d12f + - d144af39073a + - 9b5abbf50d23 + - f430a1ec7ee4 + - 81426b3cf18b 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: - - d3081540d175 + - 147de996e34f + - 1829900b5dcd - 2363ef414c9b + - d3081540d175 + - e522022137f6 - d37e313a41be - 95c6f3f4c77f - - e522022137f6 - - 1829900b5dcd - - 147de996e34f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -94,13 +94,13 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: - - 348cd212dbad - - 92c0aff8b53e - - 9b29129fb491 - - cacc9970727a - 1137ce8efc1e - 09f37afb3621 + - 92c0aff8b53e + - 348cd212dbad + - 9b29129fb491 - b14ff40958cb + - cacc9970727a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -113,11 +113,11 @@ tools: owner: iuc revisions: - 367ba501b6eb - - 4935320a59a8 - - ecc9192912b8 - - 1f2183a23823 - 55c0e906c14c + - 1f2183a23823 + - ecc9192912b8 - de68c11034f6 + - 4935320a59a8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -130,10 +130,10 @@ tools: owner: iuc revisions: - f01b2c9506b9 - - 6c790a091c7c - 7cbf3c66d4ad - - 039ea3f1dea9 - ae68ceb4cca3 + - 039ea3f1dea9 + - 6c790a091c7c - 64a8f7dae3ad tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -147,12 +147,12 @@ tools: owner: iuc revisions: - e7452697afd9 - - 656a916779fe - 277719af4dd7 - - 963a3635b2e1 - - 33bd9301568c - - cdb7b4927742 - 6ea7170a016d + - cdb7b4927742 + - 33bd9301568c + - 963a3635b2e1 + - 656a916779fe tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -166,11 +166,11 @@ tools: revisions: - 3eac729e66c9 - 5a321fab1fe4 - - 26d97cdd5410 - - a29a2f40b665 - - a1213a0b7b66 - 501bfb078342 - b7f0f59baa7e + - a1213a0b7b66 + - 26d97cdd5410 + - a29a2f40b665 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -183,13 +183,13 @@ tools: owner: iuc revisions: - 63aabc920911 - - 97d19c008d15 - 768d04526638 - - d7d1663559e9 - - 5f27e814a119 + - c803c34361e0 + - 97d19c008d15 - 81e4014fa809 + - d7d1663559e9 - 709dd8291b83 - - c803c34361e0 + - 5f27e814a119 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -201,12 +201,12 @@ tools: - name: bcftools_merge owner: iuc revisions: - - 86296490704e + - af163c712539 - b1eba148b35b + - 85ee7e6c4204 - b931e65638b8 - - af163c712539 + - 86296490704e - 7ba36babba2d - - 85ee7e6c4204 - 2215287d5cc9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -220,13 +220,13 @@ tools: owner: iuc revisions: - 37757ffb4c5f - - cf06b44624c7 - f506df85c652 - 4e1d23e5c691 - - 9c711df3258d - ce9396ddcb2b - - 5660b21a0dbd + - 9c711df3258d - 31ea13dfe5e6 + - cf06b44624c7 + - 5660b21a0dbd - 03191140c66a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -239,12 +239,12 @@ tools: - name: bcftools_norm owner: iuc revisions: - - a404f786a94c - 021693fdadaa - - 6deb4d549bc9 + - a404f786a94c - 48291658fdf6 - - 19905c025d2a - ebb2e12a6de1 + - 19905c025d2a + - 6deb4d549bc9 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 - - be6b217710af - - 97e8145d7e30 - - c450406f722b + - 69d8b7567281 - 5ad5d4243987 + - c450406f722b + - be6b217710af - 71c78e0eea52 - - 69d8b7567281 + - f7879f1e77f9 + - 97e8145d7e30 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 - - 79f7a1acc2cd - 89720ec3d58e - - cc7f9a4e186b - d31a2e310a52 + - cc7f9a4e186b + - 2514e684f8a3 - 0fe007201caf - 52f9e4a660e3 + - 79f7a1acc2cd 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: - - 75ddd081f608 - - 80e6e399ccd0 - 0a62420cb9cd - - 026a989b7cee - - 230e424bde67 - 1411bef27a75 + - 75ddd081f608 - 99f4a81a47be + - 80e6e399ccd0 + - 230e424bde67 + - 026a989b7cee 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: - - 5808f77b2bb6 - 444e6a756c35 - - bca7ce81688f + - 5808f77b2bb6 - 5acfca5a76af - - ba20340426fe - - c01be0ab9806 - e493702b19eb + - c01be0ab9806 + - bca7ce81688f + - ba20340426fe tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -328,13 +328,13 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - 7fe09ad6a939 + - d52b8947b269 - 68fec03a63b7 - - 157ffcdd3fa7 - 4d236c696844 - - d52b8947b269 - - f2482aa4862e + - 7fe09ad6a939 + - 157ffcdd3fa7 - 12152af85697 + - f2482aa4862e 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: - - 8dbce095986c + - 29ba253e2e05 - 27e2611639a9 + - cbe39e530cbf - 0e5d11004815 - - 6f8e223f78f3 + - 8dbce095986c - 8f2fc0ab30fb - - cbe39e530cbf - - 29ba253e2e05 + - 6f8e223f78f3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -364,13 +364,13 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: - - 88bb477f45f7 - - 3ff5654b4e7d - a8630d4fbaf8 - - a367a15c6de5 + - 9708e3086f32 - e0a856def0b0 + - a367a15c6de5 + - 3ff5654b4e7d + - 88bb477f45f7 - af36eb5418fe - - 9708e3086f32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_mendelian @@ -384,11 +384,11 @@ tools: revisions: - 5c9729d54721 - 03e30f06f15f - - 2f4eef1f0d22 - - 6ce175385dd9 - - 31c096c6b156 - 4ed46189d6c6 - 96d0145c041a + - 6ce175385dd9 + - 31c096c6b156 + - 2f4eef1f0d22 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: - - 2c4941386820 - - 09f5e45a8212 - 40daf124be88 - - a1aad8b559c6 + - 2c4941386820 - 46eb13bc2c73 - - 262bba5b90ef - 11af7fce71cf + - a1aad8b559c6 + - 09f5e45a8212 + - 262bba5b90ef 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 + - 882b2e649602 + - 4b796b58938b - 8cb121b6a1d2 - 12038f59c0f4 - 6cbb9c47795c - - 882b2e649602 - 743cd1472aeb - - f272b8ba0983 - 0594ea1417c8 - - 4b796b58938b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -437,12 +437,12 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: + - cced6715f926 + - eccb508bb678 - adee7e8b746f - dba06328556a - - 18cf9de1cf73 - 238f78e38a8b - - eccb508bb678 - - cced6715f926 + - 18cf9de1cf73 - 8c3ff4ef1190 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -456,12 +456,12 @@ tools: owner: iuc revisions: - 9f36041495a3 + - e0ad88dec40d + - a850902cac64 + - c9935c9e8a24 - f64e7ca2efd2 - 3ce32adc55b2 - - c9935c9e8a24 - e53501abf992 - - a850902cac64 - - e0ad88dec40d 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: + - d68c43202172 - fd3539749127 + - b7be725976b6 - 79489d5685dd - - 4db0695a6fc7 - d43eb39b989e - 8057cf55fa41 - - d68c43202172 - - b7be725976b6 + - 4db0695a6fc7 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 + - 1ccf0e7fb4f6 + - 6a636d58dfc2 - bdc67eeb0bc9 - 78cd8b69da4c - - 6a636d58dfc2 - - 1ccf0e7fb4f6 - - 58091e1be01b - - b0d39ef600a7 - 5296d26b0373 + - 58091e1be01b 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: - - baa8823f8073 - - '388983871932' - - b641062a2587 - e8af591435d1 - - 4d3ce9dc1525 + - '388983871932' - b17394940c7a + - 4d3ce9dc1525 - a2f8dc22d7c0 + - baa8823f8073 + - b641062a2587 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_stats @@ -527,13 +527,13 @@ tools: - name: bcftools_view owner: iuc revisions: + - 59fa8742285e + - d1f8f55f564d - 3ca3de4e5291 - - 38d75661c235 - 3a233c8eb814 - - 59fa8742285e - abc3ced31cd1 - e6b5cbbf449b - - d1f8f55f564d + - 38d75661c235 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -545,15 +545,15 @@ tools: - name: vcf2tsv owner: devteam revisions: - - 285060661b45 - e92b3c0f9224 + - 285060661b45 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfaddinfo owner: devteam revisions: - - 6ea73d6151ec - afc0ba768690 + - 6ea73d6151ec tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfallelicprimitives @@ -566,15 +566,15 @@ tools: - name: vcfannotate owner: devteam revisions: - - 01e0321aca98 - 6faa2c4c71d2 + - 01e0321aca98 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes owner: devteam revisions: - - 84959112d9a6 - 70bc6ced57f7 + - 84959112d9a6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect @@ -601,15 +601,15 @@ tools: - name: vcfcombine owner: devteam revisions: - - 53edb91ed051 - 1f0ba67cc85a + - 53edb91ed051 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcommonsamples owner: devteam revisions: - - f1852ecef841 - 254f285dbaaa + - f1852ecef841 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfdistance @@ -630,29 +630,29 @@ tools: - name: vcffixup owner: devteam revisions: - - 11f62f071125 - fc5a64fdd5b2 + - 11f62f071125 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - 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 owner: devteam revisions: - - a60ae8af21a1 - f5653ed90dfd + - a60ae8af21a1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom @@ -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: - - 6257ee3b50d3 - 12b570dd0bc5 + - 6257ee3b50d3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfselectsamples @@ -693,8 +693,8 @@ tools: - name: vcfsort owner: devteam revisions: - - 5b7120c66efc - dd44c3f416c3 + - 5b7120c66efc tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate @@ -724,7 +724,7 @@ tools: - name: vcfvcfintersect owner: devteam revisions: - - 166c4f50525f - 6f6bf10618d7 + - 166c4f50525f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index f231154d1..3ec306cb6 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - c2ef298da409 - 3f3e247c053d - 78c75f134c16 - 4efdca267d51 - 6e9aea89e388 + - c2ef298da409 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: - - 1aae04680c4b - - f29602ae449e - - b5d8e5475247 - 44018dd6b447 - - 4f2967b27e67 + - b5d8e5475247 - cd2480f35935 - - 133f36c29579 - 3e1f6f6d557e - fe3ca740a485 + - 133f36c29579 + - 1aae04680c4b + - f29602ae449e + - 4f2967b27e67 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash owner: bgruening revisions: - - bc88856eddab - e78e25d3b4bd + - bc88856eddab tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus_training owner: bgruening revisions: - - 6519ebe25019 - 7be22100e5e1 - dc027fa56d55 + - 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 - 7355bbf5e05f + - fe48aa4ccd5e - 8fd427007e93 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -93,8 +93,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 8bd92f2404dd - 1b9a9409831d + - 8bd92f2404dd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: cpat @@ -107,8 +107,8 @@ tools: owner: galaxyp revisions: - 63662ae295d6 - - 9d1fbff733cf - d9c3016f7283 + - 9d1fbff733cf tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -126,33 +126,33 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 3bbe70fef6df - - 9f2455341fac - - 14f588312c56 - 756376aeb1ae - - b6b5cd37f2a2 + - 14f588312c56 + - 9f2455341fac - 582fd74dc2a1 + - 3bbe70fef6df + - b6b5cd37f2a2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - 989f7c061f35 + - 73428a792541 + - 1691af4a0d17 - a230ea445788 - 0ffe5be70caf - 30fb23d4c31c - - 73428a792541 - - 1691af4a0d17 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 494f0bb4a993 - 5a5ae61da69c - - 563a19373357 - - 30f08d74024f - e94187d661df + - 30f08d74024f + - 494f0bb4a993 + - 563a19373357 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict @@ -160,8 +160,8 @@ tools: revisions: - 7abc5f6dd595 - 2bba2ff070d9 - - 1bc5a03faf2e - f31125bb85ea + - 1bc5a03faf2e - d6c7106b7b2e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -170,10 +170,10 @@ tools: revisions: - 54961e026fe4 - 520e30695ec3 - - fed64e676186 - d3af38b9c7e1 - - 52af33194019 + - fed64e676186 - b3cf4684e9c7 + - 52af33194019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -199,10 +199,10 @@ tools: - name: goseq owner: iuc revisions: - - ef2ad746b589 + - 602de62d995b - 43798b4caee0 - 8b3e3657034e - - 602de62d995b + - ef2ad746b589 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -220,16 +220,16 @@ 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: - - 74810db257cc - - 98cafcbd2578 - c55643c3d813 + - 98cafcbd2578 + - 74810db257cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -254,9 +254,9 @@ tools: - name: maker owner: iuc revisions: + - 370c210d9541 - 3c1a01127868 - d46d803ca6cc - - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 @@ -287,10 +287,10 @@ tools: - name: prokka owner: crs4 revisions: - - a17498c603ec + - bf68eb663bc3 - 8a22554cdde2 - d643e3b03500 - - bf68eb663bc3 + - a17498c603ec tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -322,29 +322,29 @@ tools: - name: snpeff owner: iuc revisions: - - 68693743661e + - 5a29ab10dba6 + - 9473cd297a76 + - 5c7b70713fb5 - 8f92c2b26e6d - 268d162b9c49 - - cfcf33df7fc0 - - 9473cd297a76 - - 5a29ab10dba6 - 5b80f544c67f - - 5c7b70713fb5 + - cfcf33df7fc0 + - 68693743661e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 2b3e65a4252f - 09d6806c609e + - 2b3e65a4252f - 5fab4f81391d tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna owner: rnateam revisions: - - 10b84b577117 - eb35257d2e29 + - 10b84b577117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -356,22 +356,22 @@ tools: - name: tbprofiler owner: iuc revisions: - - 45083d070fb8 - - 2c68b0c38785 - e1a9d6fd258d - - 809dfc93d593 - - 200c378d85f3 - ba6f87115e13 - - 37213cf56392 + - 809dfc93d593 + - 45083d070fb8 - ac8250086ac3 + - 37213cf56392 + - 2c68b0c38785 - 037a11682176 + - 200c378d85f3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - f50807720df1 - 8fc50fe60127 + - f50807720df1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: trna_prediction diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index 021d3827a..f207e2b07 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -2,23 +2,23 @@ tools: - name: abyss owner: iuc revisions: - - 7547fcab5d19 - - 841084c5fc46 - - 553bfe8bd0b5 + - 890b794c997d - fa5259cc561b - 0e93176640ac + - 841084c5fc46 + - 553bfe8bd0b5 - a929ce596a34 + - 7547fcab5d19 - 8f1b150a2487 - - 890b794c997d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - - b9e31c5c01c7 - - 94fe43e75ddc - 067592b6b312 - 21e491ad532a + - b9e31c5c01c7 + - 94fe43e75ddc - ddddce450736 - b2860df42e16 tool_panel_section_label: Assembly @@ -26,18 +26,18 @@ tools: - name: bellerophon owner: iuc revisions: - - 321347bd0494 - 25ca5d73aedf + - 321347bd0494 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - faee8629b460 - - a7f16f24e9a1 - - 22286dab5aa1 - 5258e18bbe23 - 3371c5bdc17a + - a7f16f24e9a1 + - faee8629b460 + - 22286dab5aa1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -49,28 +49,28 @@ tools: - name: busco owner: iuc revisions: - - e824f5d958d0 + - 0d243f458b53 - 46ae58b1d792 + - cf13a1e03e5b + - 2dd755c1c6ff + - 5ecdeca79a0d + - bb935709506a - 602fb8e63aa7 - e4bd1e99bacf - - 0d243f458b53 - - 5ecdeca79a0d - - 41030a6c03b7 - - cf13a1e03e5b - - 4048d82f0c88 - - 94170eee0ad8 - 2a5b8b9936bf - - 2dd755c1c6ff - - 1e62c28ba91d + - 94170eee0ad8 - 1440ae06552f - - bb935709506a + - 4048d82f0c88 + - 1e62c28ba91d + - 41030a6c03b7 + - e824f5d958d0 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - c5b7390290b1 - 5732f959936a + - c5b7390290b1 - 86f150c8019d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -84,36 +84,36 @@ tools: owner: bgruening revisions: - 3ee0ef312022 - - cb8dfd28c16f - - e27815e82dd4 - 276f5d8712d5 - 8d4f03b5fe9d + - cb8dfd28c16f - 1ce9b1d72ec3 + - e27815e82dd4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - b2f674562a18 - 01210c4e9144 - 3169a38c2656 + - b2f674562a18 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: + - 8b330a577046 - 06bcf65179fb - 7348b69e5109 - - 8b330a577046 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 3fba9c77550a + - 5127a713de83 - 3ef480892a9f + - 3fba9c77550a - 690c2caa367e - - 5127a713de83 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: - - 5f625c63b8bc - - 2061fb3b81b4 - - 3f7be05a1597 - - 366a11d316a7 - f3c89da3af16 + - 5bec28269d95 - ec9e21e9c71b - - 6505bd37670d + - 366a11d316a7 + - 2061fb3b81b4 - 41cea2aa2dce - - da9d8bf98802 - - 71740308d412 - - 5bec28269d95 - 045c7c3d8e59 - - 60024a528cbd - - 0ee0c3089254 + - 71740308d412 + - 5f625c63b8bc + - 6505bd37670d - 9ef6920c3089 + - 0ee0c3089254 + - 3f7be05a1597 + - da9d8bf98802 + - 60024a528cbd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -157,39 +157,39 @@ tools: - name: megahit owner: iuc revisions: - - de387b2b2803 + - 14ddfc8ffb93 - 7518ee87b53d - a96f3ad4e0d8 - - 14ddfc8ffb93 + - de387b2b2803 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 9d79beb19ac3 - 39edec572bae - 09c589057ee8 - f8113c25bc6b + - 9d79beb19ac3 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - - 51c2360aa807 - 29dabd8db6f2 + - 51c2360aa807 - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - eb7a370f6588 - 606b09cc9860 - f338e9942b27 - - 2ecf5a570907 - - e731ea24e48d - fd128c111ab0 - 3ca2d2a9068c + - eb7a370f6588 + - e731ea24e48d + - 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: - - 73a3846701e1 - - 80d1250bd5fd - - 8dee0218ac7d - 8b6d0d85252b + - 8dee0218ac7d - a7b889b90140 + - 73a3846701e1 + - 80d1250bd5fd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -217,8 +217,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 64a1c751d99b - 15200570e926 + - 64a1c751d99b - 7c2f5268d01c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -231,19 +231,19 @@ tools: - name: pretext_map owner: iuc revisions: - - 8fef980d48b5 - 2b16ba799da9 - 02831bf9e95f + - d256a51a656b + - 8fef980d48b5 - bbe19ef04a74 - dfb8a4497339 - - d256a51a656b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - - e9bd16ba5ebd - a315c25dc813 + - e9bd16ba5ebd - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -251,13 +251,13 @@ tools: owner: iuc revisions: - 72472698a2df - - 59db8ea8c845 - - 6fcbee531de6 - - ebb0dcdb621a - - 3061c8b029e5 - 7594365c546b - - 342a1d1fed7b - 875d0f36d66f + - ebb0dcdb621a + - 59db8ea8c845 + - 342a1d1fed7b + - 3061c8b029e5 + - 6fcbee531de6 - 675488238c96 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -265,40 +265,40 @@ tools: owner: bgruening revisions: - 78c533842eeb + - aa39b19ca11e - d865b62f501c - cd06929b224b - a199cd7ac344 - - aa39b19ca11e - 39bed8de8017 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: raven owner: iuc revisions: - - 2b2a352488fa - - f11b994b7eb2 - 3edba9afc9bc - - f8564b2d7f63 - 33b7d8481a76 + - f8564b2d7f63 + - 2b2a352488fa + - f11b994b7eb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades owner: iuc revisions: - - 378e55aeeb25 - - 53c2bc8c2ae3 - e122f9101584 + - 53c2bc8c2ae3 - 1d06c8b38e77 - ef69617ecb42 + - 378e55aeeb25 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: salsa owner: iuc revisions: - ba7b0f11e470 + - ab5b7f6b7198 - f77f7a7f3b83 - 9a22227bb6d0 - - ab5b7f6b7198 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -310,30 +310,30 @@ tools: - name: shovill owner: iuc revisions: - - 865119fcb694 + - 83ead2be47b2 - d9f6a00b6db7 - ee17a294d3a3 + - 865119fcb694 + - 196a599ec43d - ad80238462c1 - f698c7604b3b - - 196a599ec43d - - 83ead2be47b2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 24e471d13fe9 - - 5e0825476fb7 - 5a0ddb4dc3a4 + - 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 + - 1bb12736175c + - 051fd2db8a27 - 7490b213baa9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -341,39 +341,39 @@ tools: owner: iuc revisions: - fee85957cebe - - d6e617c4e338 + - ad8b536d1caa - 808b3a0a6716 - 34305b013402 - - ad8b536d1caa + - d6e617c4e338 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: - - 6b5a5842531e - 21da31ed41a1 - - 8d4b90bf9caf - - e5a3b75a271f - b8002c3f7141 + - 6b5a5842531e + - e5a3b75a271f + - 8d4b90bf9caf tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - 9de69775f512 + - 328aa71f0f3c - f1532cb33c75 - 2a10645aeadd + - 9de69775f512 - 86f66ab58e14 - - 328aa71f0f3c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - 340bc17f49cf - - 6aad515a5270 - - 85fb02c43042 - e41dcb0e913b + - 85fb02c43042 + - 6aad515a5270 - 1708851f8804 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -381,59 +381,59 @@ tools: owner: iuc revisions: - b65a43f70b99 + - 249f6a28c751 - d5fb354f745d - b3490b036c5a - - 249f6a28c751 - d159735a6a9f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - d2d1df21dfb9 - - b7829778729f - 7897763d14ec - dd7ad84f3943 - - 33368fec3b70 - 9006e5836729 + - d2d1df21dfb9 + - 33368fec3b70 + - b7829778729f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 6f4c8ad6ea01 - 8f631679571f - - 189e837009c9 + - 6f4c8ad6ea01 - ced385aa976d + - 189e837009c9 - 505a9833ab5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - d40ed4eb0c0e - 9ded6109434a - e59bee4565b3 - - 356afed970b4 + - d40ed4eb0c0e - 19bdfd1e6fe3 + - 356afed970b4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - ebd801e712bc - 6dd935e4984b - 4688ae3b49b5 - - b23249f81bc4 - 80a17897564d + - ebd801e712bc + - b23249f81bc4 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - b5e35a2ca4f3 - 59bd28f6265d - cb1e3db43020 + - b5e35a2ca4f3 - 937ea677d437 - b64696992ee9 tool_panel_section_label: Assembly @@ -441,44 +441,44 @@ tools: - name: trycycler_subsample owner: iuc revisions: + - 6015aa0303f2 + - 2628f6790eda - 383bb5ad32e2 - cb4768eeca3b - 05bd7504fdb2 - - 2628f6790eda - - 6015aa0303f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 0a3a602cd1e3 - - 9e3e80cc4ad4 - d10bdad2fd17 + - 0a3a602cd1e3 - 6e26c9afd301 + - 9e3e80cc4ad4 - e92675014ac9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: + - 920677cd220f - 8d09f8be269e - - 5da9a0e2fb2d - 08256557922f - - 920677cd220f + - 5da9a0e2fb2d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - 4a53b89fa703 - - 37d88f41c810 - 82398ba86ba7 + - 37d88f41c810 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: yahs owner: iuc revisions: - - 425e63adcc5d - 39495e107274 + - 425e63adcc5d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index fe063a25c..09a43bb24 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,24 +2,24 @@ tools: - name: integron_finder owner: iuc revisions: - - 4768f7f8e93f - 1ae00120dd24 + - 4768f7f8e93f tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - 31812e7a1315 - 1f5641a52664 - - ded48b36f3b7 + - 31812e7a1315 - 8e8dc9a1e3e5 + - ded48b36f3b7 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 24a7a95867b0 - 17fcac7ddf54 + - 24a7a95867b0 - 5c8ff92e38a9 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index 70adf3e9d..434a88153 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: - - 204a131e47db - 159b04e36791 - a9c9d768b751 + - 204a131e47db 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 6a412a17b..4b10ad5f2 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,16 +2,16 @@ tools: - name: bedtools owner: iuc revisions: - - dde39ba9c031 - - a1a923cd89e8 - - a8eabd2838f6 - - 0a5c785ac6db - - b28e0cfa7ba1 - - a68aa6c1204a - 589e7e57fd6d + - a68aa6c1204a + - b28e0cfa7ba1 + - dde39ba9c031 - e19bebe96cd2 - - ce3c7f062223 + - 0a5c785ac6db - 07e8b80f278c - 87ee588b3d45 + - ce3c7f062223 + - a8eabd2838f6 + - a1a923cd89e8 tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/blast.yml b/usegalaxy.org.au/blast.yml index 3482e4a06..b706013fb 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,28 +8,28 @@ tools: - name: diamond owner: bgruening revisions: - - f921014aba5a - - e8ac2b53f262 - 54f751e413f4 + - e8ac2b53f262 + - f921014aba5a - 62c9df8382c2 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: + - 0e3cf9594bb7 - 6f386c5dc4fb - 5edc472ec434 - 2889433c7ae1 - - acf4e47b734c - a52d2d93e595 + - acf4e47b734c - e25d3acf6e68 - - 0e3cf9594bb7 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart owner: crs4 revisions: - - e9005d1f3cfd - 1334cb4c6b68 + - e9005d1f3cfd tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index fdb9181ad..d5196bfd8 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -2,12 +2,12 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - c8cdde00b105 - - 095ad4d096d1 - 710301bc46fa - - da6bd1975a71 - - 27ee142314a9 + - 095ad4d096d1 + - c8cdde00b105 - 6ca543ec1bf8 + - 27ee142314a9 + - da6bd1975a71 - f4230f116196 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu @@ -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 @@ -106,32 +106,32 @@ tools: - name: gmx_editconf owner: chemteam revisions: + - 0fac8e2afc13 - 88076940fa94 + - bfb65cb551d8 - 79cfd9ead848 - - 0fac8e2afc13 - 3b8a9d5ced85 - - bfb65cb551d8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: + - 715cd0e87781 - d532b7e5f64b - - 55918daa5651 + - eb6564a60136 - f5d979cb4b54 - - 715cd0e87781 + - 55918daa5651 - b46d4b4d995c - - eb6564a60136 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - - dae135dfd519 - - 5579659312e6 - - fdf2cc80adb5 - d2f955aea23a + - 5579659312e6 - f26afd1b7104 + - fdf2cc80adb5 + - dae135dfd519 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files @@ -145,52 +145,52 @@ tools: - name: gmx_setup owner: chemteam revisions: + - ed736e6eee39 + - 2c349b027a01 + - 4da9ee404eab - cac1886249a2 - 070e3ecc3fda - - 4da9ee404eab - - 2c349b027a01 - - ed736e6eee39 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - da8753545526 - d1f803b5943c + - 525ca7c8065f + - c0c9a5024177 + - 73008ef1f487 + - da8753545526 - 2e219a2d9327 - f197e34c33a9 - 807aa4c9293d - - c0c9a5024177 - - 525ca7c8065f - - 73008ef1f487 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 1809414a9454 - - 61094e01eff9 - - 2c8ed1b52bf7 - 27ea4e1a3f95 - - c4fbab8e03c5 - 7568ae18908a + - 2c8ed1b52bf7 + - c4fbab8e03c5 + - 1809414a9454 + - 61094e01eff9 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: md_converter owner: chemteam revisions: - - 79e8ab8f1e81 + - ccfbd956a2d3 - ba83f0923369 - 730ef07b90ae - - ccfbd956a2d3 + - 79e8ab8f1e81 - d7ec25187599 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 @@ -202,9 +202,9 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: + - b59c91adeac1 - e2c36f62e22f - e6011617c748 - - b59c91adeac1 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_svg_depiction @@ -234,9 +234,9 @@ tools: - name: sucos_max_score owner: bgruening revisions: + - 85fad59f8168 - 9b48456a96fe - bf99565cec1f - - 85fad59f8168 - d4c67ced6abc tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 66a1ab1ed..84fe701b7 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 + - c97a786e8fb5 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: genrich @@ -23,11 +23,11 @@ tools: - name: macs2 owner: iuc revisions: - - 495a4173006f - - 424aefbd7777 + - 640d3af5d833 - 86e2413cf3f8 + - 424aefbd7777 + - 495a4173006f - f5d67c722d67 - - 640d3af5d833 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator @@ -40,7 +40,7 @@ tools: - name: sicer owner: devteam revisions: - - 74c9214cc8e6 - 5c2cc3b58c7d + - 74c9214cc8e6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index 30d2fc15e..21119e285 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -2,8 +2,8 @@ tools: - name: bundle_collections owner: nml revisions: - - 705ebd286b57 - cd6da887a5f4 + - 705ebd286b57 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections @@ -11,15 +11,15 @@ tools: revisions: - 33151a38533a - 830961c48e42 - - 25136a2b0cfe - 90981f86000f + - 25136a2b0cfe tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - dfde09461b1e - 3ddd99c7efee + - dfde09461b1e tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_to_collection @@ -33,7 +33,7 @@ tools: - 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 960bde691..9d5ad50ee 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -9,29 +9,29 @@ tools: owner: iuc revisions: - dad9da48a09a + - f3a19509108a - 0b3c3ad92827 - - 5e1240a87bcb - - 6ef0b5664c69 - 367b1ed91207 + - a3b86937ead6 + - 5e1240a87bcb - e3cbd2287f63 + - 6ef0b5664c69 - 4a6ee918c13a - - f3a19509108a - - a3b86937ead6 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - 33c99804a32f - - a4db66553a61 - - 584008e574b2 + - e177a8ea0bf1 + - 54ccb7e1f49a - 501c21cce614 - e525f9ffb9ac - - 1b5fc03380d4 + - a4db66553a61 - bd46669113b9 - - 54ccb7e1f49a + - 584008e574b2 + - 1b5fc03380d4 - 72ed72122deb - - e177a8ea0bf1 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -56,16 +56,16 @@ tools: - name: fastq_to_fasta owner: devteam revisions: + - 77b41c89d856 - 8979c288aefb - 186b8d913e6c - - 77b41c89d856 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 4b347702c4aa - 614a63f14adf + - 4b347702c4aa tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa @@ -84,8 +84,8 @@ tools: - name: gffread owner: devteam revisions: - - 4dea02886337 - 154d00cbbf2d + - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -123,11 +123,11 @@ tools: - name: thermo_raw_file_converter owner: galaxyp revisions: - - 26c6706bfb07 - - 63769c4217a7 + - 92ac8e086317 - 19e45916daf9 - b9b385097f13 - - 92ac8e086317 + - 26c6706bfb07 + - 63769c4217a7 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 de0f81747..fd93781f5 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,108 +2,108 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - e821645ef8fc - - 268e91e540ee - 29451af70c52 - - de72ba3ed6f2 + - 268e91e540ee - 5f6d123679f4 - a1ca9bccc7f2 + - de72ba3ed6f2 + - e821645ef8fc - c929a006727f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 5d11599b8a7d - - 12af64f93288 - - 7a7fd0f5f15d - - 2d2cf5c1ea8a - - bb1e4f63e0e6 - 0e49b109abc2 + - 2d2cf5c1ea8a + - 7a7fd0f5f15d - 0e143b4c3987 + - bb1e4f63e0e6 + - 5d11599b8a7d + - 12af64f93288 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - c06951d10364 - - 195e98217334 - - 1d848bc4585f - - 81b1e3e1fc6c - 7c1beb6d6eca + - 81b1e3e1fc6c + - 195e98217334 + - c06951d10364 - dc059492a995 + - 1d848bc4585f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 3d211717a775 - - a67ac707496a - - 93eb012d9eed - bfff7454b59a + - 93eb012d9eed - 71aa86af6762 - - 07418a30ed01 - 26e7304d6737 + - 07418a30ed01 + - 3d211717a775 + - a67ac707496a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: + - 26983857c91a + - 2bc10a9ca58b - 5be24eba848d - - 56d5b797ce84 - dd0b7398bb96 + - 56d5b797ce84 - b8858746dc1f - 29fcfd36e90a - - 26983857c91a - - 2bc10a9ca58b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - 7e6bcd2e5128 - - c3e012dfe21f - - 72bfafe3330b - 7ef978dc1b8a - - e6d0bff01239 - 9384cd033f30 + - 7e6bcd2e5128 + - 72bfafe3330b + - c3e012dfe21f - ee3a1b0f45f1 + - e6d0bff01239 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - 9470f29702f8 - - a60c359ec43c - - b73e213add0c - 167788df3b46 - - d9a637e83828 - fd1275e01605 - 514fa53b5efb - fb9cf9c97ec4 + - d9a637e83828 + - 9470f29702f8 + - b73e213add0c + - a60c359ec43c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - ca0616bb2cdf - - e479c7ca5570 - - 2c37ce318bc3 - - c34d11ea4ba6 - 86febdcc4283 + - e479c7ca5570 - 5bffaa8354a1 + - c34d11ea4ba6 + - 2c37ce318bc3 + - ca0616bb2cdf - a02cfa31e9cb tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 01fb6a7654e6 - - 2d466b530754 - - 192ef85c0b0b - - 004aea905d4d - 69a8621ca2f0 - 78f405266706 + - 192ef85c0b0b + - 004aea905d4d + - 01fb6a7654e6 + - 2d466b530754 - 1fcb7adc39b8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu @@ -111,37 +111,37 @@ tools: owner: bgruening revisions: - d9ce4897dbb2 - - d580d6acd1df - 2f9e4843f480 + - db940c262830 + - d580d6acd1df + - 137c4beed34b - 3c9f0c486cca - 459cfa861f0b - - 137c4beed34b - 9ecba5e225a6 - - db940c262830 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - f264afa9fa6f - - 32e451def88c - - 2c66e43f1c86 - - bd7db9e2f2cb - - fd408d755394 - bad3ca889618 - fbe773640707 + - bd7db9e2f2cb + - 2c66e43f1c86 + - f264afa9fa6f + - fd408d755394 + - 32e451def88c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 7e361d147872 + - 231994413f89 - 56bce3c82278 - 9368fbc49c8b - - 231994413f89 - 7fda5607e777 - - 4e12ea27f788 - 3b9d990a0a0e + - 7e361d147872 + - 4e12ea27f788 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment @@ -149,36 +149,36 @@ tools: revisions: - 4431f39ede55 - ce4ce3316f74 - - b1779366c8e9 - c03c3384cd81 - - d9114ef1c8a5 + - b1779366c8e9 - e65d16fb2724 - 94ca68515826 + - d9114ef1c8a5 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: + - 4ed32329e0ed - 23f7c5f1fdaf - d57251071381 - 793665fff0f8 + - f8fc4e5aff9d - b88ebb3672a1 - - 4ed32329e0ed - 2da482e408b8 - - f8fc4e5aff9d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - 010e58e9d822 - 512155688d98 - - a4dfb122e52b + - 010e58e9d822 + - 25d830337d31 - a7849312d328 - ba6efa77fb79 - c60570fa602f + - a4dfb122e52b - e4c7985d4585 - - 25d830337d31 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca @@ -186,21 +186,21 @@ tools: revisions: - 00d869ea03a1 - aa200e4f3939 - - 4d678170d29b + - c899e0ccff8c - 443d9a9d6d11 - - 69264da0ce77 - 38e3f226248b - - c899e0ccff8c + - 4d678170d29b + - 69264da0ce77 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - 6662b1a8d326 - - 10301d137111 - - d806504e96d9 - a2d70c4fd406 - - aac8444d6681 + - d806504e96d9 + - 10301d137111 - c361b12d207a + - aac8444d6681 + - 6662b1a8d326 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/dna_metabarcoding.yml b/usegalaxy.org.au/dna_metabarcoding.yml index 97ca2b947..2589993fa 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -9,22 +9,22 @@ 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 owner: iuc revisions: - - 374fd9feb032 - 4d705e3443a7 + - 374fd9feb032 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep owner: iuc revisions: - - fe7ec8a3d35e - e9e49cf06b42 + - fe7ec8a3d35e tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend @@ -51,21 +51,21 @@ tools: - name: obi_stat owner: iuc revisions: - - 39320fee9d70 - 723a93febe89 + - 39320fee9d70 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab owner: iuc revisions: - - 3299c7d5268f - 5f7003111e32 + - 3299c7d5268f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq owner: iuc revisions: - - c0f7b58b4ce4 - ec215ed98831 + - c0f7b58b4ce4 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index aaf7a1b11..58b655034 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,8 +2,8 @@ tools: - name: emboss_5 owner: devteam revisions: - - dba489bfcd62 - 63dd26468588 + - dba489bfcd62 - ce385837c160 - 832c20329690 tool_panel_section_label: EMBOSS diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index f1ace70e3..e8ca914ea 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -2,10 +2,10 @@ tools: - name: bwameth owner: iuc revisions: + - 6da3972210ee + - 62f5fab76dfb - 29bdbc353f20 - d82648ad25a3 - - 62f5fab76dfb - - 6da3972210ee 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: - - d6787bab7b11 - 183cb55b1729 + - d6787bab7b11 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index f5f87b6fe..752baa4b5 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,37 +8,37 @@ tools: - name: cutadapt owner: lparsons revisions: - - de6cebe3c043 - 48f587c13075 - - 49370cb85f0f - - 5915ea1ec9b1 - - 44e2cc14f75b - - 288f97432497 + - 093678460093 - 660cffd8d92a - - 135b80fb1ac2 - 8665bcc8b847 - - c053d4cad713 - - 4e5056fefd88 - - 093678460093 + - 5915ea1ec9b1 - c5e2e5902201 - - e4691e1589d3 - - c4b82dce8335 - 8c0175e03cee + - c4b82dce8335 + - e4691e1589d3 + - c053d4cad713 + - 4e5056fefd88 + - de6cebe3c043 + - 49370cb85f0f + - 44e2cc14f75b + - 135b80fb1ac2 + - 288f97432497 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: - 8889eb864cef - - 9db07fd39f85 - f666895cbebd + - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - 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 @@ -56,9 +56,9 @@ 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_merge_files_and_filter_unique_sequences @@ -71,40 +71,40 @@ tools: - name: fasta_nucleotide_changer owner: devteam revisions: + - f81d4362b6c1 - ec0b5076173a - f773e98b26cf - - f81d4362b6c1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: - - 56022eb50bbd - cd0874854f51 - - 9c620a950d3a - 0dbb995c7d35 + - 56022eb50bbd + - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - 1d8fe9bc4cb0 - dbf9c561ef29 - 65b93b623c77 + - 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 owner: devteam revisions: - - 10b75444feae - 81a9090d6df3 + - 10b75444feae tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -117,36 +117,36 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 7861f3b10c68 - 5b87038565bb + - 7861f3b10c68 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality 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 owner: devteam revisions: - - 3e396e702cea - 2ccb8dcabddc + - 3e396e702cea 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 @@ -160,8 +160,8 @@ tools: - name: fastq_quality_converter owner: devteam revisions: - - 54053ea6c77e - 74db4cffab1f + - 54053ea6c77e - 045f0e1043f7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -188,9 +188,9 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: + - d5e9e83cd3d8 - 567d5b3c52b1 - 09070cacefd8 - - d5e9e83cd3d8 - 529bccd5e4a1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -206,8 +206,8 @@ tools: owner: devteam revisions: - 90858c306551 - - bdf1ce174e39 - cb1e251cac37 + - bdf1ce174e39 - 736b8f6ee456 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -215,35 +215,35 @@ tools: owner: devteam revisions: - 421f0af4ee95 - - 07497255281e - 7ce1891db6f5 + - 07497255281e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - - f984bb114520 + - b29d37ca9e41 - 3599f5451ee2 - 02f8a17a4ebd - - b29d37ca9e41 + - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: + - 177f0621c266 - e246088b6e34 - 6027ef51ef91 - - 177f0621c266 - 0c2907307ba4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: + - 547e8d00f11c - 61b4cedc8934 - 73194cdd4f57 - 377ac2829eac - - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -255,8 +255,8 @@ tools: - name: pear owner: iuc revisions: - - 2f804526f5fd - b4c6f054210a + - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id @@ -290,11 +290,11 @@ tools: - name: umi_tools_count owner: iuc revisions: - - a535cf1e5da4 - - e654095ab143 - - 24013bf85a6f - 8250ea3a1501 - b557acca0b56 + - 24013bf85a6f + - e654095ab143 + - a535cf1e5da4 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: - - 7accf7407811 - - 27ac32a22ad2 - f3759eec3018 - - 6a675c3aa610 - 828dba98cdb4 + - 7accf7407811 + - 27ac32a22ad2 - 9fa7803d1c51 + - 6a675c3aa610 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 3872b9078..5cfbb2fb2 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,10 +2,10 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - ce9cd02d5b88 - 64e9a6afdd0c - e41385662e5e - 7b4468117008 + - ce9cd02d5b88 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,65 +18,65 @@ tools: - name: fastqc owner: devteam revisions: - - 2b0c9d9fc6ca - ff9530579d1f - - f2e8552cf1d0 + - 9da02be9c6cc - e7b2202befea - 3d0c7bdf12f5 + - f2e8552cf1d0 - 5ec9f6bceaee - - 9da02be9c6cc + - 2b0c9d9fc6ca tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: - - a252d8415583 - 89d299153577 + - a252d8415583 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - 18a51655db17 - b6b54ba71bd8 - ad116ae3f4d9 + - 18a51655db17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - 59003d0543cd - cc0fd298cc17 - 7306ec78632a + - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: + - a72af9de6bf5 - 1f296803dfa3 - 8880fb74ef56 - - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - 1c2db0054039 + - abfd8a6544d7 - c1a4b5f3b432 - - 75c93c70d094 - 9a913cdee30e - - 3d93dd18d9f8 - - bf675f34b056 + - 1c2db0054039 - b2f1f75d49c4 - - abfd8a6544d7 - 5e33b465d8d5 + - 75c93c70d094 + - 3d93dd18d9f8 + - bf675f34b056 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: + - 084bbd8ba7b8 - 949f01671246 - cd7e644cae1d - - 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 789344242..dd060751b 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - dff7df6fcab5 - 3c623e81be77 + - dff7df6fcab5 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs @@ -15,7 +15,7 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: - - 83a19df00eab - 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 7737be1cd..d2805aee1 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -9,16 +9,16 @@ tools: - name: gemini_amend owner: iuc revisions: - - 4bd4870ecd33 - be828b79bd4d + - 4bd4870ecd33 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - - 8f53b238a360 - f2f3bc622a16 - 0c8f7322f8fc + - 8f53b238a360 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden @@ -45,8 +45,8 @@ tools: - name: gemini_de_novo owner: iuc revisions: - - d5b01cc263be - 9db3e299b1c8 + - d5b01cc263be tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -59,15 +59,15 @@ tools: - name: gemini_fusions owner: iuc revisions: - - 8151a5a0e4f6 - 91d53f89ca54 + - 8151a5a0e4f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise owner: iuc revisions: - - d46017ddbf94 - 452104bdc655 + - d46017ddbf94 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -79,30 +79,30 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 184aa4e686e2 - 2550239feed5 + - 184aa4e686e2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load owner: iuc revisions: - - 45296e47d565 - cf61daf064fe + - 45296e47d565 - b2c25142267e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve owner: iuc revisions: - - 90021fffff70 - 2969a1f43b7d + - 90021fffff70 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors owner: iuc revisions: - - 61343646155c - 00c2734b3bea + - 61343646155c tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways @@ -130,8 +130,8 @@ tools: - name: gemini_recessive_and_dominant owner: iuc revisions: - - 05124dc72dba - 86f3aac4418d + - 05124dc72dba tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region @@ -151,15 +151,15 @@ 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 owner: iuc revisions: - - ee894347fcd6 - 5c9efee9cb1e + - ee894347fcd6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 2e186f768..2b81e95ea 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: - - b946929d31c4 - d46e36492bff + - b946929d31c4 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index d6fa7dbe1..07f79e113 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: + - 983bf725dfc2 + - e9df53a75f3c - b39347891609 - c1b437242fee - - e9df53a75f3c - - 983bf725dfc2 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_acc_download owner: iuc revisions: - - e063168e0a81 - 28587613264f + - e063168e0a81 - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 4df8de2d0e48 - - 83c7d564b128 - 6ea73833cf67 - - e08a7ad4378b - - 7068f48d0ef9 - - 5e6237d58b0c - - 653e89d73fc4 - - c441583adae5 - - 9a776b080193 - - 1790dcf3c32d - 4317d3cb6cba + - 7068f48d0ef9 - e407b9da183a - - 69ebb7f46e45 + - 4df8de2d0e48 - aad3885b3216 + - 5e6237d58b0c - 6591f049cf7e - - 734abc7ac21d + - 1790dcf3c32d - f5ea3ce9b9b0 + - 653e89d73fc4 + - e08a7ad4378b + - 69ebb7f46e45 + - 734abc7ac21d + - 9a776b080193 + - 83c7d564b128 + - c441583adae5 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - - 75b3b3d0adbf - 34758ab8aaa4 - 9aaa46d45472 + - 75b3b3d0adbf - 7863f1abcdda tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -51,7 +51,7 @@ tools: owner: bgruening revisions: - 054483e27a35 - - af5eccf83605 - bfdc6a7ffd3a + - af5eccf83605 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/graphdisplay_data.yml b/usegalaxy.org.au/graphdisplay_data.yml index 41e6078f2..704d96acf 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - 740057a5126d - - 290a11559985 - fd59d783248a + - 740057a5126d - c4bde687c846 + - 290a11559985 + - ae9994cf526f - 4b519282a05b + - df7356989ac1 - a64dc31ab7f2 - 7f13dc906cb9 - - df7356989ac1 - - ae9994cf526f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,8 +28,8 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 7cf5b1d072b5 - 867ab348287d + - 7cf5b1d072b5 - f95284aa2946 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -44,29 +44,29 @@ tools: revisions: - 3b37b1b1c3a7 - ca7cb0eaad62 - - '566197475670' - 53460afd5115 + - '566197475670' tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - d3a9e32672ec - - 10515715c940 - da4c086cff5b - 3d059e9c2fba - 391a4cc45fea + - 10515715c940 + - d3a9e32672ec tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 299307abd804 - - e3a675da7fd0 + - 1acf88921176 - d0fc8b746d57 + - e3a675da7fd0 - 5fe1dc76176e - 3b12bf9b4b87 - - 1acf88921176 + - 299307abd804 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -78,15 +78,15 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 5d6f8f0bef7c - cf1df6b2220a + - 5d6f8f0bef7c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan owner: iuc revisions: - - a490b70e46fc - 8f62f666dcb6 + - a490b70e46fc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram @@ -98,17 +98,17 @@ tools: - name: jbrowse owner: iuc revisions: + - 4542035c1075 - a6e57ff585c0 - 667e17248bfe - - 2bb2e07a7a21 - - 17359b808b01 - - ca2def38369c - - 4542035c1075 - - 1cfc579079a6 - 6cd09d7b5f37 - 112eb40ba6cf - - fd5dbf0f732e + - 2bb2e07a7a21 - 836d1aa3e89a + - ca2def38369c + - fd5dbf0f732e + - 17359b808b01 + - 1cfc579079a6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -127,8 +127,8 @@ tools: owner: iuc revisions: - f1691de443a7 - - fe154a7af404 - 03c13085aecc + - fe154a7af404 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram @@ -147,8 +147,8 @@ tools: - 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 @@ -173,21 +173,21 @@ tools: - name: pygenometracks owner: iuc revisions: - - 7dd841a32245 - a1abfa420d9d - - 360df4999907 - 14e7c35f3d00 - - 2824d77cd8f8 - - 326a3db8d9d1 - - 59fd173ac850 - 4ac4e7083b7e + - 7dd841a32245 + - 59fd173ac850 + - 326a3db8d9d1 + - 2824d77cd8f8 + - 360df4999907 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 44608d0193ed - 73b8cb5bddcd + - 44608d0193ed - 83c573f2e73c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/hca_single_cell.yml b/usegalaxy.org.au/hca_single_cell.yml index c2bb385d2..565534d9b 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 1a642de6db01 - 14b3f2a4523b + - 1a642de6db01 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - e42c217a450f - 88f5a0a6a818 + - e42c217a450f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph @@ -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/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index 5d30a2266..1873a5cbf 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,8 +2,8 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 9edf8894a22d - ed2cca6b5de4 + - 9edf8894a22d - 921a2da49a0c - 29f66c353bcb tool_panel_section_label: HiCExplorer @@ -11,26 +11,26 @@ tools: - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 5746d61f0a91 - 78fb5e286609 - ec4b948dc6f0 - d404277cc87a + - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: + - 4d511437b1e5 - 03dd3c16ae4e - - 9e357a8b2ec3 - 977dc15add20 - - 4d511437b1e5 + - 9e357a8b2ec3 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 3b5b54ed6392 - 77919cc3618e + - 3b5b54ed6392 - 0ba4f56a3613 - 41dbf4d162a2 tool_panel_section_label: HiCExplorer @@ -38,9 +38,9 @@ tools: - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 9939786dd9c9 - - 7babd8a46fe0 - 5308ca68ef3d + - 9939786dd9c9 - b63363075c2e + - 7babd8a46fe0 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index 8e9c41778..fec13577d 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,23 +2,23 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 3df9f0a4bf34 - 81f0cbca04a7 - 0c777d708acc + - 3df9f0a4bf34 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5791a7f65275 - 0a53256b48c6 + - 5791a7f65275 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_filter_segmentation_by_features owner: imgteam revisions: - - 6ad1d3cfdea1 - e576b73a2e2f + - 6ad1d3cfdea1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_histogram_equalization @@ -31,8 +31,8 @@ tools: - name: 2d_simple_filter owner: imgteam revisions: - - dba87c4b32d3 - f70b215d155c + - dba87c4b32d3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert @@ -54,24 +54,24 @@ tools: - name: count_objects owner: imgteam revisions: - - 5bf8eb50b280 - - b58447a2eed2 - 664232d2a3f7 + - b58447a2eed2 + - 5bf8eb50b280 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: - - eb6c08714244 - 0e4dccaafef5 - e917a2424690 + - eb6c08714244 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 @@ -85,97 +85,97 @@ tools: - name: cp_convert_objects_to_image owner: bgruening revisions: + - ef4aed1d34c4 - df3ad3ba5c6f - cdf8e3c57dae - - ef4aed1d34c4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_display_data_on_image owner: bgruening revisions: + - 6a7da2e5f696 - 5d28ac336861 - 2484086dee41 - - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - f2ed92b011a9 - bace5a93a97c + - f2ed92b011a9 - 11f177b1a59e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - 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: - - 3245681b2f6d - 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 - 993faa34333b - 87d4d92d7487 + - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - 6100a22bf4f2 - - c09dcda1143f - ff1a86a87364 + - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - b178453ea8d1 - - 667a513e67e4 - 3a05117669cf + - 667a513e67e4 + - b178453ea8d1 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - ac5bea85a391 - a1a961c46d4b - 2564f461de62 + - ac5bea85a391 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - a32c3f810ade - 20dbb1f7ec7b - 91e03287f285 + - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: + - b64af54c5c09 - 5499dc6f8ac1 - 8536b1ae0254 - - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - e972e07c7845 - - 6f4715b8540a - d3890df07463 + - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity @@ -205,24 +205,24 @@ tools: - name: cp_overlay_outlines owner: bgruening revisions: - - b44b081bcf37 - 91560258e972 + - b44b081bcf37 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_relate_objects owner: bgruening revisions: + - 48102a685037 - 3a3033222f61 - 8083a87d2fdf - - 48102a685037 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: + - 4ecf93628f97 - 27edbb90ab2b - 33f4fa1413fb - - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -234,14 +234,14 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 1fd453cd757b - 972d2c365739 + - 1fd453cd757b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: image_info owner: imgteam revisions: - - 236ec78b2e53 - 7b6d9412c7f8 + - 236ec78b2e53 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index e67663fd8..45de865f7 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,88 +2,88 @@ tools: - name: ivar_consensus owner: iuc revisions: + - e319b5b65879 + - 17f911830a8c + - 78bbd17d0703 + - 1069f6db0a0e - f362150bef41 - e4ee04da1c19 - - 1069f6db0a0e - - 3e4f434a69c6 - - 17f911830a8c - d6e72da3ec35 - - e319b5b65879 + - 3e4f434a69c6 - a38934e303b9 - - 78bbd17d0703 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 9537184d421f - - 0135f1d487a0 - f91cfb73d369 - - 7fe36019c073 - 2b95d5c04908 - - c88553ec696e + - 0135f1d487a0 - 1ef5b6e3e09d + - c88553ec696e - 72ddd32392cd + - 9537184d421f + - 7fe36019c073 - 8f8df367470d tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - d7e79eb3bcb3 + - ad0dc9f4c9e2 - fafb3d685fa9 + - d7e79eb3bcb3 - 2cf4a1cafc16 - - ad0dc9f4c9e2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: + - 28a6f1908fcc - 6a1515bb0687 + - 8c05afb547fa - 3d18f8c3c0f6 - - ee29337f905c - - 69797fa273c3 - - 8d36959b000d - - ee2beb764a7b + - 7f1cfa4c0e32 + - bd2a7d1316b9 - 9eaadf03e0df + - ee2beb764a7b + - 8d36959b000d + - ee29337f905c - 94df24c6bc00 - - 28a6f1908fcc - - 8c05afb547fa - - 7f1cfa4c0e32 - 43aac8d29685 - - bd2a7d1316b9 + - 69797fa273c3 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 5671e1d3d5ee - - db536ad45f28 + - bcaa0d571ce2 + - 0893a1dbb807 - e3bb03cf207a + - 5671e1d3d5ee + - c092052ed673 - 5d6ed46cc101 - - 8858fa037a15 - - 0893a1dbb807 - - d37ede8589b2 - cb903c9dc33d - - bcaa0d571ce2 + - db536ad45f28 + - d37ede8589b2 - 364f4ffec275 - - c092052ed673 + - 8858fa037a15 - 9f978da6528a tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - 49236b03e4fd - - 230b05597996 - c5c9f02b6167 - - 12d66d0d05ac - - 3b6a16d82c1b - - 38b91a3190cd - - 584beffa972b - e1a015876aa9 - - 045d6d00f606 + - 584beffa972b + - 3b6a16d82c1b + - 49236b03e4fd - ed28dd32141c + - 045d6d00f606 - f95f403841ad + - 38b91a3190cd + - 230b05597996 + - 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 b9a9b8cc4..23e32c176 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -4,17 +4,17 @@ tools: revisions: - 17e3b698dd52 - b8a457820315 - - f198773344e4 - 0f1724dd59d2 + - f198773344e4 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - 22c2a1ac7ae3 - - ac092723240d - - 374cb875d38a - ba0c40780ecf - a513e3fbb4c5 + - ac092723240d + - 22c2a1ac7ae3 + - 374cb875d38a tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index 7be8d0192..ceec2f8ef 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: + - 66d7efc06000 - 522137aaa9c4 - 772e0e89fc68 - - 66d7efc06000 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_model_config owner: bgruening revisions: - - f22a9297440f - - 4d81e3e2fb63 - 8a794e6d3388 + - 4d81e3e2fb63 + - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: + - e1317b5502fa - 818f9b69d8a0 + - 2af1346e68c9 - b6ef6d0cb6b7 - f1b9a42d6809 - - 2af1346e68c9 - - e1317b5502fa tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - c80db5d6fd8c - - 8334dc98c48e - - 05143043ca13 - 1588f9076e32 + - c80db5d6fd8c - 947c2eacccb8 + - 05143043ca13 + - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - 9991c4ddde14 - - 25b46af53232 - - 29e4122c90de - 1552b8cb4a94 + - 25b46af53232 - 83228baae3c5 + - 29e4122c90de tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 060ca94ac049 + - 841a6cc5fc58 - a07ab242b0b5 + - 060ca94ac049 + - 1a53edc4b438 - f3dfa4bdf87e - - 841a6cc5fc58 - 53616c8b0865 - - 1a53edc4b438 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - - 91c4e3331208 - - 927586a18553 + - d4808d5b83da - 40f4447733b2 - dc4b5fd604a6 - - d4808d5b83da + - 91c4e3331208 - 2fc89dcd41c8 + - 927586a18553 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - c6ae57f774c6 - - 36e8d6d5d01b - - 25ab6b4e376e - - 301e07345c93 - e5a5ad882f1f + - 25ab6b4e376e - 7626ea9c2e1b + - c6ae57f774c6 + - 301e07345c93 + - 36e8d6d5d01b tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - - 4ed102b922cb - - 0630258dcf35 + - b7c3e9a3b954 - 02d2be90dedb - - f9639b488779 - 80852884053f - - b7c3e9a3b954 + - 0630258dcf35 + - f9639b488779 + - 4ed102b922cb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - - caeb57858702 + - 61634a87efc7 - ec69cbe34b73 + - caeb57858702 - 14180f9c831e - - 61634a87efc7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index 31c9e9f4c..3d03c296a 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,15 +2,15 @@ tools: - name: bowtie2 owner: devteam revisions: - - 03e9b2fbc005 - - f6877ad76b00 - - a6d65b0c67af - 17062a0decb7 - - 3ba8d4563129 - - 937aa69e715f - 017aba02828d + - 3ba8d4563129 - cd659e8cc5fa + - f6877ad76b00 + - 03e9b2fbc005 - 749c918495f7 + - a6d65b0c67af + - 937aa69e715f tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -29,10 +29,10 @@ tools: - name: bwa owner: devteam revisions: - - 64f11cf59c6e - - 3fe632431b68 - e188dc7a68e6 + - 3fe632431b68 - dfd8b7f78c37 + - 64f11cf59c6e - 53646aaaafef tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -45,42 +45,42 @@ tools: - name: lastz owner: devteam revisions: - - e7f19d6a9af8 - - 2ff111fac1d7 - - 3e1ea2facca6 - 60afcc2c1d05 - 37b497aa133f + - 2ff111fac1d7 + - e7f19d6a9af8 + - 3e1ea2facca6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: + - 037c6e54df11 + - b3eab4b67562 - 3f4d6399997b - - 77b2770508f6 + - f54f5baedfdd + - c0c2d0941de8 - be1d967337e4 - - 53c0b7a1a0c3 + - 11a0d50a54e6 - 09b53c1d4ab1 - - b3eab4b67562 - 8c6cd2650d1f - - 11a0d50a54e6 - - c0c2d0941de8 + - 77b2770508f6 - 6b1e195506a3 - - f54f5baedfdd - - 037c6e54df11 + - 53c0b7a1a0c3 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - 178bdbdb6d24 + - 5ef7ec16b04f + - b8f5f6e87f5c - 1cd2511a396e - 00fbfac99d39 - - 13022c3d3076 + - e403d27e8f24 - 79b885ce78d7 - ec9cbd6b9a49 - - b8f5f6e87f5c - - 5ef7ec16b04f - - e403d27e8f24 + - 178bdbdb6d24 + - 13022c3d3076 - 9ee34ba73ebf 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 b86373803..5e61a68a7 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -22,28 +22,28 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: + - 76d3d2b10738 - 7c2100246a2f - 63f86089423e - 5b5a7af9fbb4 - - 76d3d2b10738 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 18a502a9d287 - - 1c35dadbe76f - 96336c6a2bb7 - 84fd33a60b35 + - 18a502a9d287 + - 1c35dadbe76f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: - - f732237754fc - 34e55239e68b - - addaf9d22850 - a9f4a217dcd6 + - addaf9d22850 + - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors @@ -51,92 +51,92 @@ tools: revisions: - 75403243703a - 04c15826a0b8 - - 8c202e741d68 - 0776d824d896 + - 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 - - 43c99742158b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 84743da21318 - - 1d75bd0595e2 - 5c865a382933 + - 84743da21318 - 306a40d4bb8f + - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - - ac72310b038a - 8daf4564ccda - - 78faebd0879c + - ac72310b038a - 555ccac8a4c5 + - 78faebd0879c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - d60df8727f59 + - a58e4a43f49c - 7b8cb2b02978 - f947b4bb5107 - - a58e4a43f49c + - d60df8727f59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - 04144473e59e - - 7f3b59dee073 - 7136e9ab70db - 1bc3657cd694 + - 7f3b59dee073 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - 9058d8943303 - - 19299bb1c6af - 0a1224c4b781 + - 19299bb1c6af - d943081510da + - 9058d8943303 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree owner: iuc revisions: - - e005e659ae21 - c7e73acfa3eb + - e005e659ae21 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: gtdbtk_classify_wf owner: iuc revisions: - - dbf1798c0dcc - 6501b5b33988 - c4db8c4de66f + - dbf1798c0dcc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 15dbb444df71 - fa35f1106d3e + - 15dbb444df71 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 6c84982ee6f7 - - 6d364c65c946 - 654548ae1357 + - 6d364c65c946 + - 6c84982ee6f7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_join_tables @@ -148,9 +148,9 @@ tools: - name: humann2_regroup_table owner: iuc revisions: + - e66ab198ec15 - 6aad8ca3918b - bd7a9c6efb10 - - e66ab198ec15 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table @@ -164,9 +164,9 @@ tools: - name: humann2_unpack_pathways owner: iuc revisions: + - 9704f1a3b32d - 7f208f1eb64f - cad93abecac9 - - 9704f1a3b32d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -178,59 +178,59 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - c409a495841f - 31c6d107e7a5 - 79706f10d680 + - c409a495841f - e88b731dad59 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 714d5a28cc5c - - 094ad9c068af - d24841f5c3d2 - - 71ea608ddfa3 + - 094ad9c068af - 172920f67a84 + - 714d5a28cc5c + - 71ea608ddfa3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - 4137b492233e - - a293a742194f - - d7e9a3c41657 - a4d7148ccee4 + - d7e9a3c41657 + - a293a742194f - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_stratified_table owner: iuc revisions: - - 64bc7acc22a9 + - 6fcb8ac37a3e - 97f7bb0851e7 - - 75bedfb2078b - - cf87759761eb - e2c71b852aba - - 6fcb8ac37a3e + - 64bc7acc22a9 + - cf87759761eb + - 75bedfb2078b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_unpack_pathways owner: iuc revisions: - - 080ea153677c - - c82508e76ad1 - 2d35528d2141 - 5e5a999ffaa9 + - 080ea153677c + - c82508e76ad1 - 4033827c76b8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 95bf7479d53c - - 2cd76b089570 - 6b7622dda516 + - 2cd76b089570 + - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: jellyfish @@ -291,8 +291,8 @@ tools: owner: iuc revisions: - 4a9da2b6c2e3 - - 328c607150ff - e674066930b2 + - 328c607150ff tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -311,15 +311,15 @@ tools: - name: kraken_filter owner: devteam revisions: - - 3d6570bffdb1 - 5bee9adae474 + - 3d6570bffdb1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report owner: devteam revisions: - - 6c09bed3444f - 1902d3de4a4f + - 6c09bed3444f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -331,8 +331,8 @@ tools: - name: kraken owner: devteam revisions: - - aec58624706f - 8ba2174315aa + - aec58624706f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads @@ -344,8 +344,8 @@ tools: - name: krakentools_kreport2krona owner: iuc revisions: - - 2deaada69b14 - 88d274322340 + - 2deaada69b14 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: mash_sketch @@ -369,19 +369,19 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: + - 27250f92a01a - e073891b2afc - - 2cff76cf35c6 - 4fd3b5d8706b + - 2cff76cf35c6 - 0270541aaf46 - - 27250f92a01a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - - eb50e7eca3dc - - 76bc4efa1aeb - 708abf08a626 + - 76bc4efa1aeb + - eb50e7eca3dc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -454,13 +454,13 @@ tools: - name: metaphlan owner: iuc revisions: - - a92a632c4d9b - - 2131d7dca455 - b89b0765695d + - a16313517e55 - ff8f55893e7d - - 6dee4abadccb - 1a6cdf55390f - - a16313517e55 + - a92a632c4d9b + - 2131d7dca455 + - 6dee4abadccb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -570,20 +570,20 @@ tools: - name: staramr owner: nml revisions: + - 141afacabcfa + - aeaa20b96ef2 - 2fd4d4c9c5c2 + - 4b9a8031ab74 - be818ae858e4 - - 141afacabcfa - 3b22de20bd4b - - 4b9a8031ab74 - - aeaa20b96ef2 - 4d83eccf5f81 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - - 576963db5f1b - 9495df9dd6ef - b3c7199d8786 + - 576963db5f1b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index ddadef270..3a4bc2787 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - f4d7d5755f01 - 63b74bfc8052 + - f4d7d5755f01 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - 67cb43432196 - e866e31f6da3 + - 67cb43432196 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index ef9bd301b..0a5fb4ad3 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: - - 48c13389050d + - 2263989660f5 + - bdfbaf0c10aa - 6ae5a7b5a0a2 - - 9baa871cb1d1 - - 9422c5a87ee2 - - 