From 67a601f8288e09854ef43081cb84f8e7cb792288 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Thu, 15 Aug 2024 10:29:56 +0200 Subject: [PATCH 1/5] updated tools --- umsa_tool_list.yaml.lock | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/umsa_tool_list.yaml.lock b/umsa_tool_list.yaml.lock index 537db09..1eab7b7 100644 --- a/umsa_tool_list.yaml.lock +++ b/umsa_tool_list.yaml.lock @@ -7,6 +7,7 @@ tools: - name: split_file_to_collection owner: bgruening revisions: + - 2dae863c8f42 - 6cbe2f30c2d7 tool_panel_section_label: Collection Operations - name: collapse_collections @@ -92,6 +93,7 @@ tools: - name: xtb_molecular_optimization owner: recetox revisions: + - 6e1ef071fffc - cba7123c2741 - d5633eaf3552 tool_panel_section_label: RECETOX @@ -106,6 +108,7 @@ tools: revisions: - 1a2aeb8137bf - 6480c6d5fa36 + - bf32ae95a06f tool_panel_section_label: RECETOX - name: ramclustr owner: recetox @@ -751,10 +754,12 @@ tools: revisions: - 11ab2081bd4a - 12def6edac2f + - 6de175c1f6ef tool_panel_section_label: XCMS - name: xcms_xcmsset owner: lecorguille revisions: + - 6550698fe60f - b02d1992a43a - f5d51091cf84 tool_panel_section_label: XCMS @@ -763,29 +768,34 @@ tools: revisions: - 018a9771de28 - 2a2850fdf29e + - 444e3ed135e3 tool_panel_section_label: XCMS - name: xcms_retcor owner: lecorguille revisions: - 8242376d9f35 - aa252eec9229 + - d2b82d89f848 tool_panel_section_label: XCMS - name: xcms_plot_chromatogram owner: lecorguille revisions: - 024974037c4e - 8846a03995d3 + - c8bef8f6a1cb tool_panel_section_label: XCMS - name: xcms_merge owner: lecorguille revisions: - 58b5a4b6e1da - 5bd125a3f3b0 + - 6d475a389abc tool_panel_section_label: XCMS - name: xcms_group owner: lecorguille revisions: - 2b676d5eb848 + - 71572faf938e - d45a786cbc40 tool_panel_section_label: XCMS - name: xcms_fillpeaks @@ -793,10 +803,12 @@ tools: revisions: - 26d77e9ceb49 - bb9ee352fce0 + - ec9aebabc1d2 tool_panel_section_label: XCMS - name: xcms_export_samplemetadata owner: lecorguille revisions: + - 4ea32e46b2d6 - 94eb263cfab4 - cdab04a1d1d7 tool_panel_section_label: XCMS @@ -819,6 +831,7 @@ tools: - name: xcms_refine owner: workflow4metabolomics revisions: + - 090b33a9981c - 20f8ebc3a391 tool_panel_section_label: W4M - name: qualitymetrics @@ -1028,6 +1041,7 @@ tools: owner: recetox revisions: - 04892b463957 + - 17a48d0a80f4 - dd7bbc2b99d1 tool_panel_section_label: recetox-aplcms - name: recetox_aplcms_compute_template @@ -1035,11 +1049,13 @@ tools: revisions: - 481d769e2f7a - 4963811b6dec + - dfebc82ba1f0 tool_panel_section_label: recetox-aplcms - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - 6ba3526237e0 + - b3413f335327 - e7305ba0dd38 tool_panel_section_label: recetox-aplcms - name: recetox_aplcms_remove_noise @@ -1047,22 +1063,26 @@ tools: revisions: - b5a1f35abd8a - d90187b0f247 + - ffbabefbd2e2 tool_panel_section_label: recetox-aplcms - name: recetox_aplcms_correct_time owner: recetox revisions: - 02c772a49998 - 1574b8a29e6f + - 9064aecc78a7 tool_panel_section_label: recetox-aplcms - name: recetox_aplcms_compute_clusters owner: recetox revisions: - 149b9cc7499b - b9b19a74ac01 + - f3a18e020cdd tool_panel_section_label: recetox-aplcms - name: recetox_aplcms_align_features owner: recetox revisions: + - 79ad928a0dae - 7b42ee54d757 - d5c638b72ce4 tool_panel_section_label: recetox-aplcms @@ -1070,29 +1090,34 @@ tools: owner: recetox revisions: - 99d118321d5f + - d7f5878a98c3 - e0536ff73f36 tool_panel_section_label: recetox-aplcms - name: matchms_subsetting owner: recetox revisions: + - 6d2f2c565431 - a598091029ad - cab0e4dcf372 tool_panel_section_label: matchms - name: matchms_metadata_merge owner: recetox revisions: + - 84ead993862c - ec25de0f0c58 - fc1a698a71e8 tool_panel_section_label: matchms - name: matchms_add_key owner: recetox revisions: + - 1d10d32fa3b3 - 51da674b945d - 7c5b86026e57 tool_panel_section_label: matchms - name: matchms_networking owner: recetox revisions: + - 1d74ae228df3 - 3cd1cf3034d1 - ab8a33c370f5 tool_panel_section_label: matchms @@ -1100,6 +1125,7 @@ tools: owner: recetox revisions: - 05a7fc94e66c + - 1d443ed476a1 - 844d32c59314 tool_panel_section_label: matchms - name: matchms_spectral_similarity @@ -1107,10 +1133,12 @@ tools: revisions: - 26c92af1bd28 - 44e7027714d7 + - 7627b40601f6 tool_panel_section_label: matchms - name: matchms_metadata_export owner: recetox revisions: + - b576ed720711 - cbadbec49b5d - dd49ef90297c tool_panel_section_label: matchms @@ -1119,16 +1147,19 @@ tools: revisions: - 1d3ee4f9f63d - ad9d2d1b2b8d + - d7b517f2c5fe tool_panel_section_label: matchms - name: matchms_convert owner: recetox revisions: - 692471e62c68 - bff7bfcf975e + - c990df6afc24 tool_panel_section_label: matchms - name: matchms_filtering owner: recetox revisions: + - 00e66c401366 - 07cac38cbd29 - da15e8ea3b28 tool_panel_section_label: matchms @@ -1137,11 +1168,13 @@ tools: revisions: - 80df426e7e47 - c24ebd41dd53 + - fbe335d27d25 tool_panel_section_label: matchms - name: matchms_split owner: recetox revisions: - 446fddefcee7 + - 500f473df7e4 - fc1bc38ede0b tool_panel_section_label: matchms - name: matchms_remove_key @@ -1149,10 +1182,12 @@ tools: revisions: - 0a64e2bcce96 - 19367db5cf3c + - 9d1b01d3fedd tool_panel_section_label: matchms - name: matchms_formatter owner: recetox revisions: - 6501d0287dcd + - 9e3c83d2afc3 - f76a397afbe1 tool_panel_section_label: matchms From 801be77a15b4143b1271236c370a686916725c7e Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Thu, 15 Aug 2024 13:51:08 +0200 Subject: [PATCH 2/5] added spec2vec similarity tool --- umsa_tool_list.yaml | 6 ++++-- umsa_tool_list.yaml.lock | 15 +++++++++++++++ 2 files changed, 19 insertions(+), 2 deletions(-) diff --git a/umsa_tool_list.yaml b/umsa_tool_list.yaml index 66489ac..0ab1b5c 100644 --- a/umsa_tool_list.yaml +++ b/umsa_tool_list.yaml @@ -1,3 +1,4 @@ +tool_shed_url: toolshed.g2.bx.psu.edu tools: - name: collapse_collections owner: nml @@ -123,10 +124,11 @@ tools: tool_shed_url: toolshed.g2.bx.psu.edu - name: spec2vec_training owner: recetox - revisions: - - e1e22ada831e tool_panel_section_label: RECETOX tool_shed_url: toolshed.g2.bx.psu.edu +- name: spec2vec_similarity + owner: recetox + tool_panel_section_label: RECETOX - name: riassigner owner: recetox revisions: diff --git a/umsa_tool_list.yaml.lock b/umsa_tool_list.yaml.lock index 1eab7b7..150f770 100644 --- a/umsa_tool_list.yaml.lock +++ b/umsa_tool_list.yaml.lock @@ -195,6 +195,7 @@ tools: owner: bgruening revisions: - 4e3b2049a4d3 + - f70b83b730ac tool_panel_section_label: ChemicalToolBox - name: msconvert owner: galaxyp @@ -308,16 +309,19 @@ tools: revisions: - 50ca8845e7f5 - b2569e22b40c + - c5de6c19eb06 tool_panel_section_label: ChemicalToolBox - name: openbabel_addh owner: bgruening revisions: - 43167f164076 - 6e4b7e0c61a6 + - 7b6fd1c273cd tool_panel_section_label: ChemicalToolBox - name: openbabel_filter owner: bgruening revisions: + - 988085c7a0ea - df4dc55197dd - ff2dd4b7d918 tool_panel_section_label: ChemicalToolBox @@ -325,17 +329,20 @@ tools: owner: bgruening revisions: - 171c94786a56 + - 9adf3fae2771 - c19608db6b15 tool_panel_section_label: ChemicalToolBox - name: openbabel_compound_convert owner: bgruening revisions: - 1c66bf08f687 + - 4242b4d68e9c - e2c36f62e22f tool_panel_section_label: ChemicalToolBox - name: openbabel_remove_protonation_state owner: bgruening revisions: + - 22a866858b81 - bf4e668b6690 - e376ba0fcde0 tool_panel_section_label: ChemicalToolBox @@ -344,10 +351,12 @@ tools: revisions: - 330514267c57 - afd14e10a318 + - f5d7ffbb2d33 tool_panel_section_label: ChemicalToolBox - name: openbabel_svg_depiction owner: bgruening revisions: + - 75ee9c410951 - 7672039a0bb0 - d3b48303045b tool_panel_section_label: ChemicalToolBox @@ -359,6 +368,7 @@ tools: - name: openbabel_genprop owner: bgruening revisions: + - 50eaae9df8d3 - a72ae2711a97 - b249bf9be0d1 tool_panel_section_label: ChemicalToolBox @@ -367,16 +377,19 @@ tools: revisions: - 01ab890bf0ad - 3ecaa9634126 + - a638d8d13bb3 tool_panel_section_label: ChemicalToolBox - name: openbabel_obgrep owner: bgruening revisions: - 274193d6c443 - 78640d0127ce + - 985ab0acd514 tool_panel_section_label: ChemicalToolBox - name: openbabel_remsmall owner: bgruening revisions: + - 81836d586797 - aebc671bae78 - d7f0ca1f2669 tool_panel_section_label: ChemicalToolBox @@ -385,6 +398,7 @@ tools: revisions: - 5486f7a2b0cb - de4c80d17527 + - fac2c28b4c55 tool_panel_section_label: ChemicalToolBox - name: biomd_neqgamma owner: chemteam @@ -637,6 +651,7 @@ tools: revisions: - 2c5c7da26e08 - 4c9d6b47045c + - 8302ab092300 tool_panel_section_label: ChemicalToolBox - name: ctb_frankenstein_ligand owner: bgruening From b68e86af736ba98b40c02feee07f60b7b2ef4a1e Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Thu, 15 Aug 2024 17:14:48 +0200 Subject: [PATCH 3/5] added revisions and lockfile --- umsa_tool_list.yaml | 251 +++++++++------------------------------ umsa_tool_list.yaml.lock | 52 ++++++-- 2 files changed, 95 insertions(+), 208 deletions(-) diff --git a/umsa_tool_list.yaml b/umsa_tool_list.yaml index 0ab1b5c..5e1b9ca 100644 --- a/umsa_tool_list.yaml +++ b/umsa_tool_list.yaml @@ -5,127 +5,106 @@ tools: revisions: - 90981f86000f tool_panel_section_label: Collection Operations - tool_shed_url: toolshed.g2.bx.psu.edu - name: scatterplot owner: devteam revisions: - efda9a4a50e7 tool_panel_section_label: Visualization - tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - dfd5d981b5a4 tool_panel_section_label: Visualization - tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - 391a4cc45fea tool_panel_section_label: Visualization - tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_pca owner: iuc revisions: - 7e616a1bdb07 tool_panel_section_label: Visualization - tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram owner: iuc revisions: - 398e5104f8a2 tool_panel_section_label: Visualization - tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap2 owner: iuc revisions: - ca7cb0eaad62 tool_panel_section_label: Visualization - tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - e3a675da7fd0 tool_panel_section_label: Visualization - tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - 22c2a1ac7ae3 - a513e3fbb4c5 tool_panel_section_label: Text Manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: diff owner: bgruening revisions: - 95a9dc82fc9a tool_panel_section_label: Text Manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: - ddf54b12c295 - fbf99087e067 tool_panel_section_label: Text Manipulation - tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column owner: bgruening revisions: - ff2a81aa3f08 tool_panel_section_label: Filter and Sort - tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder owner: recetox revisions: - e7eff0c9baa3 tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: msmetaenhancer owner: recetox revisions: - 3e2cb0bc6959 tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: xtb_molecular_optimization owner: recetox revisions: - d5633eaf3552 tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_xmsannotator_advanced owner: recetox revisions: - cfd2e19f00a9 tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: waveica owner: recetox revisions: - 6480c6d5fa36 tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr owner: recetox revisions: - 050cfef6ba65 tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: rmassbank owner: recetox revisions: - 0b28816c1c2c tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: biotransformer owner: recetox revisions: - 0b86600b715e tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: spec2vec_training owner: recetox tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: spec2vec_similarity owner: recetox tool_panel_section_label: RECETOX @@ -135,7 +114,6 @@ tools: - c702620c22b1 - af25aa61c611 tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: assign_ri_from_comment owner: recetox revisions: @@ -143,835 +121,696 @@ tools: - 7226eba9c09d - 97ccdb1ba47c tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr_define_experiment owner: recetox revisions: - 25625114618e tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: msp_split owner: recetox revisions: - ae0263faa819 tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: filter_compounds owner: recetox revisions: - 72b687d21f65 tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - 19e45916daf9 tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature owner: recetox revisions: - 268fcec93d9c tool_panel_section_label: RECETOX - tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_annotate owner: lecorguille revisions: - abf1775ac14d tool_panel_section_label: CAMERA - tool_shed_url: toolshed.g2.bx.psu.edu - name: camera_combinexsannos owner: mmonsoor revisions: - 961089e21ae2 tool_panel_section_label: CAMERA - tool_shed_url: toolshed.g2.bx.psu.edu - name: rem_complex owner: recetox revisions: - a0e07a0bc047 tool_panel_section_label: ChemicalToolBox - tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remions owner: bgruening revisions: - 4e3b2049a4d3 tool_panel_section_label: ChemicalToolBox - tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert owner: galaxyp revisions: - 6153e8ada1ee tool_panel_section_label: ChemicalToolBox - tool_shed_url: toolshed.g2.bx.psu.edu - name: smina owner: earlhaminst revisions: - 7c0bb0c48a27 tool_panel_section_label: ChemicalToolBox - tool_shed_url: toolshed.g2.bx.psu.edu - name: apoc owner: earlhaminst revisions: - 67d2a6f3b4e3 tool_panel_section_label: ChemicalToolBox - tool_shed_url: toolshed.g2.bx.psu.edu - name: parmconv owner: chemteam revisions: - 6c6cecf51bd0 tool_panel_section_label: ChemicalToolBox - 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tool_shed_url: toolshed.g2.bx.psu.edu - name: ambertools_acpype owner: chemteam revisions: - f4230f116196 tool_panel_section_label: ChemicalToolBox - tool_shed_url: toolshed.g2.bx.psu.edu - name: mordred owner: bgruening revisions: - cc0f89287ecf tool_panel_section_label: ChemicalToolBox - tool_shed_url: toolshed.g2.bx.psu.edu - name: get_pdb owner: bgruening revisions: - 538790c6c21b tool_panel_section_label: ChemicalToolBox - tool_shed_url: toolshed.g2.bx.psu.edu - name: get_pubchem owner: bgruening revisions: - 4d966d5bdd17 tool_panel_section_label: ChemicalToolBox - tool_shed_url: toolshed.g2.bx.psu.edu - name: get_online_data owner: bgruening revisions: - 2538366eb8fb tool_panel_section_label: ChemicalToolBox - tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina owner: bgruening revisions: - 7a871df65202 tool_panel_section_label: ChemicalToolBox - tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_ligand owner: bgruening revisions: - 50871000e977 tool_panel_section_label: ChemicalToolBox - 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80df426e7e47 tool_panel_section_label: matchms - tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split owner: recetox revisions: - fc1bc38ede0b tool_panel_section_label: matchms - tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_key owner: recetox revisions: - 0a64e2bcce96 tool_panel_section_label: matchms - tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter owner: recetox revisions: - f76a397afbe1 tool_panel_section_label: matchms - tool_shed_url: toolshed.g2.bx.psu.edu + +- name: mfassignr_snplot + owner: recetox + tool_panel_section_label: mfassignr + revisions: + - 6a34bc7afd61 + +- name: mfassignr_histnoise + owner: recetox + tool_panel_section_label: mfassignr + revisions: + - faf7108f3b48 + +- name: mfassignr_kmdnoise + owner: recetox + tool_panel_section_label: mfassignr + revisions: + - f60df05dd038 + +- name: mfassignr_isofiltr + owner: recetox + tool_panel_section_label: mfassignr + revisions: + - 079ae9aa6ed5 + +- name: mfassignr_mfassign + owner: recetox + tool_panel_section_label: mfassignr + revisions: + - 5aa9380f397b + +- name: mfassignr_mfassigncho + owner: recetox + tool_panel_section_label: mfassignr + revisions: + - 11949bd6837a + +- name: mfassignr_recal + owner: recetox + tool_panel_section_label: mfassignr + revisions: + - 235878c45443 + +- name: mfassignr_recallist + owner: recetox + tool_panel_section_label: mfassignr + revisions: + - 6e1813883a9a + +- name: rcx_tk + owner: recetox + tool_panel_section_label: RECETOX + revisions: + - 54401f9d1a30 diff --git a/umsa_tool_list.yaml.lock b/umsa_tool_list.yaml.lock index 150f770..7528cae 100644 --- a/umsa_tool_list.yaml.lock +++ b/umsa_tool_list.yaml.lock @@ -1,15 +1,4 @@ tools: -- name: compose_text_param - owner: iuc - revisions: - - e188c9826e0f - tool_panel_section_label: Text Manipulation -- name: split_file_to_collection - owner: bgruening - revisions: - - 2dae863c8f42 - - 6cbe2f30c2d7 - tool_panel_section_label: Collection Operations - name: collapse_collections owner: nml revisions: @@ -126,6 +115,7 @@ tools: owner: recetox revisions: - 0b86600b715e + - 6cd2a9e6ac49 - e5fcba090b10 tool_panel_section_label: RECETOX - name: spec2vec_training @@ -134,6 +124,10 @@ tools: - 9d917de87cca - e1e22ada831e tool_panel_section_label: RECETOX +- name: spec2vec_similarity + owner: recetox + revisions: [] + tool_panel_section_label: RECETOX - name: riassigner owner: recetox revisions: @@ -1206,3 +1200,39 @@ tools: - 9e3c83d2afc3 - f76a397afbe1 tool_panel_section_label: matchms +- name: mfassignr_snplot + owner: recetox + revisions: [] + tool_panel_section_label: mfassignr +- name: mfassignr_histnoise + owner: recetox + revisions: [] + tool_panel_section_label: mfassignr +- name: mfassignr_kmdnoise + owner: recetox + revisions: [] + tool_panel_section_label: mfassignr +- name: mfassignr_isofiltr + owner: recetox + revisions: [] + tool_panel_section_label: mfassignr +- name: mfassignr_mfassign + owner: recetox + revisions: [] + tool_panel_section_label: mfassignr +- name: mfassignr_mfassigncho + owner: recetox + revisions: [] + tool_panel_section_label: mfassignr +- name: mfassignr_recal + owner: recetox + revisions: [] + tool_panel_section_label: mfassignr +- name: mfassignr_recallist + owner: recetox + revisions: [] + tool_panel_section_label: mfassignr +- name: rcx_tk + owner: recetox + revisions: [] + tool_panel_section_label: RECETOX From 5261171b2b0d842362f0e2302820b9c95194b07f Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Thu, 15 Aug 2024 17:38:57 +0200 Subject: [PATCH 4/5] updated tools and lockfile --- umsa_tool_list.yaml | 13 +-- umsa_tool_list.yaml.lock | 213 ++++----------------------------------- 2 files changed, 25 insertions(+), 201 deletions(-) diff --git a/umsa_tool_list.yaml b/umsa_tool_list.yaml index 5e1b9ca..55f6c82 