diff --git a/tool_list.yaml.lock b/tool_list.yaml.lock index d941293..f1df386 100644 --- a/tool_list.yaml.lock +++ b/tool_list.yaml.lock @@ -5,17 +5,17 @@ tools: - name: autodock_vina owner: bgruening revisions: - - 7b2f205b3f68 - - 90ea16534012 - 3c8e86318a81 - 7a871df65202 + - 7b2f205b3f68 + - 90ea16534012 tool_panel_section_label: Computational chemistry - name: autodock_vina_prepare_box owner: bgruening revisions: - - ad35eaa204ea - - 908880455b2d - 8f766d9652a2 + - 908880455b2d + - ad35eaa204ea tool_panel_section_label: Computational chemistry - name: autodock_vina_prepare_ligand owner: bgruening @@ -32,46 +32,48 @@ tools: - name: cutadapt owner: lparsons revisions: - - 8c0175e03cee - - 48f587c13075 - - e4691e1589d3 - 093678460093 - - c4b82dce8335 + - 104d86c98776 - 135b80fb1ac2 + - 48f587c13075 - 49370cb85f0f - 660cffd8d92a - - 104d86c98776 + - 8c0175e03cee + - b1c926deaa2d + - c4b82dce8335 + - e4691e1589d3 tool_panel_section_label: Fastq Manipulation - name: multiqc owner: iuc revisions: - - f7985e0479b9 - 161f4383df15 + - 1c2db0054039 + - 3d93dd18d9f8 + - 467486f1c568 - abfd8a6544d7 - bf675f34b056 - - 467486f1c568 - e4574a4d09d8 - - 1c2db0054039 - - 3d93dd18d9f8 + - f7985e0479b9 tool_panel_section_label: Fastq Manipulation - name: fastqc owner: devteam revisions: - - ff9530579d1f - - 5ec9f6bceaee - - f2e8552cf1d0 - - 3d0c7bdf12f5 - 2d094334f61e - - e7b2202befea + - 3d0c7bdf12f5 + - 5ec9f6bceaee - 9da02be9c6cc - d2cf2c0c8a11 + - e7b2202befea + - f2e8552cf1d0 + - ff9530579d1f tool_panel_section_label: Fastq Manipulation - name: trimmomatic owner: pjbriggs revisions: - 32f1f56bd970 - - d94aff5ee623 - 898b67846b47 + - b9aaed85cbd1 + - d94aff5ee623 tool_panel_section_label: Fastq Manipulation - name: fastq_to_tabular owner: devteam @@ -81,8 +83,8 @@ tools: - name: blast_rbh owner: peterjc revisions: - - d8d9a9069586 - b2f91cbed8d9 + - d8d9a9069586 tool_panel_section_label: Sequence Analysis - name: chromeister owner: iuc @@ -95,18 +97,20 @@ tools: - name: mafft owner: rnateam revisions: - - a65296ffb4a0 - - f1a5908ea2cb - 4de39704d423 + - a65296ffb4a0 - aaefa93c2dd2 + - bf28a8cff401 + - f1a5908ea2cb tool_panel_section_label: Sequence Analysis - name: hmmer_jackhmmer owner: iuc revisions: - 036df14999e8 - 5113c71c7031 - - 793967b6ae8a - 6e27bb3f0fa6 + - 793967b6ae8a + - 9fdeca68a6b5 - d9ce554da9b4 tool_panel_section_label: Sequence Analysis - name: hmmer_hmmsearch @@ -114,110 +118,122 @@ tools: revisions: - 192a5046d9a2 - 284d40d6f5a1 - - b774ae8e1609 - 6867ed975e25 + - b774ae8e1609 - d753d9169482 + - df7a52791be9 tool_panel_section_label: Sequence Analysis - name: hmmer_phmmer owner: iuc revisions: - - c1de05e20868 + - 37bcc9fb0bb1 - 74fc6d7d40f1 - - ff6e24314c63 - - 8a791afd99fb - 8267b6ad0b45 + - 8a791afd99fb + - c1de05e20868 + - ff6e24314c63 tool_panel_section_label: Sequence Analysis - name: hmmer_hmmbuild owner: iuc revisions: - - 7ea31fc35394 + - 4b996c837ec8 - 6846f8789e33 - - dc8860ba75d1 - - d0875d3f6544 - 750269125dc9 + - 7ea31fc35394 + - d0875d3f6544 + - dc8860ba75d1 tool_panel_section_label: Sequence Analysis - name: hmmer_nhmmer owner: iuc revisions: - 314b778b8ffa - - be0cc39776f9 - - b4fe2f703b4b + - 54b92ae4f75b - b28e8ed99424 + - b4fe2f703b4b + - be0cc39776f9 - c8e81e43bff1 tool_panel_section_label: Sequence Analysis - name: hmmer_hmmscan owner: iuc