80f03df2e2ce + - a74dbfee5a86 - 9eeb13a92d79 - - 8b67dd48fec1 - - bdfbaf0c10aa - cd07731e4434 - - 2263989660f5 - 94b8c6013083 - - a74dbfee5a86 + - 48c13389050d + - 8b67dd48fec1 + - 9baa871cb1d1 + - 80f03df2e2ce + - 9422c5a87ee2 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - 3ff17bad4006 - - be78f13134e2 - - 5abf2c2249aa - - fc2e49f91e52 - f0af8936ed41 + - 2e093badc689 + - fc2e49f91e52 + - c18157c68134 - f14193ec1f50 - '764845535798' - - 4a60927aaca5 + - d390fe1567dc + - d7ce0ec78e51 - bc3831dd65c1 - - c18157c68134 - - 2e093badc689 + - 5abf2c2249aa + - be78f13134e2 + - 4a60927aaca5 + - 3ff17bad4006 - aaa0d6a8b808 - - d7ce0ec78e51 - - d390fe1567dc tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -51,8 +51,8 @@ tools: - name: clustalw owner: devteam revisions: - - d6694932c5e0 - 5b097fde95dd + - d6694932c5e0 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: gecko @@ -65,52 +65,52 @@ tools: owner: rnateam revisions: - f1a5908ea2cb - - f0d493f8f84f - - 15974dd17515 - c5908940967d + - 15974dd17515 - 6f28e90db932 - a65296ffb4a0 + - f0d493f8f84f 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: - - c9685bc0407c - 60698466facd + - c9685bc0407c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - - 48823c9635a4 - bcd65de9725b + - 48823c9635a4 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - ebe3b0f84de9 - 4fc0cb2ac8ae + - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - 636b049e6141 - e18267f90096 + - 636b049e6141 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - 959c1f8dae95 - b4124df98b26 + - 959c1f8dae95 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index 4d7f91eb5..ba3d02476 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -2,42 +2,42 @@ tools: - name: medaka_consensus_pipeline owner: iuc revisions: + - 0e9e7fcdd543 + - fc8804320156 - cb34f00cc10f - a7228a7ea146 - - 79e9a869f40e - - 0e9e7fcdd543 - 72b5e9dda577 - - fc8804320156 + - 79e9a869f40e tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - db25ec99c3ea - - d6cddc06aeae - fa11aa8103b2 + - d6cddc06aeae - 18505fe2bdb1 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant owner: iuc revisions: + - ec699520444c + - 2bf63b38ee9b - cc36773a3681 - - edf6d4003fad - - eb746fa6f514 - - 19f3b583a9b3 - - 222669c4afb6 - 0f5f4a208660 - - 2bf63b38ee9b + - 222669c4afb6 + - edf6d4003fad - 43815fa60f3a - - ec699520444c + - 19f3b583a9b3 + - eb746fa6f514 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp owner: iuc revisions: - - b833eff63b10 - c0fb573c1e8d + - b833eff63b10 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanofilt @@ -49,33 +49,33 @@ tools: - name: nanoplot owner: iuc revisions: - - 645159bcee2d - - edbb6c5028f5 - 0f1c34698076 - a3c4fe6f49ab + - 645159bcee2d + - edbb6c5028f5 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 85a394edc247 - 3b6f94fc7e1d - d219b6d8158a + - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - 90a922f32523 - a8d4be409446 + - 90a922f32523 - be95355fef8d tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 449e9aeded2d - d376944466bf + - 449e9aeded2d - 4857d5bcce52 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -83,23 +83,23 @@ tools: owner: bgruening revisions: - bec636361cfd - - de5b3d8f5b90 - a3afc5f0a96c + - de5b3d8f5b90 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: - - 543cbeef3949 - 5f76b20953e5 - 93d623d9979c + - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events owner: iuc revisions: - - 28d7819c312f - 1d835c691480 + - 28d7819c312f 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: - - 47936349f3e9 - 5a82eb9e1b89 + - 47936349f3e9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index ff21a9c1f..da51271b2 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -28,9 +28,9 @@ tools: - name: data_manager_bowtie2_index_builder owner: devteam revisions: - - 83da94c0e4a6 - - 9dd107db92c2 - 1586b111d2a3 + - 9dd107db92c2 + - 83da94c0e4a6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -43,15 +43,15 @@ tools: owner: iuc revisions: - 2f27f3b86827 - - 19b6a2f0dbe2 - ed1518ce2237 + - 19b6a2f0dbe2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam revisions: - - 46066df8813d - 9e993022c762 + - 46066df8813d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwameth_index_builder @@ -70,8 +70,8 @@ tools: owner: iuc revisions: - 48a42ca61006 - - 5711fc06a63e - 38ccd4589990 + - 5711fc06a63e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder @@ -84,8 +84,8 @@ tools: - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - fcb8bdd124f4 - 81a286e4c5a2 + - fcb8bdd124f4 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco @@ -111,17 +111,17 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 6287d0ee459e - 9a40272f56d0 + - 6287d0ee459e tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: + - 52b6a4d98009 - 172815da3d41 - - 27a6a256cd23 - b4b2b284230a - - 52b6a4d98009 + - 27a6a256cd23 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -133,8 +133,8 @@ tools: - name: data_manager_hisat2_index_builder owner: iuc revisions: - - d74c740bdb25 - d210e1f185bd + - d74c740bdb25 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_humann2_database_downloader @@ -147,8 +147,8 @@ tools: owner: iuc revisions: - 87febc68b45b - - fea85c467896 - 19bbd19b74b3 + - fea85c467896 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -179,9 +179,9 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 5fe20c915fa6 - - 4ba60cb14cb0 - 9c43baa60906 + - 4ba60cb14cb0 + - 5fe20c915fa6 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -201,25 +201,25 @@ tools: - name: data_manager_pangolearn owner: iuc revisions: - - ed7a967cb11b - 29c738066906 - - 6e24e79d3d69 + - ed7a967cb11b - df30a2f1db55 + - 6e24e79d3d69 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - 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 - name: data_manager_snpeff owner: iuc revisions: - - def511e8e005 - d107d20dc6bd + - def511e8e005 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_sortmerna_database_downloader @@ -240,8 +240,8 @@ tools: owner: devteam revisions: - 94a50db37d1a - - 625fd9476402 - 9946bc39c834 + - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -289,8 +289,8 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 22e573b7dcb1 - 8ad39f493587 + - 22e573b7dcb1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: package_atlas_3_10 diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index 5563e3f48..e8e77c0d4 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -33,115 +33,115 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - '841557158611' - - a6619171428e - 5a7c56a5cc08 + - f04a1264e2a2 + - 81e66674859e - b89cac5156ec + - 8834daeb9892 - 26de3a7b1cb9 - - f73435dc282b - - 81e66674859e - - cce7b18495e4 + - 107d3ba7024a - 3f59ebfbfe3d - - f04a1264e2a2 + - d033ffc1c161 - 6a457678efcb - - 8834daeb9892 + - a6619171428e + - '841557158611' + - 3b8b5bde0bd9 + - cce7b18495e4 - c78f3d7dd1db - - 107d3ba7024a + - f73435dc282b - d7c7ef3353fe - - 3b8b5bde0bd9 - - d033ffc1c161 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: - - 3b96e92e8ec3 - - a185b079b095 - - b0af57c1a968 - 5fcd1ece3a6e + - 6a726db04d4b - aa8cc71438cf - - 88c4aa435ded - 659517798cc4 + - df47d4845b62 - 02b8758214b0 + - 7a2092844346 + - 5b777002c2de + - b0af57c1a968 + - 3b96e92e8ec3 + - a185b079b095 - 6223845127ea - - 6a726db04d4b - - df47d4845b62 + - 88c4aa435ded - 4755f52427c4 - - 7a2092844346 - e75442c7f4da - 6283babe736e - - 5b777002c2de tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - f97743d52b87 - 9b892d7f82cc - - c1d53e95327f + - f97743d52b87 - d1c340a5664b - b8476e82ac20 + - c1d53e95327f tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - 128ba8da994f - - daddf188c13f - 9e10ba792be2 + - daddf188c13f - feb40665d7cd tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: pangolin owner: iuc revisions: - - 437e28791761 - ca337cce3888 - - 36912871ccdc - - ca0d8cf80567 + - 03ed9524dcd1 - 42a174224817 - - 81804a978fc0 - - 5f8727ff21e7 - - 2fa9d4f1b48f - - abf6dbe8c9d7 - - 9d61d3fa046c - - b7e297c2ede6 - 2f1019071464 - - 7bb8726be37c - - a2099fb98cdb + - b7e297c2ede6 - 14ae456b8cc5 - - 03ed9524dcd1 + - 2fa9d4f1b48f + - ca0d8cf80567 - 83a69484cb87 - - 3a43c3982401 + - 5f8727ff21e7 + - 36912871ccdc - b6abccb1f25b + - a2099fb98cdb + - 81804a978fc0 + - 437e28791761 + - 7bb8726be37c + - 9d61d3fa046c + - abf6dbe8c9d7 + - 3a43c3982401 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 7157a5b34a68 - 2bf47d57ebb5 + - 7157a5b34a68 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: raxml owner: iuc revisions: - - ea30d3089354 - - a4b71be30c3c + - b1e68bbe4cef + - 73a469f7dc96 - 29ff6a849eac + - a4b71be30c3c - ba29b5e2a4be - - 73a469f7dc96 - - b1e68bbe4cef + - ea30d3089354 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - dbe2b2204555 - - 809e42326fc2 - f1ccc8a6eb05 - - e88a7de55d6e - 15ac71df11a0 + - e88a7de55d6e + - dbe2b2204555 - 91887494eb97 + - 809e42326fc2 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 fada91cfc..e996a962f 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -4,11 +4,11 @@ tools: revisions: - a1f0b3f4b781 - 881d7645d1bf + - f6ced08779c4 - fc288950c3b7 - b502c227b5e6 + - f9242e01365a - 1aac2a13842a - 7d34178f2812 - - f9242e01365a - - f6ced08779c4 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 f364fcd01..2de56a6bd 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -4,12 +4,12 @@ tools: revisions: - 7fbec959cf2b - e4a053d67e24 - - c0e71cb2bd1b - - d00e15139065 - - 5b85006245f3 - - eb085b3dbaf8 - - ca90d17ff51b - a58f7eb0df2c + - 5b85006245f3 + - c0e71cb2bd1b - 3bd420ec162d + - ca90d17ff51b + - eb085b3dbaf8 + - 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 1fa0cfbc0..42addb5fa 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,49 +2,49 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - f28ad96b76dc + - 277dc652246e - b574b84afc4d + - f28ad96b76dc - 0a18ac48ac53 - - b18329a8ac14 - ece627528a78 - - 277dc652246e + - b18329a8ac14 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - 525f201b86c1 - - e988563cc6e5 - bf06d196e23d - - b41107d8fe89 - e215f71d7983 + - e988563cc6e5 + - 525f201b86c1 + - b41107d8fe89 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - - bb6397b94018 - 4fbffddde8cd - 8da3511c9467 + - bb6397b94018 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering owner: galaxyp revisions: - f23d67e28cc8 + - a8157342d9a3 - b8c79e70516d - 528fb09022be - - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 59e85306eae5 - 80600735685d - - a69865da6f80 - a95a82eb4d50 - 25b83cbd596a + - 59e85306eae5 + - a69865da6f80 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing @@ -52,9 +52,9 @@ tools: revisions: - ed9ed1e6cca2 - 798da6bdff3d - - e0669b1854b1 - 611d80c0e29d - f1897eb07081 + - e0669b1854b1 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report @@ -68,19 +68,19 @@ tools: - name: cardinal_segmentations owner: galaxyp revisions: - - 82f6c2f4332d - df2187f9013b - cc430977c8ff + - 82f6c2f4332d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - - d2483487e077 - 043f9c91f686 - - 1693b2126f30 - - c5aa9fca18c6 + - d2483487e077 - 10566783d718 + - c5aa9fca18c6 + - 1693b2126f30 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -98,8 +98,8 @@ tools: - name: diann owner: galaxyp revisions: - - ae4dc0c041f9 - 9fa3dbf06f17 + - ae4dc0c041f9 - bf0728e000cd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -119,8 +119,8 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: - - 0fa397f4f40b - 1c5cbf8f79ce + - 0fa397f4f40b - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -155,8 +155,8 @@ tools: - 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 @@ -169,24 +169,24 @@ tools: - name: maxquant owner: galaxyp revisions: - - 37d669de2828 + - 1f39c833f65f - e42225f8a659 - - f522c08e900c + - 37d669de2828 - 2133b0be850a - - 97a7f34fcb6a - 7f432d87c82c + - 97a7f34fcb6a + - 4d17fcdeb8ff - 837224ad1694 + - f522c08e900c - 8934bc76bb52 - - 4d17fcdeb8ff - - 1f39c833f65f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_db owner: galaxyp revisions: - 0ed07016d668 - - 85b8866f06d7 - '860429737408' + - 85b8866f06d7 - a72ac2c7cc5b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -195,26 +195,26 @@ tools: revisions: - 4187b6df1a40 - 