100644 --- a/umsa_tool_list.yaml +++ b/umsa_tool_list.yaml @@ -105,9 +105,13 @@ tools: - name: spec2vec_training owner: recetox tool_panel_section_label: RECETOX + revisions: + - 9d917de87cca - name: spec2vec_similarity owner: recetox tool_panel_section_label: RECETOX + revisions: + - 721a4e666191 - name: riassigner owner: recetox revisions: @@ -1021,55 +1025,46 @@ tools: revisions: - f76a397afbe1 tool_panel_section_label: matchms - - name: mfassignr_snplot owner: recetox tool_panel_section_label: mfassignr revisions: - 6a34bc7afd61 - - name: mfassignr_histnoise owner: recetox tool_panel_section_label: mfassignr revisions: - faf7108f3b48 - - name: mfassignr_kmdnoise owner: recetox tool_panel_section_label: mfassignr revisions: - f60df05dd038 - - name: mfassignr_isofiltr owner: recetox tool_panel_section_label: mfassignr revisions: - 079ae9aa6ed5 - - name: mfassignr_mfassign owner: recetox tool_panel_section_label: mfassignr revisions: - 5aa9380f397b - - name: mfassignr_mfassigncho owner: recetox tool_panel_section_label: mfassignr revisions: - 11949bd6837a - - name: mfassignr_recal owner: recetox tool_panel_section_label: mfassignr revisions: - 235878c45443 - - name: mfassignr_recallist owner: recetox tool_panel_section_label: mfassignr revisions: - 6e1813883a9a - - name: rcx_tk owner: recetox tool_panel_section_label: RECETOX diff --git a/umsa_tool_list.yaml.lock b/umsa_tool_list.yaml.lock index 7528cae..38f0e7e 100644 --- a/umsa_tool_list.yaml.lock +++ b/umsa_tool_list.yaml.lock @@ -1,3 +1,4 @@ +tool_shed_url: toolshed.g2.bx.psu.edu tools: - name: collapse_collections owner: nml @@ -12,37 +13,31 @@ tools: - name: ggplot2_violin owner: iuc revisions: - - 0e7290688b50 - dfd5d981b5a4 tool_panel_section_label: Visualization - name: ggplot2_heatmap owner: iuc revisions: - - 10515715c940 - 391a4cc45fea tool_panel_section_label: Visualization - name: ggplot2_pca owner: iuc revisions: - 7e616a1bdb07 - - b1268b7544d3 tool_panel_section_label: Visualization - name: ggplot2_histogram owner: iuc revisions: - 398e5104f8a2 - - b0d96516e6a5 tool_panel_section_label: Visualization - name: ggplot2_heatmap2 owner: iuc revisions: - - 374e9062d874 - ca7cb0eaad62 tool_panel_section_label: Visualization - name: ggplot2_point owner: iuc revisions: - - 3b12bf9b4b87 - e3a675da7fd0 tool_panel_section_label: Visualization - name: datamash_transpose @@ -54,7 +49,6 @@ tools: - name: diff owner: bgruening revisions: - - 156d0908e232 - 95a9dc82fc9a tool_panel_section_label: Text Manipulation - name: text_processing @@ -77,56 +71,46 @@ tools: owner: recetox revisions: - 3e2cb0bc6959 - - b5467dead5b1 tool_panel_section_label: RECETOX - name: xtb_molecular_optimization owner: recetox revisions: - - 6e1ef071fffc - - cba7123c2741 - d5633eaf3552 tool_panel_section_label: RECETOX - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 6b5dec818827 - cfd2e19f00a9 tool_panel_section_label: RECETOX - name: waveica owner: recetox revisions: - - 1a2aeb8137bf - 6480c6d5fa36 - - bf32ae95a06f tool_panel_section_label: RECETOX - name: ramclustr owner: recetox revisions: - 050cfef6ba65 - - da7722f665f4 tool_panel_section_label: RECETOX - name: rmassbank owner: recetox revisions: - 0b28816c1c2c - - 5a6bb93ec656 tool_panel_section_label: RECETOX - name: biotransformer owner: recetox revisions: - 0b86600b715e - - 6cd2a9e6ac49 - - e5fcba090b10 tool_panel_section_label: RECETOX - name: spec2vec_training owner: recetox revisions: - 9d917de87cca - - e1e22ada831e tool_panel_section_label: RECETOX - name: spec2vec_similarity owner: recetox - revisions: [] + revisions: + - 721a4e666191 tool_panel_section_label: RECETOX - name: riassigner owner: recetox @@ -145,7 +129,6 @@ tools: owner: recetox revisions: - 25625114618e - - f2c1d0bbb074 tool_panel_section_label: RECETOX - name: msp_split owner: recetox @@ -155,7 +138,6 @@ tools: - name: filter_compounds owner: recetox revisions: - - 6c5df3eeb768 - 72b687d21f65 tool_panel_section_label: RECETOX - name: thermo_raw_file_converter @@ -171,7 +153,6 @@ tools: - name: camera_annotate owner: lecorguille revisions: - - 4b9ab71be05e - abf1775ac14d tool_panel_section_label: CAMERA - name: camera_combinexsannos @@ -182,19 +163,16 @@ tools: - name: rem_complex owner: recetox revisions: - - 60db8070a5c3 - a0e07a0bc047 tool_panel_section_label: ChemicalToolBox - name: openbabel_remions owner: bgruening revisions: - 4e3b2049a4d3 - - f70b83b730ac tool_panel_section_label: ChemicalToolBox - name: msconvert owner: galaxyp revisions: - - 545054b15d7c - 6153e8ada1ee tool_panel_section_label: ChemicalToolBox - name: smina @@ -205,31 +183,26 @@ tools: - name: apoc owner: earlhaminst revisions: - - 451f90534945 - 67d2a6f3b4e3 tool_panel_section_label: ChemicalToolBox - name: parmconv owner: chemteam revisions: - 6c6cecf51bd0 - - 6d0677a148fe tool_panel_section_label: ChemicalToolBox - name: enumerate_charges owner: bgruening revisions: - 36360fa103d6 - - 67ee76f0e497 tool_panel_section_label: ChemicalToolBox - name: sdf_to_tab owner: bgruening revisions: - - 4beb3e026bbb - 55553120df69 tool_panel_section_label: ChemicalToolBox - name: fpocket owner: bgruening revisions: - - 4cc9d85c3bae - 4fb73be7f4cb tool_panel_section_label: ChemicalToolBox - name: chembl_structure_pipeline @@ -241,24 +214,20 @@ tools: owner: bgruening revisions: - 1d6fb7967ae9 - - a446ea7e2bc1 tool_panel_section_label: ChemicalToolBox - name: ambertools_parmchk2 owner: chemteam revisions: - 96b872138d3b - - ecc43bf27a49 tool_panel_section_label: ChemicalToolBox - name: ambertools_antechamber owner: chemteam revisions: - 29aa7091e533 - - 8a839e6a1e3e tool_panel_section_label: ChemicalToolBox - name: ambertools_acpype owner: chemteam revisions: - - 095ad4d096d1 - f4230f116196 tool_panel_section_label: ChemicalToolBox - name: mordred @@ -285,7 +254,6 @@ tools: owner: bgruening revisions: - 7a871df65202 - - 90ea16534012 tool_panel_section_label: ChemicalToolBox - name: autodock_vina_prepare_ligand owner: bgruening @@ -295,63 +263,46 @@ tools: - name: autodock_vina_prepare_box owner: bgruening revisions: - - 8f766d9652a2 - ad35eaa204ea tool_panel_section_label: ChemicalToolBox - name: openbabel_remduplicates owner: bgruening