revisions: - - d92dd2f040cd - 01219a31c48e + - 1a83249ddfff + - 4a54e4c9188b - be072920a53e - be7097d6e3ff - - 1a83249ddfff + - d92dd2f040cd tool_panel_section_label: Sequence Analysis - name: hmmer_nhmmscan owner: iuc revisions: - - e07176c0925d - - c3075b7fdbdd - 24a67ef302dd - 2d406da5d34e + - c3075b7fdbdd + - e07176c0925d - f68b43be32d7 + - fb1305d0d1c6 tool_panel_section_label: Sequence Analysis - name: t_coffee owner: earlhaminst revisions: - - ae69d14b6fbf - 0a189243186d + - ae69d14b6fbf tool_panel_section_label: Sequence Analysis - name: gffread owner: devteam revisions: - - 4dea02886337 - 154d00cbbf2d + - 3e436657dcd0 + - 4dea02886337 tool_panel_section_label: Sequence Analysis - name: cd_hit owner: iuc revisions: - - e0da3400ac2f - 7807800a3d03 + - e0da3400ac2f tool_panel_section_label: Sequence Analysis - name: diamond owner: bgruening revisions: - 1e3323a44643 - - 64be1ac21109 - 62c9df8382c2 + - 64be1ac21109 + - e8ac2b53f262 - f921014aba5a tool_panel_section_label: Sequence Analysis - name: fastp owner: iuc revisions: - - 65b93b623c77 - 1d8fe9bc4cb0 + - 65b93b623c77 - 6c2351178f8d - - dbf9c561ef29 - a935cbdf1c0e + - c59d48774d03 + - dbf9c561ef29 tool_panel_section_label: Sequence Analysis - name: hmmer_alimask owner: iuc revisions: - - 80c713789d13 - 274d66a6368b - - 92227c141aa5 + - 80c713789d13 - 819d044451ed + - 92227c141aa5 + - e3e5f208e93c tool_panel_section_label: Sequence Analysis - name: hmmer_hmmemit owner: iuc revisions: - - 96b127c59e6a - - a6f41287ef2b - 1cd4d0cf8fd9 - 7b7ff4d209f7 + - 96b127c59e6a + - a6f41287ef2b + - be03abdc6451 tool_panel_section_label: Sequence Analysis - name: hmmer_hmmconvert owner: iuc revisions: - 649b289b4ccc + - a9dace1a1e36 - b03487ad64c8 - db8a5a3195e7 - f92edeb5e4c4 @@ -225,25 +241,27 @@ tools: - name: hmmer_hmmfetch owner: iuc revisions: - - a28fd001de59 - - cd078bda9921 - 01c842e297f5 + - 34b09461bf87 - 74089c182a50 + - a28fd001de59 + - cd078bda9921 tool_panel_section_label: Sequence Analysis - name: hmmer_hmmalign owner: iuc revisions: - - ca0b674e895b + - 24fa8e890f08 + - 71863d3bf721 - a9c62fc8187b + - ca0b674e895b - d430c68061f7 - - 24fa8e890f08 tool_panel_section_label: Sequence Analysis - name: trim_galore owner: bgruening revisions: - - cd7e644cae1d - 084bbd8ba7b8 - 949f01671246 + - cd7e644cae1d tool_panel_section_label: Sequence Analysis - name: ucsc_blat owner: yating-l @@ -255,13 +273,14 @@ tools: owner: devteam revisions: - 4daabc25df00 + - 5b097fde95dd - d6694932c5e0 tool_panel_section_label: Sequence Analysis - name: repeat_masker owner: bgruening revisions: - - bfc70c8cc5ca - ba6d2c32f797 + - bfc70c8cc5ca tool_panel_section_label: Sequence Analysis - name: prokka owner: crs4 @@ -276,6 +295,7 @@ tools: - name: kofamscan owner: iuc revisions: + - 8ec7636fa875 - c3c46f14c7a4 tool_panel_section_label: Sequence Analysis - name: blat @@ -286,20 +306,20 @@ tools: - name: locarna_pairwise_p owner: rnateam revisions: - - 535f2e41d4f7 - 53583f715a8c + - 535f2e41d4f7 tool_panel_section_label: RNA - Utilities for RNA - name: locarna_exparnap owner: rnateam revisions: - - e66514da3a99 - 8723e3f8e422 + - e66514da3a99 tool_panel_section_label: RNA - Utilities for RNA - name: locarna_multiple owner: rnateam revisions: - - 94b0468f0db8 - 7554c0df9139 + - 94b0468f0db8 tool_panel_section_label: RNA - Utilities for RNA - name: locarna_reliability_profile owner: rnateam @@ -310,14 +330,14 @@ tools: - name: locarna_pairwise owner: rnateam revisions: - - f3f08a777c10 - 433601e9f132 + - f3f08a777c10 tool_panel_section_label: RNA - Utilities for RNA - name: sortmerna owner: rnateam revisions: - - eb35257d2e29 - 10b84b577117 + - eb35257d2e29 tool_panel_section_label: RNA - Utilities for RNA - name: muscle owner: crs4 @@ -332,41 +352,46 @@ tools: - name: samtools_flagstat owner: devteam revisions: - - db17d5321bad + - 0072bf593791 - 22970df7a40e + - db17d5321bad - fe34990e5ce7 - - 0072bf593791 + - fefd89ab563c tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: picard owner: devteam revisions: - - 881d7645d1bf - - 7d34178f2812 + - 3f254c5ced1d - 7615ac66c6e5 + - 7d34178f2812 + - 881d7645d1bf tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_mpileup owner: devteam revisions: - 329deb17a9f7 - - aa0ef6f0ee89 - 9da0311ab1dd + - aa0ef6f0ee89 + - b61f5d6a7f25 - fa7ad9b89f4a tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_slice_bam owner: devteam revisions: - - 344fc91e1bfd - 2b474ebbfc7d + - 344fc91e1bfd - a4a10c7924d1 + - b5c88b7b153e tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_view owner: iuc revisions: - - c370440f901e - 0dbf49c414ae - - ff313de5f7f4 - 5826298f6a73 + - 6be888be75f9 - bf328cec6a42 + - c370440f901e + - ff313de5f7f4 tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_coverage owner: iuc @@ -374,20 +399,23 @@ tools: - 8a477224dfee - 90f2dd176d80 - ae36fab06bc2 + - c4ff13d2aab3 tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_depth owner: iuc revisions: - - 56faa6a57e50 - 2ee8dc1aeda9 - 44de678a44c4 + - 56faa6a57e50 + - 971dc85e9441 tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_fastx owner: iuc revisions: - - b3d99709fe1a - - a8d69aee190e + - 66e23b11feae - 720217c23995 + - a8d69aee190e + - b3d99709fe1a tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_fixmate owner: iuc @@ -395,145 +423,161 @@ tools: - 41e36c99a008 - 595ae1ba934a - bc0cc7bfbfe9 + - e5ece8fa99de tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_markdup owner: iuc revisions: - - ce32171c6d44 - - b5527cc104ab + - 046cbf29795a - 83b8e36e9cbe - 8c440c3002bc - - 046cbf29795a + - a389f74c3630 + - b5527cc104ab + - ce32171c6d44 tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_merge owner: iuc revisions: - 36677f429310 - - b40e2d865d52 + - 65a38e8c8e2a - 740ce0a18f0d + - b40e2d865d52 tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_split owner: devteam revisions: + - 135c85f4cfaf - 57f3e32f809d - b7f7826ef1cd - - 135c85f4cfaf - bcedabb53ddf + - bd850490c7f1 tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_stats owner: devteam revisions: - - 8cfc17e27132 - - 5a08c09b9311 - - 3a0efe14891f + - 145f6d74ff5e - 1cc79f49b8d5 + - 3a0efe14891f + - 5a08c09b9311 + - 8cfc17e27132 - 95a7ddf617e7 - - 145f6d74ff5e + - fed4aa48ba09 tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_sort owner: devteam revisions: - 6c2c1836728b - - f56bdb93ae58 - - e613c1ad4c4c - a430da4f04cd + - a577ea614bed + - e613c1ad4c4c + - f56bdb93ae58 tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_bedcov owner: devteam revisions: - - 9149ad20699a + - 12749212f61b - 46c6639921f1 + - 6856f8a01905 - 8c3472790020 - - 12749212f61b + - 9149ad20699a tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: sam_to_bam owner: devteam revisions: + - 9bd1568619cd - d04d9f1c6791 tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: bam_to_sam owner: devteam revisions: - - af7c50162f0b - 88eedb4abea0 + - a53efedba9e7 + - af7c50162f0b tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_calmd owner: devteam revisions: - - 1ebb4ecdc1ef - 06dc50b7b711 + - 1ebb4ecdc1ef - 92ec40abcdcf + - c89806670ab9 tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_idxstats owner: devteam revisions: + - 7a6034296ae9 - 7def34e6cf4d - 811fc2d75ad4 - - 7a6034296ae9 - 87398ae795c7 + - fa5d3e61e429 tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: samtools_reheader owner: devteam revisions: - - 30388d878f81 - 020e144b5f78 + - 30388d878f81 - bb8cfc6f6e0c + - d7b4851d1971 - db000c6007a0 tool_panel_section_label: SAM - Tools for manipulating alignments in the SAM format - name: abyss owner: iuc revisions: - - 8f1b150a2487 + - 0124fce4654a - 0a5c7992b1ac + - 3ce74eab308b - 7547fcab5d19 + - 8f1b150a2487 - fa5259cc561b - - 3ce74eab308b tool_panel_section_label: Assembly - name: rnaquast owner: iuc revisions: - - f89e3c318453 - 33c060ec0ac9 + - 8e66f695d859 - e989670c7fc7 + - f89e3c318453 tool_panel_section_label: Assembly - name: velvetoptimiser owner: simon-gladman revisions: + - 37d88f41c810 - 82398ba86ba7 - d81360ea69d8 - - 37d88f41c810 tool_panel_section_label: Assembly - name: velvet owner: devteam revisions: - - 5da9a0e2fb2d - - 920677cd220f - 08256557922f + - 5da9a0e2fb2d - 8d09f8be269e + - 920677cd220f tool_panel_section_label: Assembly - name: quast owner: iuc revisions: - 0834c823d4b9 - - ebb0dcdb621a - - 875d0f36d66f - - 72472698a2df - 3061c8b029e5 - 59db8ea8c845 - 6fcbee531de6 + - 72472698a2df + - 875d0f36d66f + - ebb0dcdb621a tool_panel_section_label: Assembly - name: spades owner: nml revisions: - - b8c00ce5dfa0 - 884dc0264950 - - a789e163a670 - 9006e5836729 + - a789e163a670 + - b8c00ce5dfa0 + - d5887ace0dd4 tool_panel_section_label: Assembly - name: spades_rnaviralspades owner: iuc revisions: - 48cf45a53456 + - 6357b127161e - b3490b036c5a tool_panel_section_label: Assembly - name: spades_plasmidspades @@ -541,43 +585,50 @@ tools: revisions: - 6aad515a5270 - 75405f5e2cc5 + - 8cc856b935ee tool_panel_section_label: Assembly - name: spades_metaviralspades owner: iuc revisions: - - e060c3987513 + - 7922870efcca - 86f66ab58e14 + - e060c3987513 tool_panel_section_label: Assembly - name: spades_metaplasmidspades owner: iuc revisions: - 21da31ed41a1 - 4a01e0d2892c + - 7e27faaad80e tool_panel_section_label: Assembly - name: spades_coronaspades owner: iuc revisions: - - ff41a00a6745 + - 655fa188c3cc - fee85957cebe + - ff41a00a6745 tool_panel_section_label: Assembly - name: spades_biosyntheticspades owner: iuc revisions: - 1fc82fe7ebef + - c33a476f4001 - d89ced9439f3 tool_panel_section_label: Assembly - name: rnaspades owner: iuc revisions: - - 675ee1aa5952 - 378e55aeeb25 + - 5fc94b3a4704 + - 675ee1aa5952 tool_panel_section_label: Assembly - name: metaspades owner: nml revisions: - 05c394313b1c - - 6563e22a9fd0 - 606b09cc9860 + - 6563e22a9fd0 + - 99ecfdafc64f tool_panel_section_label: Assembly - name: ball owner: luis @@ -587,47 +638,49 @@ tools: - name: join owner: devteam revisions: + - 718d04143c31 - a10f49d9218a tool_panel_section_label: Join, Subtract and Group - name: regex_find_replace owner: galaxyp revisions: + - 209b7c5ee9d7 + - 399da6b5ec21 - 503bcd6ebe4b - ae8c4b2488e7 - - 399da6b5ec21 - - 209b7c5ee9d7 tool_panel_section_label: Text Manipulation - name: datamash_transpose owner: iuc revisions: + - 22c2a1ac7ae3 - 374cb875d38a + - a513e3fbb4c5 - ac092723240d - - 22c2a1ac7ae3 tool_panel_section_label: Text Manipulation - name: datamash_ops owner: iuc revisions: - - 562f3c677828 - - 4c07ddedc198 - 2f3c6f2dcf39 + - 4c07ddedc198 + - 562f3c677828 - 746e8e4bf929 tool_panel_section_label: Text Manipulation - name: datamash_reverse owner: iuc revisions: - 0f1724dd59d2 - - f198773344e4 - b8a457820315 + - f198773344e4 tool_panel_section_label: Text Manipulation - name: column_maker owner: devteam revisions: - 02026300aa45 - - be25c075ed54 - - 6e8d94597139 - 464b9305180e - - 6595517c2dd8 - 626658afe4cb + - 6595517c2dd8 + - 6e8d94597139 + - be25c075ed54 tool_panel_section_label: Text Manipulation - name: singularity_scriptrunner owner: mbernt @@ -637,20 +690,21 @@ tools: - name: query_tabular owner: iuc revisions: - - cf34c344508d - - 33d61c89fb8d - 0c95a3f1654f - 1ea4e668bf73 - 2e8f945f7285 + - 33d61c89fb8d - 3a6b78c39dca + - cf34c344508d tool_panel_section_label: Text Manipulation - name: text_processing owner: bgruening revisions: - - d698c222f354 - - 74a8bef53a00 - 0a8c6b61f0f4 + - 74a8bef53a00 + - d698c222f354 - fb4ff3c42cd3 + - fbf99087e067 tool_panel_section_label: Text Manipulation - name: get_flanks owner: devteam @@ -661,118 +715,121 @@ tools: owner: devteam revisions: - 33b3f3688db4 + - 69c10b56f46d tool_panel_section_label: Genomic Interval Operations - name: xcms_xcmsset owner: lecorguille revisions: - - 378ddb410225 - - 9eebe9690ced - 14b1c52fae62 - 15646e937936 - - eb15a3841da4 + - 363cce459fff + - 378ddb410225 - 793f87231d49 - - f5d51091cf84 + - 9eebe9690ced - b02d1992a43a - - 363cce459fff + - eb15a3841da4 + - f5d51091cf84 tool_panel_section_label: Metabolomics - W4M - name: xcms_group owner: lecorguille revisions: + - 0d05d0458376 - 13558e8a4778 - 2b676d5eb848 - - fe4002ac5193 - - d45a786cbc40 - - 761913919c21 - 4c8507667cd6 - - 0d05d0458376 + - 761913919c21 + - d45a786cbc40 + - fe4002ac5193 tool_panel_section_label: Metabolomics - W4M - name: xcms_merge owner: lecorguille revisions: - - 5bd125a3f3b0 - - a301f001835c - 090cf284d9ff - 39797c768bba - 3a5204f14fff - 58b5a4b6e1da + - 5bd125a3f3b0 + - a301f001835c tool_panel_section_label: Metabolomics - W4M - name: xcms_plot_chromatogram owner: lecorguille revisions: - 024974037c4e - - 8846a03995d3 - 0cab69429e1e - 271c9d5f0d10 + - 8846a03995d3 - dbd877060ac3 tool_panel_section_label: Metabolomics - W4M - name: xcms_retcor owner: lecorguille revisions: + - 36480435e92b + - 4bfef820569b + - 7faadba7c625 + - 8242376d9f35 - aa252eec9229 + - c914743e3f2f - e4e0254a3c0a - - 36480435e92b - faf4a6b67304 - - c914743e3f2f - - 7faadba7c625 - - 4bfef820569b tool_panel_section_label: Metabolomics - W4M - name: xcms_fillpeaks owner: lecorguille revisions: - - 999f9db0ca2c - 26d77e9ceb49 - - de0d85537ee3 - - dcb9041cb9ea - 3bc94c3abb28 + - 999f9db0ca2c - bb9ee352fce0 + - dcb9041cb9ea + - de0d85537ee3 tool_panel_section_label: Metabolomics - W4M - name: xcms_summary owner: lecorguille revisions: - - a5347d57899f - - acc66e5c23d7 + - 018a9771de28 - 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