990b4560ead7 - - 1974224d63c2 - 352b37c66d97 + - 1974224d63c2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: + - 4f359549383c - 99450519d727 - - deaf035bbe9f - a1daafbf5233 - - 4f359549383c + - deaf035bbe9f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_sample owner: galaxyp revisions: - - e79958768a2c + - c1343e3389ca - c7745841de24 - 40ca115438d2 - - c1343e3389ca + - e79958768a2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat @@ -222,16 +222,16 @@ tools: revisions: - da986f83631b - d2eac53666f0 - - b648e45fd3cf - d46d64e7964d + - b648e45fd3cf tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_viz owner: galaxyp revisions: - - 944b43462104 - eb811f3018ea - 9bf325045235 + - 944b43462104 - 1199751329b0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -250,10 +250,10 @@ tools: - name: msstats owner: galaxyp revisions: - - 593839e1f2c3 - - 8212e342e482 - 28434abe6c5c + - 593839e1f2c3 - b7034eff0db1 + - 8212e342e482 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msstatstmt @@ -266,9 +266,9 @@ tools: - name: openms_consensusid owner: galaxyp revisions: + - 4e77b8f12cd3 - 01dbaf6a57e0 - 8960fb791701 - - 4e77b8f12cd3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase @@ -282,24 +282,24 @@ tools: owner: galaxyp revisions: - c9eff69a7c62 - - 9cdf15d3cfc8 - - 518b1730cf2a - f7fef900f5b2 + - 518b1730cf2a + - 9cdf15d3cfc8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - ca88bd28f116 - dff6c756eee5 + - ca88bd28f116 - 5e948629bc73 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: - - 890025d6e426 - 41859bbdc16e + - 890025d6e426 - 658494a2cb00 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -307,23 +307,23 @@ tools: owner: galaxyp revisions: - 9b7977080f6d - - 6634cad7d797 - 5ad0b5bf1deb + - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filefilter owner: galaxyp revisions: + - d6878d27f051 - 05d5e1ddc985 - 0bb5056cb775 - - d6878d27f051 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 5ad830edc021 - febd569ad26f + - 5ad830edc021 - 52ba9695e752 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -338,9 +338,9 @@ tools: - name: openms_highresprecursormasscorrector owner: galaxyp revisions: + - 9e26f5c770f8 - 0efbc235f314 - d413dc49d650 - - 9e26f5c770f8 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver @@ -354,43 +354,43 @@ tools: - name: openms_idfilter owner: galaxyp revisions: - - c55dddc5844a - - c427a8628cbe - 382cde407f81 + - c427a8628cbe - ca799a7246e7 + - c55dddc5844a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: + - b5d0905419da - 8ddb7bab1138 - 39caaa778d2e - - b5d0905419da tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - - 8d4db262964c - - 1c5f31b8d632 - 18f93351f8b6 - f817513840a9 + - 8d4db262964c + - 1c5f31b8d632 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idposteriorerrorprobability owner: galaxyp revisions: + - 5d9f175dff81 - 111c3a00136d - c69f69d7867a - - 5d9f175dff81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idscoreswitcher owner: galaxyp revisions: - - 0e52c85f3b15 - - be74a8cd7d66 - 476b5e296979 + - be74a8cd7d66 + - 0e52c85f3b15 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_msfraggeradapter @@ -403,9 +403,9 @@ tools: - name: openms_msgfplusadapter owner: galaxyp revisions: + - 2b2a7551a857 - a407b6790342 - c18d8efa4474 - - 2b2a7551a857 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_multiplexresolver @@ -418,9 +418,9 @@ tools: - name: openms_mztabexporter owner: galaxyp revisions: - - bf32e0bcf554 - 8098330f6d91 - ee860980edc6 + - bf32e0bcf554 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathanalyzer @@ -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 @@ -489,25 +489,25 @@ tools: - name: openms_peakpickerhires owner: galaxyp revisions: - - decc397c3b7e - 5ae104d0da6e - 3d8d4ada5405 + - decc397c3b7e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - e039cc5c7aed + - 5182338d5e7c - 539a3a4dcc9e + - e039cc5c7aed - dd173849c3d8 - - 5182338d5e7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 8a45fd5a608a - 16026cdb1330 + - 8a45fd5a608a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter @@ -519,8 +519,8 @@ tools: - name: openms_textexporter owner: galaxyp revisions: - - d063e2fe4ba4 - 9020199dba0a + - d063e2fe4ba4 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator @@ -533,35 +533,35 @@ tools: owner: galaxyp revisions: - fb52e95a370c - - c8b225c69a7f - 7f6a1f27553e + - c8b225c69a7f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pep_pointer owner: galaxyp revisions: - - 073a2965e3b2 - a6282baa8c6f + - 073a2965e3b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptide_genomic_coordinate owner: galaxyp revisions: - - cb0378d2d487 - 5f49ffce52cb + - cb0378d2d487 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: - - 1beff3ddce58 - - a72c48001f7c + - 3634c90301af - da885ca16cb2 + - 1beff3ddce58 - 943a34df6047 - 7fdd9119cc4f - - 07ff622ec007 - - 3634c90301af + - a72c48001f7c - 3ec27b4cee7c + - 07ff622ec007 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -616,9 +616,9 @@ tools: owner: galaxyp revisions: - 265c35540faa + - 12692567c7f9 - 1a5690a5eedc - a371252a2cf6 - - 12692567c7f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: xtandem diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index a41d7b055..2a21a4f59 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -2,11 +2,11 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: - - 289b7d6b69a4 - - 42201b90e3f4 - - e345aadf914f - 2f1d464ebfd2 + - 289b7d6b69a4 - 110a346daf36 + - e345aadf914f + - 42201b90e3f4 - cd5f98911089 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -14,31 +14,31 @@ tools: owner: iuc revisions: - 8501601a118d - - 0cd2df8af811 - - fcce77c09289 - c207119ba5f6 - 42d9087b4789 - 0345dbaaa79b + - fcce77c09289 + - 0cd2df8af811 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap owner: iuc revisions: - - 405a212b32ab + - 421c33b8bf17 - 89eb29319bf4 + - 405a212b32ab - 33486216eec0 - - ad5ab22ffe24 - 04db7fd6b238 - - 421c33b8bf17 + - ad5ab22ffe24 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks owner: iuc revisions: - - f6e91108b7b1 - 1d839ead7ad3 - - 7b72fde3d27e - eb784fa07f80 + - f6e91108b7b1 + - 7b72fde3d27e - fa51dc5e8386 - 7370bb65bad4 tool_panel_section_label: RAD-seq @@ -46,88 +46,88 @@ tools: - name: stacks2_kmerfilter owner: iuc revisions: - - 1544278c272e - 8a55d29c8fcf + - a3e86cd9cac7 - 3d70c2996730 + - 1544278c272e - c9b77ced9a78 - - a3e86cd9cac7 - d30e36c48c93 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations owner: iuc revisions: + - a5969aa9347e + - 7b881f5f5ad5 + - b242deb58952 - 564c33e5c3e3 - 887cf585cafc - - 7b881f5f5ad5 - e2db212d64ad - - b242deb58952 - - a5969aa9347e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_procrad owner: iuc revisions: - - 8cff84759bf6 - - 9a171f9a450b - - b4bab607eb05 - e897c74a48bb - bd5ff77e2036 + - b4bab607eb05 + - 9a171f9a450b + - 8cff84759bf6 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap owner: iuc revisions: - - 6dafad990086 - - 5e10f396979e - 4f65e343ecdf - 887e0991eb24 - 33f0793edf93 + - 5e10f396979e + - 6dafad990086 - adc7a7610d4f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads owner: iuc revisions: - - 97575d01f06b + - c5d7050e4ad7 - 4e280b27a831 - 17d39bf0a63a - - 43e3eeb2e0ec - c287418eb288 - - c5d7050e4ad7 + - 43e3eeb2e0ec + - 97575d01f06b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - d9bf483266a1 - cd034465d4a4 - - 9586f08634c0 - - 0b8c84a7fdb5 - 09b8edb56d80 + - 0b8c84a7fdb5 - a819ec3b362d + - d9bf483266a1 + - 9586f08634c0 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - - 2645575d1bf2 - - bf0e43ab0416 - - 95351dd0fd3f + - a9c34a289493 - a4b4bd84f69e - 69842dd5aa48 - - a9c34a289493 + - 95351dd0fd3f + - 2645575d1bf2 + - bf0e43ab0416 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - 8a35a3bc6752 - - bb0475c884ff - - cfb504394ae1 - d033e1ccb386 - 912f904a6e1e + - bb0475c884ff - d1fda11e602f + - 8a35a3bc6752 + - cfb504394ae1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -163,9 +163,9 @@ tools: - name: stacks_populations owner: iuc revisions: + - 95286af4139b - d504d945a655 - d1fad35bdb4a - - 95286af4139b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad @@ -195,8 +195,8 @@ tools: - name: stacks_sstacks owner: iuc revisions: - - 96de7538bf0c - 563af4497055 + - 96de7538bf0c tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_stats diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 9c3111685..9c345d513 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -10,9 +10,9 @@ tools: - name: arriba_get_filters owner: iuc revisions: + - 703a2cb3fb38 - 125d20cb23d7 - 32e542c2a773 - - 703a2cb3fb38 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -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 @@ -57,8 +57,8 @@ tools: - name: cufflinks owner: devteam revisions: - - d080005cffe1 - e04dbae2abe0 + - d080005cffe1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -97,47 +97,47 @@ tools: - name: describe_samples owner: iuc revisions: + - 3b36efd62b3e - 0693ccd171c4 - e3b16fd7dd08 - 8f0181aacb7a - - 3b36efd62b3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: + - d027d1f4984e - 24a09ca67621 - - 8fe98f7094de - 9a882d108833 - 6a3a025714d3 - - 0696db066a5b - cd9874cb9019 - - d027d1f4984e + - 0696db066a5b + - 8fe98f7094de tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - - df929f257179 + - 2872c633f07e - b47c006d90c5 - 62adf13b86ea - - 2872c633f07e + - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 555659de7321 - - 334ce9b1bac5 - - a8305cf0c951 - - df0c8d0a5992 - - 3d89af8a44f0 - 5bf899c13979 + - 3d89af8a44f0 + - 555659de7321 - f2843df56434 + - 0cb907a2a810 + - 6e53e565fc6a - 9bdff28ae1b1 - 070900306913 - - 6e53e565fc6a - - 0cb907a2a810 + - 334ce9b1bac5 + - df0c8d0a5992 + - a8305cf0c951 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -156,17 +156,17 @@ tools: - name: featurecounts owner: iuc revisions: + - 7db9d3ea71c9 + - f3a5f075498f - e6a2a912677a - a56fbe2d6ba7 + - af814359d244 - f9d49f5cb597 - - f3a5f075498f - - 6f66ae7c5f7a - 38b6d12edc68 - ea04b737afa0 - - af814359d244 - - 90d16db017d7 - - 7db9d3ea71c9 - a37612abf7f9 + - 6f66ae7c5f7a + - 90d16db017d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_transcripts_via_tracking @@ -184,9 +184,9 @@ tools: - name: gffcompare owner: iuc revisions: + - 0f710191a66d - f99dd58de04f - 3c97c841a443 - - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -198,20 +198,20 @@ tools: - name: hisat2 owner: iuc revisions: - - 6c19daec423d + - f4af63aaf57a - 6ab42baa56e9 - a86e80d3c09c - 3fb01a8c902d - - f4af63aaf57a - - d4b55e2beb12 - 26371a1df031 + - d4b55e2beb12 + - 6c19daec423d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - - 916cb26bd9d3 - 67b0b160903a + - 916cb26bd9d3 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -223,32 +223,32 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 1c75aa5de15e - 87c11c05d238 - - 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: - - 10c98fab6c5a - 40985510cd98 - c971db6f0fe5 + - 10c98fab6c5a - 4f9c4e6566e5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 32511f586472 - - d6f5fa4ee473 - 708348a17fa1 + - d6f5fa4ee473 - 0921444c832d - - e827f9aae031 - - 58c35179ebf0 - 97e06a4c7c75 + - 58c35179ebf0 + - e827f9aae031 + - 32511f586472 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -297,19 +297,19 @@ tools: - name: rgrnastar owner: iuc revisions: - - 3ea5a2a63fa2 + - 0a563fd2f22e - 4df95e2d7f61 - - c7c55b694974 - - 99b17b74a8cd - - 5ec75f5dae3c - - 4074fc1940e2 - - b9e04854e2bb - 980d2a2e1180 - c772497b2c32 - - e132e7d02a3e - - 0a563fd2f22e - 7ed2edc1337f + - b9e04854e2bb + - 99b17b74a8cd - 79de45b5069b + - 4074fc1940e2 + - c7c55b694974 + - e132e7d02a3e + - 3ea5a2a63fa2 + - 5ec75f5dae3c 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: - - 49121db48873 - - ebab418107f5 - cc05793bb896 - e3d32471da11 + - ebab418107f5 - 53e9709776a0 - - 15cd64d7c58b + - 49121db48873 - 2c0ca397d302 + - 15cd64d7c58b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: + - 8c28affc7c48 - fab6ff46e019 - c0fd285eb553 - - 8c28affc7c48 - 56242ff81c84 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - ae618321f34a - cef79931dda5 - dd4df992d93d - 914cfcba0ec8 - 