revisions: - 50ca8845e7f5 - - b2569e22b40c - - c5de6c19eb06 tool_panel_section_label: ChemicalToolBox - name: openbabel_addh owner: bgruening revisions: - 43167f164076 - - 6e4b7e0c61a6 - - 7b6fd1c273cd tool_panel_section_label: ChemicalToolBox - name: openbabel_filter owner: bgruening revisions: - - 988085c7a0ea - - df4dc55197dd - ff2dd4b7d918 tool_panel_section_label: ChemicalToolBox - name: openbabel_subsearch owner: bgruening revisions: - 171c94786a56 - - 9adf3fae2771 - - c19608db6b15 tool_panel_section_label: ChemicalToolBox - name: openbabel_compound_convert owner: bgruening revisions: - 1c66bf08f687 - - 4242b4d68e9c - - e2c36f62e22f tool_panel_section_label: ChemicalToolBox - name: openbabel_remove_protonation_state owner: bgruening revisions: - - 22a866858b81 - bf4e668b6690 - - e376ba0fcde0 tool_panel_section_label: ChemicalToolBox - name: openbabel_spectrophore_search owner: bgruening revisions: - - 330514267c57 - afd14e10a318 - - f5d7ffbb2d33 tool_panel_section_label: ChemicalToolBox - name: openbabel_svg_depiction owner: bgruening revisions: - - 75ee9c410951 - - 7672039a0bb0 - d3b48303045b tool_panel_section_label: ChemicalToolBox - name: openbabel_multi_obgrep @@ -362,61 +313,47 @@ tools: - name: openbabel_genprop owner: bgruening revisions: - - 50eaae9df8d3 - a72ae2711a97 - - b249bf9be0d1 tool_panel_section_label: ChemicalToolBox - name: openbabel_change_title owner: bgruening revisions: - - 01ab890bf0ad - 3ecaa9634126 - - a638d8d13bb3 tool_panel_section_label: ChemicalToolBox - name: openbabel_obgrep owner: bgruening revisions: - - 274193d6c443 - 78640d0127ce - - 985ab0acd514 tool_panel_section_label: ChemicalToolBox - name: openbabel_remsmall owner: bgruening revisions: - - 81836d586797 - aebc671bae78 - - d7f0ca1f2669 tool_panel_section_label: ChemicalToolBox - name: prepare_ligands_for_docking owner: bgruening revisions: - - 5486f7a2b0cb - de4c80d17527 - - fac2c28b4c55 tool_panel_section_label: ChemicalToolBox - name: biomd_neqgamma owner: chemteam revisions: - 4f3222cb5cf6 - - afcb925def69 tool_panel_section_label: ChemicalToolBox - name: biomd_rmsd_clustering owner: chemteam revisions: - b001ebc8bf58 - - b9c46dbe9605 tool_panel_section_label: ChemicalToolBox - name: biomd_extract_clusters owner: chemteam revisions: - 078dfd7fb26d - - e0ecaf2d05fb tool_panel_section_label: ChemicalToolBox - name: fastpca owner: chemteam revisions: - 6f2029791c94 - - 9ca30ad95444 tool_panel_section_label: ChemicalToolBox - name: bio3d_dccm owner: chemteam @@ -446,25 +383,21 @@ tools: - name: mdanalysis_extract_rmsd owner: chemteam revisions: - - 589f8ef21e58 - 743bd6aa3c7a tool_panel_section_label: ChemicalToolBox - name: mdanalysis_ramachandran_protein owner: chemteam revisions: - - 060b9d9ec8cf - 0f270722aca6 tool_panel_section_label: ChemicalToolBox - name: mdanalysis_endtoend owner: chemteam revisions: - 78aa3659fcd1 - - 795a5996cdc8 tool_panel_section_label: ChemicalToolBox - name: mdanalysis_cosine_analysis owner: chemteam revisions: - - 48d6a6eb438b - a842da7ef42b tool_panel_section_label: ChemicalToolBox - name: vmd_hbonds @@ -476,36 +409,30 @@ tools: owner: chemteam revisions: - 4c36f5ad2799 - - b17ce46509ad tool_panel_section_label: ChemicalToolBox - name: mdanalysis_ramachandran_plot owner: chemteam revisions: - 70a2d548e62c - - be5eaea0b2d1 tool_panel_section_label: ChemicalToolBox - name: mdanalysis_distance owner: chemteam revisions: - - fd987ff06ceb - ffd6f8d159e1 tool_panel_section_label: ChemicalToolBox - name: mdanalysis_dihedral owner: chemteam revisions: - - 976cfd44b921 - aaa130695a2b tool_panel_section_label: ChemicalToolBox - name: mdanalysis_rdf owner: chemteam revisions: - 1a220575ad7a - - 49076afc90b1 tool_panel_section_label: ChemicalToolBox - name: mdanalysis_angle owner: chemteam revisions: - - 567f8c5d4680 - a0d210b9d287 tool_panel_section_label: ChemicalToolBox - name: packmol @@ -516,7 +443,6 @@ tools: - name: ctb_rdkit_descriptors owner: bgruening revisions: - - 0993ac4f4a23 - cf725c82c865 tool_panel_section_label: ChemicalToolBox - name: alchemical_analysis @@ -527,31 +453,26 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - 88076940fa94 - bfb65cb551d8 tool_panel_section_label: ChemicalToolBox - name: gmx_makendx owner: chemteam revisions: - d9eb276dfa32 - - e3e536aa2633 tool_panel_section_label: ChemicalToolBox - name: gmx_restraints owner: chemteam revisions: - - 509aa136d4e3 - ca6a4740114e tool_panel_section_label: ChemicalToolBox - name: gmx_energy owner: chemteam revisions: - c8d2c0162b6e - - f26afd1b7104 tool_panel_section_label: ChemicalToolBox - name: gmx_trj owner: chemteam revisions: - - 32052c6c3310 - 9363254ef848 tool_panel_section_label: ChemicalToolBox - name: gmx_fep @@ -563,12 +484,10 @@ tools: owner: chemteam revisions: - a97dcfc23b4b - - c0c9a5024177 tool_panel_section_label: ChemicalToolBox - name: gmx_merge_topology_files owner: chemteam revisions: - - bc31d02be922 - ced8ec975548 tool_panel_section_label: ChemicalToolBox - name: gmx_nvt @@ -585,25 +504,21 @@ tools: owner: chemteam revisions: - 27ea4e1a3f95 - - c4fbab8e03c5 tool_panel_section_label: ChemicalToolBox - name: gmx_em owner: chemteam revisions: - 55918daa5651 - - b46d4b4d995c tool_panel_section_label: ChemicalToolBox - name: gmx_setup owner: chemteam revisions: - - 070e3ecc3fda - 4da9ee404eab tool_panel_section_label: ChemicalToolBox - name: md_converter owner: chemteam revisions: - 79e8ab8f1e81 - - d7ec25187599 tool_panel_section_label: ChemicalToolBox - name: gmx_npt owner: chemteam @@ -614,38 +529,31 @@ tools: owner: bgruening revisions: - 30c673b5b061 - - a84bcb007b09 tool_panel_section_label: ChemicalToolBox - name: qed owner: bgruening revisions: - - 52a8d34dd08f - fc45bf8b6e01 tool_panel_section_label: ChemicalToolBox - name: sucos_docking_scoring owner: bgruening revisions: - - 4f1896782f7c - fe318c648502 tool_panel_section_label: ChemicalToolBox - name: sucos_clustering owner: bgruening revisions: - 12725d4b90f3 - - b8725fec8c7b tool_panel_section_label: ChemicalToolBox - name: sucos_max_score owner: bgruening revisions: - 55ac04db36aa - - 9b48456a96fe tool_panel_section_label: ChemicalToolBox - name: openbabel_structure_distance_finder owner: bgruening revisions: - - 2c5c7da26e08 - 4c9d6b47045c - - 8302ab092300 tool_panel_section_label: ChemicalToolBox - name: ctb_frankenstein_ligand owner: bgruening @@ -690,7 +598,6 @@ tools: - name: mmpbsa_mmgbsa owner: chemteam revisions: - - 608098b3668d - d09f116dfca5 tool_panel_section_label: ChemicalToolBox - name: ctb_im_pbf_ev @@ -762,70 +669,51 @@ tools: owner: lecorguille revisions: - 11ab2081bd4a - - 12def6edac2f - - 6de175c1f6ef tool_panel_section_label: XCMS - name: xcms_xcmsset owner: lecorguille revisions: - - 6550698fe60f - b02d1992a43a - - f5d51091cf84 tool_panel_section_label: XCMS - name: xcms_summary owner: lecorguille revisions: - 018a9771de28 - - 2a2850fdf29e - - 444e3ed135e3 tool_panel_section_label: XCMS - name: xcms_retcor owner: lecorguille revisions: - - 8242376d9f35 - aa252eec9229 - - d2b82d89f848 tool_panel_section_label: XCMS - name: xcms_plot_chromatogram owner: lecorguille revisions: - 024974037c4e - - 8846a03995d3 - - c8bef8f6a1cb tool_panel_section_label: XCMS - name: xcms_merge owner: lecorguille revisions: - - 58b5a4b6e1da - 5bd125a3f3b0 - - 6d475a389abc tool_panel_section_label: XCMS - name: xcms_group owner: lecorguille revisions: - - 2b676d5eb848 - - 71572faf938e - d45a786cbc40 tool_panel_section_label: XCMS - name: xcms_fillpeaks owner: lecorguille revisions: - 26d77e9ceb49 - - bb9ee352fce0 - - ec9aebabc1d2 tool_panel_section_label: XCMS - name: xcms_export_samplemetadata owner: lecorguille revisions: - - 4ea32e46b2d6 - 94eb263cfab4 - - cdab04a1d1d7 tool_panel_section_label: XCMS - name: secimtools owner: malex revisions: - 2e7d47c0b027 - - caba07f41453 tool_panel_section_label: SECIMTools - name: metams_plot owner: workflow4metabolomics @@ -840,7 +728,6 @@ tools: - name: xcms_refine owner: workflow4metabolomics revisions: - - 090b33a9981c - 20f8ebc3a391 tool_panel_section_label: W4M - name: qualitymetrics @@ -876,68 +763,57 @@ tools: - name: mspurity_frag4feature owner: computational-metabolomics revisions: - - 174a523cb1da - e9fbb65451f6 tool_panel_section_label: msPurity - name: mspurity_spectralmatching owner: computational-metabolomics revisions: - 20f4fdaf36bb - - c33b92eeb1fb tool_panel_section_label: msPurity - name: mspurity_filterfragspectra owner: computational-metabolomics revisions: - 2e10c13085c9 - - a8842e5e75a7 tool_panel_section_label: msPurity - name: mspurity_puritya owner: computational-metabolomics revisions: - - 10e56e53668c - 55f1691db108 tool_panel_section_label: msPurity - name: mspurity_dimspredictpuritysingle owner: computational-metabolomics revisions: - 2ce66d2f6a24 - - 548fed2ef792 tool_panel_section_label: msPurity - name: mspurity_combineannotations owner: computational-metabolomics revisions: - d7104112fac6 - - f11c129a4227 tool_panel_section_label: msPurity - name: mspurity_purityx owner: computational-metabolomics revisions: - - 374022b7b469 - 942e676515fe tool_panel_section_label: msPurity - name: mspurity_createmsp owner: computational-metabolomics revisions: - - 3d92b95cf6c0 - 8512923bdd37 tool_panel_section_label: msPurity - name: mspurity_createdatabase owner: computational-metabolomics revisions: - 0cc6b67dccb8 - - 751b7378a683 tool_panel_section_label: msPurity - name: mspurity_averagefragspectra owner: computational-metabolomics revisions: - 94eb1fcfde88 - - ac284b969836 tool_panel_section_label: msPurity - name: mspurity_flagremove owner: computational-metabolomics revisions: - 69ed543767b2 - - da36e8bbcfbd tool_panel_section_label: msPurity - name: frag_hires_mass owner: ljocha @@ -973,13 +849,11 @@ tools: owner: galaxyp revisions: - 2735db4dd8d9 - - 748dfbdf2201 tool_panel_section_label: OpenMS - name: openms_featurelinkerunlabeled owner: galaxyp revisions: - b46263c3ee99 - - fbe41f0cc71e tool_panel_section_label: OpenMS - name: openms_featurefindersuperhirn owner: galaxyp @@ -990,249 +864,204 @@ tools: owner: galaxyp revisions: - 1a709ba66f2f - - d0c5325cb998 tool_panel_section_label: OpenMS - name: openms_featurefindermetabo owner: galaxyp revisions: - 2451315543f9 - - a49dde5a836e tool_panel_section_label: OpenMS - name: openms_fileconverter owner: galaxyp revisions: - 2a93a25f0599 - - 8b6336c903ef tool_panel_section_label: OpenMS - name: openms_peakpickerwavelet owner: galaxyp revisions: - 2077efa205de - - bf0b36140329 tool_panel_section_label: OpenMS - name: openms_peakpickerhires owner: galaxyp revisions: - - 401f500aae50 - 6b01678ec2fc tool_panel_section_label: OpenMS - name: openms_noisefiltergaussian owner: galaxyp revisions: - - 464f7877215b - 47982606f542 tool_panel_section_label: OpenMS - name: openms_noisefiltersgolay owner: galaxyp revisions: - - 35468667de97 - cf86c9091cb3 tool_panel_section_label: OpenMS - name: openms_filefilter owner: galaxyp revisions: - - 86a9dd43dd09 - fe4e4587d265 tool_panel_section_label: OpenMS - name: openms_baselinefilter owner: galaxyp revisions: - - 84bd73e60367 - ddbae9eb797e tool_panel_section_label: OpenMS - name: openms_fileinfo owner: galaxyp revisions: - 4af67edd5aef - - 5a45e6ac9aae tool_panel_section_label: OpenMS - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - 04892b463957 - - 17a48d0a80f4 - dd7bbc2b99d1 tool_panel_section_label: recetox-aplcms - name: recetox_aplcms_compute_template owner: recetox revisions: - 481d769e2f7a - - 4963811b6dec - - dfebc82ba1f0 tool_panel_section_label: recetox-aplcms - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - 6ba3526237e0 - - b3413f335327 - e7305ba0dd38 tool_panel_section_label: recetox-aplcms - name: recetox_aplcms_remove_noise owner: recetox revisions: - - b5a1f35abd8a - d90187b0f247 - - ffbabefbd2e2 tool_panel_section_label: recetox-aplcms - name: recetox_aplcms_correct_time owner: recetox revisions: - 02c772a49998 - - 1574b8a29e6f - - 9064aecc78a7 tool_panel_section_label: recetox-aplcms - name: recetox_aplcms_compute_clusters owner: recetox revisions: - 149b9cc7499b - - b9b19a74ac01 - - f3a18e020cdd tool_panel_section_label: recetox-aplcms - name: recetox_aplcms_align_features owner: recetox revisions: - - 79ad928a0dae - 7b42ee54d757 - - d5c638b72ce4 tool_panel_section_label: recetox-aplcms - name: recetox_aplcms_recover_weaker_signals owner: recetox revisions: - 99d118321d5f - - d7f5878a98c3 - - e0536ff73f36 tool_panel_section_label: recetox-aplcms - name: matchms_subsetting owner: recetox revisions: - - 6d2f2c565431 - a598091029ad - - cab0e4dcf372 tool_panel_section_label: matchms - name: matchms_metadata_merge owner: recetox revisions: - - 84ead993862c - ec25de0f0c58 - - fc1a698a71e8 tool_panel_section_label: matchms - name: matchms_add_key owner: recetox revisions: - - 1d10d32fa3b3 - 51da674b945d - - 7c5b86026e57 tool_panel_section_label: matchms - name: matchms_networking owner: recetox revisions: - - 1d74ae228df3 - 3cd1cf3034d1 - - ab8a33c370f5 tool_panel_section_label: matchms - name: matchms_metadata_match owner: recetox revisions: - 05a7fc94e66c - - 1d443ed476a1 - - 844d32c59314 tool_panel_section_label: matchms - name: matchms_spectral_similarity owner: recetox revisions: - - 26c92af1bd28 - 44e7027714d7 - - 7627b40601f6 tool_panel_section_label: matchms - name: matchms_metadata_export owner: recetox revisions: - - b576ed720711 - cbadbec49b5d - - dd49ef90297c tool_panel_section_label: matchms - name: matchms_fingerprint_similarity owner: recetox revisions: - 1d3ee4f9f63d - - ad9d2d1b2b8d - - d7b517f2c5fe tool_panel_section_label: matchms - name: matchms_convert owner: recetox revisions: - - 692471e62c68 - bff7bfcf975e - - c990df6afc24 tool_panel_section_label: matchms - name: matchms_filtering owner: recetox revisions: - - 00e66c401366 - - 07cac38cbd29 - da15e8ea3b28 tool_panel_section_label: matchms - name: matchms_remove_spectra owner: recetox revisions: - 80df426e7e47 - - c24ebd41dd53 - - fbe335d27d25 tool_panel_section_label: matchms - name: matchms_split owner: recetox revisions: - - 446fddefcee7 - - 500f473df7e4 - fc1bc38ede0b tool_panel_section_label: matchms - name: matchms_remove_key owner: recetox revisions: - 0a64e2bcce96 - - 19367db5cf3c - - 9d1b01d3fedd tool_panel_section_label: matchms - name: matchms_formatter owner: recetox revisions: - - 6501d0287dcd - - 9e3c83d2afc3 - f76a397afbe1 tool_panel_section_label: matchms - name: mfassignr_snplot owner: recetox - revisions: [] + revisions: + - 6a34bc7afd61 tool_panel_section_label: mfassignr - name: mfassignr_histnoise owner: recetox - revisions: [] + revisions: + - faf7108f3b48 tool_panel_section_label: mfassignr - name: mfassignr_kmdnoise owner: recetox - revisions: [] + revisions: + - f60df05dd038 tool_panel_section_label: mfassignr - name: mfassignr_isofiltr owner: recetox - revisions: [] + revisions: + - 079ae9aa6ed5 tool_panel_section_label: mfassignr - name: mfassignr_mfassign owner: recetox - revisions: [] + revisions: + - 5aa9380f397b tool_panel_section_label: mfassignr - name: mfassignr_mfassigncho owner: recetox - revisions: [] + revisions: + - 11949bd6837a tool_panel_section_label: mfassignr - name: mfassignr_recal owner: recetox - revisions: [] + revisions: + - 235878c45443 tool_panel_section_label: mfassignr - name: mfassignr_recallist owner: recetox - revisions: [] + revisions: + - 6e1813883a9a tool_panel_section_label: mfassignr - name: rcx_tk owner: recetox - revisions: [] + revisions: + - 54401f9d1a30 tool_panel_section_label: RECETOX From 8f66762d63f3ca0047b5da92b5bd32d0b01eca2d Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Fri, 16 Aug 2024 10:35:49 +0200 Subject: [PATCH 5/5] finished updates with fixed tools --- umsa_tool_list.yaml | 13 +++- umsa_tool_list.yaml.lock | 152 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 164 insertions(+), 1 deletion(-) diff --git a/umsa_tool_list.yaml b/umsa_tool_list.yaml index 55f6c82..5e6f76e 100644 --- a/umsa_tool_list.yaml +++ b/umsa_tool_list.yaml @@ -5,6 +5,17 @@ tools: revisions: - 90981f86000f tool_panel_section_label: Collection Operations +- name: compose_text_param + owner: iuc + revisions: + - e188c9826e0f + tool_panel_section_label: Text Manipulation +- name: split_file_to_collection + owner: bgruening + revisions: + - 6cbe2f30c2d7 + - 2dae863c8f42 + tool_panel_section_label: Collection Operations - name: scatterplot owner: devteam revisions: @@ -1027,9 +1038,9 @@ tools: tool_panel_section_label: matchms - name: mfassignr_snplot owner: recetox - tool_panel_section_label: mfassignr revisions: - 6a34bc7afd61 + tool_panel_section_label: mfassignr - name: mfassignr_histnoise owner: recetox tool_panel_section_label: mfassignr diff --git a/umsa_tool_list.yaml.lock b/umsa_tool_list.yaml.lock index 38f0e7e..e18f41b 100644 --- a/umsa_tool_list.yaml.lock +++ b/umsa_tool_list.yaml.lock @@ -5,6 +5,17 @@ tools: revisions: - 90981f86000f tool_panel_section_label: Collection Operations +- name: compose_text_param + owner: iuc + revisions: + - e188c9826e0f + tool_panel_section_label: Text Manipulation +- name: split_file_to_collection + owner: bgruening + revisions: + - 2dae863c8f42 + - 6cbe2f30c2d7 + tool_panel_section_label: Collection Operations - name: scatterplot owner: devteam revisions: @@ -13,31 +24,37 @@ tools: - name: ggplot2_violin owner: iuc revisions: + - 0e7290688b50 - dfd5d981b5a4 tool_panel_section_label: Visualization - name: ggplot2_heatmap owner: iuc revisions: + - 10515715c940 - 391a4cc45fea tool_panel_section_label: Visualization - name: ggplot2_pca owner: iuc revisions: - 7e616a1bdb07 + - b1268b7544d3 tool_panel_section_label: Visualization - name: ggplot2_histogram owner: iuc revisions: - 398e5104f8a2 + - b0d96516e6a5 tool_panel_section_label: Visualization - name: ggplot2_heatmap2 owner: iuc revisions: + - 374e9062d874 - ca7cb0eaad62 tool_panel_section_label: Visualization - name: ggplot2_point owner: iuc revisions: + - 3b12bf9b4b87 - e3a675da7fd0 tool_panel_section_label: Visualization - name: datamash_transpose @@ -49,6 +66,7 @@ tools: - name: diff owner: bgruening revisions: + - 156d0908e232 - 95a9dc82fc9a tool_panel_section_label: Text Manipulation - name: text_processing @@ -71,36 +89,43 @@ tools: owner: recetox revisions: - 3e2cb0bc6959 + - b5467dead5b1 tool_panel_section_label: RECETOX - name: xtb_molecular_optimization owner: recetox revisions: + - 6e1ef071fffc - d5633eaf3552 tool_panel_section_label: RECETOX - name: recetox_xmsannotator_advanced owner: recetox revisions: + - 6b5dec818827 - cfd2e19f00a9 tool_panel_section_label: RECETOX - name: waveica owner: recetox revisions: - 