258d696dbd7e - 1ebd14235b92 - 76d290331481 + - ae618321f34a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -372,81 +372,81 @@ tools: - name: transdecoder owner: iuc revisions: - - c6334cb383ff - - d0d4cef4f967 - ffd1300599a1 - 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: - - 74217fbfba4d + - d6a479fd4281 - ba3720d7e68b + - 74217fbfba4d - bcc5f03f1900 - - d6a479fd4281 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: - - 56162e446004 - - 2fb4ee002432 - c2b82a94493e - 478f36effca1 + - 56162e446004 + - 2fb4ee002432 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: - - 3f4094b6a565 - 9ff3765e7172 + - 3f4094b6a565 - fab23c3b5258 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - - be3f26533209 + - 4687ecf0eb2d - 34a018cbee9c + - be3f26533209 - 870ac06dff8e - - 4687ecf0eb2d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: + - 5192f657f305 - 05ab8d5e04a2 + - 33406f5a445c - 65e7dea767ea - - 5192f657f305 - c5fbddcac63a - - 33406f5a445c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts owner: iuc revisions: - - 1fdb25a8384d - 6f0fb35b799c - a35cba31d904 + - 1fdb25a8384d - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map owner: iuc revisions: - - 7c7fbf13aadd - - 964b7efe2639 - c2c039e421af + - 964b7efe2639 - 37a1129c89d2 + - 7c7fbf13aadd tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis owner: iuc revisions: - - 047c22569787 - eafea3083352 - 24e94d84adc9 + - 047c22569787 - 1d689e4e1caf tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -454,23 +454,23 @@ tools: owner: iuc revisions: - 04bb8bb7c198 - - 3a4ac03d1266 - - 9871104ea630 - 1812dbc5bb7b + - 9871104ea630 + - 3a4ac03d1266 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity owner: iuc revisions: - - c9cfec002f71 - - db1f362cca3e - 32b86cd8eb50 - - 8f1c3df4dd49 - - cee61b3fcf78 - - d2bc35f3d1c5 + - db1f362cca3e - 9fa24d5aac68 + - 8f1c3df4dd49 + - c9cfec002f71 - 48636f857c4b - d84caa5a98ad + - d2bc35f3d1c5 + - cee61b3fcf78 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 ba833d62f..b41c54fe8 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,8 +2,8 @@ tools: - name: rseqc owner: nilesh revisions: - - 473382134e56 - - 1a052c827e88 - 080fd5739bb4 + - 1a052c827e88 + - 473382134e56 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/sambam.yml b/usegalaxy.org.au/sambam.yml index fe32c1619..9189d7ae3 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,16 +2,16 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 88eedb4abea0 - a53efedba9e7 + - 88eedb4abea0 - 10184eaa85fc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - - cb20f99fd45b - 108db6635177 + - cb20f99fd45b - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -42,9 +42,9 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - e7fd6754d093 - - 5f8e69cc4c6e - 19ece8afbaab + - 5f8e69cc4c6e + - e7fd6754d093 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc @@ -68,8 +68,8 @@ tools: - name: sam_pileup owner: devteam revisions: - - a3b4ad6858ff - 890d97772e2a + - a3b4ad6858ff tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam @@ -88,74 +88,74 @@ 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 - 6856f8a01905 - 9149ad20699a + - 46c6639921f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: - - 06dc50b7b711 - 92ec40abcdcf - - c89806670ab9 + - 06dc50b7b711 - 33208952b99d + - c89806670ab9 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx owner: iuc revisions: - 720217c23995 - - a8d69aee190e - 66e23b11feae + - a8d69aee190e - b3d99709fe1a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - fe34990e5ce7 - - fefd89ab563c - cc61ade70eb8 - - db17d5321bad - 22970df7a40e + - db17d5321bad + - fefd89ab563c + - fe34990e5ce7 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - 88b8c2916784 - 7def34e6cf4d + - 88b8c2916784 - 811fc2d75ad4 - - fa5d3e61e429 - 7a6034296ae9 + - fa5d3e61e429 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - b40e2d865d52 - - 65a38e8c8e2a - - 740ce0a18f0d - 36677f429310 + - 740ce0a18f0d + - 65a38e8c8e2a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - - b61f5d6a7f25 + - 8da515fbc1bf - 583abf29fc8e - 9da0311ab1dd - - 8da515fbc1bf - 329deb17a9f7 + - b61f5d6a7f25 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase @@ -168,10 +168,10 @@ tools: - name: samtools_reheader owner: devteam revisions: - - d7b4851d1971 - 30388d878f81 - - db000c6007a0 - bb8cfc6f6e0c + - db000c6007a0 + - d7b4851d1971 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: + - a4a10c7924d1 - 344fc91e1bfd - b5c88b7b153e - - a4a10c7924d1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - a577ea614bed - - e613c1ad4c4c - 6c2c1836728b - cab3f8d35989 + - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - b7f7826ef1cd + - 5d9ae78f34d3 - 135c85f4cfaf + - b7f7826ef1cd - bcedabb53ddf - - 5d9ae78f34d3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 145f6d74ff5e - - 1cc79f49b8d5 - 3a0efe14891f - - 5a08c09b9311 + - 1cc79f49b8d5 - 24c5d43cb545 - fed4aa48ba09 + - 5a08c09b9311 + - 145f6d74ff5e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: + - b72793637686 - 350bbc5c2ffd - - 0dbf49c414ae - 6be888be75f9 + - 0dbf49c414ae - bf328cec6a42 - - 5826298f6a73 - c370440f901e - b01db2684fa5 - - b72793637686 + - 5826298f6a73 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 ddbd052c7..dd0ba40c5 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -2,10 +2,10 @@ tools: - name: ena_upload owner: iuc revisions: - - 480d9e9d156b + - 4aab5ae907b6 - 59bb6d34fca6 + - 480d9e9d156b - a62c4a11a67d - - 4aab5ae907b6 - 6f6537780379 - d147d6455873 tool_panel_section_label: Send Data diff --git a/usegalaxy.org.au/single_cell.yml b/usegalaxy.org.au/single_cell.yml index ff8324e8e..60f69da72 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -3,31 +3,31 @@ tools: owner: iuc revisions: - 32e547223c9e - - 00712416fdaa - - cfc3f5a57dc6 - - 55e35e9203cf - 93dd15e13e6a + - cfc3f5a57dc6 - fb9e030ffae4 + - 00712416fdaa + - 55e35e9203cf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - 038e32885fec - - 39e945f0b2c1 - b9fac48532eb - - ee98d611afc6 - 688357ad5e61 + - ee98d611afc6 + - 39e945f0b2c1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - 43cb7b5a6fe7 - - b85871dd69f9 - 9bd945a03d7b + - 43cb7b5a6fe7 - 3d748954434b - d4af736e7b83 + - b85871dd69f9 - ed4996a16f7f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -49,22 +49,22 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 7ffaa0968da3 - 282819d09a4f + - 7ffaa0968da3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 56371b5a2da9 - 2ba99a52bd44 + - 56371b5a2da9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset owner: bgruening revisions: - - 8c64a2da3869 - 7705cc75ac18 + - 8c64a2da3869 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -97,8 +97,8 @@ tools: - 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 @@ -113,78 +113,78 @@ tools: - name: scanpy_filter owner: iuc revisions: - - b409c2486353 - - a97abb8cd15b - 3c86f71498bc - a03ff8633507 + - b409c2486353 + - a97abb8cd15b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: - 6bd82ed14acd - - 5e9171dc8244 - - c5d3684f7c4c - 3081ff5c84a3 + - c5d3684f7c4c + - 5e9171dc8244 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - 94c19fb1281c - - a407e7f8bdc1 - 3bcd5445cd7a - ab55fe8030b6 + - a407e7f8bdc1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - aa0c474463c2 + - 9b0cdb8cf6be - dbbe1ea8ecb1 - 6adf98e782f3 - - 9b0cdb8cf6be + - aa0c474463c2 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - bf2017df9837 + - 73ab2ac53d06 - 215733a383f2 + - bf2017df9837 - f2f6c703da06 - 458e8f43a775 - - 73ab2ac53d06 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - - b834074a9aff - - 8f333f90d8d6 - fd808de478b1 + - 8f333f90d8d6 + - b834074a9aff tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter owner: iuc revisions: - - 652923ce664f - - b7ea9f09c02f - 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: + - 2e41b35b5bdd - ef4c80837bc5 - 81e5bdff4853 - - 2e41b35b5bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_pca owner: iuc revisions: + - 46fc6751d746 - c99ba278dfa9 - 9e5c0bb18d08 - - 46fc6751d746 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 c8de8f25d..b33c770b9 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: - - 562f3c677828 - - 746e8e4bf929 - 2f3c6f2dcf39 - - 4c07ddedc198 + - 562f3c677828 - 419027d822d6 + - 4c07ddedc198 + - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all @@ -63,16 +63,16 @@ tools: - name: dwt_var_perclass owner: devteam revisions: - - cb422b6f49d2 - 781e68074f84 + - cb422b6f49d2 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perfeature owner: devteam revisions: - - cb1c59d69557 - 7a15159140d1 - 6c29c7e347e8 + - cb1c59d69557 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -114,32 +114,32 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: + - aef56d0e7a61 + - 4c4ec859c31a - 7442b94d6a1e - - 9c3e1d3235c8 - 840f29aad145 + - 9c3e1d3235c8 - b1eda492f063 - - 4c4ec859c31a - - aef56d0e7a61 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: + - 30d21a6041f6 - 9fda0b82f419 + - d0352e8b4c10 - 07843f917990 - 375bbd555f4a - - d0352e8b4c10 - - 30d21a6041f6 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 8b1b2b91f8d0 - cd02bf168d23 - - 7ae443e6217d - - 4cc980df6265 + - 8b1b2b91f8d0 - 2c58b83c9bad + - 4cc980df6265 + - 7ae443e6217d tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering @@ -147,10 +147,10 @@ tools: revisions: - bb9fc9d46ea4 - 7dd3fb35904f - - 4bbaf77573ef - ad7e0b4291ee - - 1dd433d2c92c + - 4bbaf77573ef - e10e776f2109 + - 1dd433d2c92c tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index 832d7c945..802858a54 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: - - 745871c0b055 - 023f0a3760b3 + - 745871c0b055 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -21,20 +21,20 @@ tools: - name: column_arrange_by_header owner: bgruening revisions: - - f18f67056946 - 6c6d26ff01ff + - f18f67056946 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_maker owner: devteam revisions: - - 6595517c2dd8 - 9cd341095afd - 464b9305180e - 02026300aa45 - - 13b6f0007d9e - 6e8d94597139 + - 13b6f0007d9e - be25c075ed54 + - 6595517c2dd8 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -46,8 +46,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 3a4694d4354f - 6f54dc6b37da + - 3a4694d4354f tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: concatenate_multiple_datasets @@ -71,10 +71,10 @@ tools: - 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a8a4f94aa321 + - 57a16b310fe8 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotate owner: devteam revisions: - - 6faa2c4c71d2 - 01e0321aca98 + - 6faa2c4c71d2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes owner: devteam revisions: - - 84959112d9a6 - 70bc6ced57f7 + - 84959112d9a6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfbedintersect @@ -412,8 +412,8 @@ tools: - name: vcfcheck owner: devteam revisions: - - aa8e8c96ca06 - 5e850c85ba32 + - aa8e8c96ca06 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -433,23 +433,23 @@ tools: - name: vcfdistance owner: devteam revisions: - - 5822b40f3037 - 48e458c721b3 + - 5822b40f3037 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffilter owner: devteam revisions: - - eae7c08ebb6f - 6b935ab36d7b + - eae7c08ebb6f - fa24bf0598f4 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - 11f62f071125 - fc5a64fdd5b2 + - 11f62f071125 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten @@ -462,22 +462,22 @@ tools: - name: vcfgeno2haplo owner: devteam revisions: - - a3dea556218d - b890055e07bd + - a3dea556218d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes owner: devteam revisions: - - a60ae8af21a1 - f5653ed90dfd + - a60ae8af21a1 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfhethom owner: devteam revisions: - - b07ef36cf7e6 - 8254e0fe7358 + - b07ef36cf7e6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfleftalign @@ -490,8 +490,8 @@ tools: - name: vcfprimers owner: devteam revisions: - - d226a7327946 - 17096387c0e6 + - d226a7327946 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfrandomsample @@ -504,8 +504,8 @@ tools: - name: vcfselectsamples owner: devteam revisions: - 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