6480c6d5fa36 + - bf32ae95a06f tool_panel_section_label: RECETOX - name: ramclustr owner: recetox revisions: - 050cfef6ba65 + - da7722f665f4 tool_panel_section_label: RECETOX - name: rmassbank owner: recetox revisions: - 0b28816c1c2c + - 5a6bb93ec656 tool_panel_section_label: RECETOX - name: biotransformer owner: recetox revisions: - 0b86600b715e + - 6cd2a9e6ac49 tool_panel_section_label: RECETOX - name: spec2vec_training owner: recetox @@ -129,6 +154,7 @@ tools: owner: recetox revisions: - 25625114618e + - f2c1d0bbb074 tool_panel_section_label: RECETOX - name: msp_split owner: recetox @@ -138,6 +164,7 @@ tools: - name: filter_compounds owner: recetox revisions: + - 6c5df3eeb768 - 72b687d21f65 tool_panel_section_label: RECETOX - name: thermo_raw_file_converter @@ -153,6 +180,7 @@ tools: - name: camera_annotate owner: lecorguille revisions: + - 4b9ab71be05e - abf1775ac14d tool_panel_section_label: CAMERA - name: camera_combinexsannos @@ -163,17 +191,20 @@ tools: - name: rem_complex owner: recetox revisions: + - 60db8070a5c3 - a0e07a0bc047 tool_panel_section_label: ChemicalToolBox - name: openbabel_remions owner: bgruening revisions: - 4e3b2049a4d3 + - f70b83b730ac tool_panel_section_label: ChemicalToolBox - name: msconvert owner: galaxyp revisions: - 6153e8ada1ee + - ab6c14374bc0 tool_panel_section_label: ChemicalToolBox - name: smina owner: earlhaminst @@ -183,26 +214,31 @@ tools: - name: apoc owner: earlhaminst revisions: + - 451f90534945 - 67d2a6f3b4e3 tool_panel_section_label: ChemicalToolBox - name: parmconv owner: chemteam revisions: - 6c6cecf51bd0 + - 6d0677a148fe tool_panel_section_label: ChemicalToolBox - name: enumerate_charges owner: bgruening revisions: - 36360fa103d6 + - 67ee76f0e497 tool_panel_section_label: ChemicalToolBox - name: sdf_to_tab owner: bgruening revisions: + - 4beb3e026bbb - 55553120df69 tool_panel_section_label: ChemicalToolBox - name: fpocket owner: bgruening revisions: + - 4cc9d85c3bae - 4fb73be7f4cb tool_panel_section_label: ChemicalToolBox - name: chembl_structure_pipeline @@ -214,20 +250,24 @@ tools: owner: bgruening revisions: - 1d6fb7967ae9 + - a446ea7e2bc1 tool_panel_section_label: ChemicalToolBox - name: ambertools_parmchk2 owner: chemteam revisions: - 96b872138d3b + - ecc43bf27a49 tool_panel_section_label: ChemicalToolBox - name: ambertools_antechamber owner: chemteam revisions: - 29aa7091e533 + - 8a839e6a1e3e tool_panel_section_label: ChemicalToolBox - name: ambertools_acpype owner: chemteam revisions: + - 095ad4d096d1 - f4230f116196 tool_panel_section_label: ChemicalToolBox - name: mordred @@ -254,6 +294,7 @@ tools: owner: bgruening revisions: - 7a871df65202 + - 90ea16534012 tool_panel_section_label: ChemicalToolBox - name: autodock_vina_prepare_ligand owner: bgruening @@ -263,46 +304,55 @@ tools: - name: autodock_vina_prepare_box owner: bgruening revisions: + - 8f766d9652a2 - ad35eaa204ea tool_panel_section_label: ChemicalToolBox - name: openbabel_remduplicates owner: bgruening revisions: - 50ca8845e7f5 + - c5de6c19eb06 tool_panel_section_label: ChemicalToolBox - name: openbabel_addh owner: bgruening revisions: - 43167f164076 + - 7b6fd1c273cd tool_panel_section_label: ChemicalToolBox - name: openbabel_filter owner: bgruening revisions: + - 988085c7a0ea - ff2dd4b7d918 tool_panel_section_label: ChemicalToolBox - name: openbabel_subsearch owner: bgruening revisions: - 171c94786a56 + - 9adf3fae2771 tool_panel_section_label: ChemicalToolBox - name: openbabel_compound_convert owner: bgruening revisions: - 1c66bf08f687 + - 4242b4d68e9c tool_panel_section_label: ChemicalToolBox - name: openbabel_remove_protonation_state owner: bgruening revisions: + - 22a866858b81 - bf4e668b6690 tool_panel_section_label: ChemicalToolBox - name: openbabel_spectrophore_search owner: bgruening revisions: - afd14e10a318 + - f5d7ffbb2d33 tool_panel_section_label: ChemicalToolBox - name: openbabel_svg_depiction owner: bgruening revisions: + - 75ee9c410951 - d3b48303045b tool_panel_section_label: ChemicalToolBox - name: openbabel_multi_obgrep @@ -313,47 +363,56 @@ tools: - name: openbabel_genprop owner: bgruening revisions: + - 50eaae9df8d3 - a72ae2711a97 tool_panel_section_label: ChemicalToolBox - name: openbabel_change_title owner: bgruening revisions: - 3ecaa9634126 + - a638d8d13bb3 tool_panel_section_label: ChemicalToolBox - name: openbabel_obgrep owner: bgruening revisions: - 78640d0127ce + - 985ab0acd514 tool_panel_section_label: ChemicalToolBox - name: openbabel_remsmall owner: bgruening revisions: + - 81836d586797 - aebc671bae78 tool_panel_section_label: ChemicalToolBox - name: prepare_ligands_for_docking owner: bgruening revisions: - de4c80d17527 + - fac2c28b4c55 tool_panel_section_label: ChemicalToolBox - name: biomd_neqgamma owner: chemteam revisions: - 4f3222cb5cf6 + - afcb925def69 tool_panel_section_label: ChemicalToolBox - name: biomd_rmsd_clustering owner: chemteam revisions: - b001ebc8bf58 + - b9c46dbe9605 tool_panel_section_label: ChemicalToolBox - name: biomd_extract_clusters owner: chemteam revisions: - 078dfd7fb26d + - e0ecaf2d05fb tool_panel_section_label: ChemicalToolBox - name: fastpca owner: chemteam revisions: - 6f2029791c94 + - 9ca30ad95444 tool_panel_section_label: ChemicalToolBox - name: bio3d_dccm owner: chemteam @@ -383,21 +442,25 @@ tools: - name: mdanalysis_extract_rmsd owner: chemteam revisions: + - 589f8ef21e58 - 743bd6aa3c7a tool_panel_section_label: ChemicalToolBox - name: mdanalysis_ramachandran_protein owner: chemteam revisions: + - 060b9d9ec8cf - 0f270722aca6 tool_panel_section_label: ChemicalToolBox - name: mdanalysis_endtoend owner: chemteam revisions: - 78aa3659fcd1 + - 795a5996cdc8 tool_panel_section_label: ChemicalToolBox - name: mdanalysis_cosine_analysis owner: chemteam revisions: + - 48d6a6eb438b - a842da7ef42b tool_panel_section_label: ChemicalToolBox - name: vmd_hbonds @@ -409,30 +472,36 @@ tools: owner: chemteam revisions: - 4c36f5ad2799 + - b17ce46509ad tool_panel_section_label: ChemicalToolBox - name: mdanalysis_ramachandran_plot owner: chemteam revisions: - 70a2d548e62c + - be5eaea0b2d1 tool_panel_section_label: ChemicalToolBox - name: mdanalysis_distance owner: chemteam revisions: + - fd987ff06ceb - ffd6f8d159e1 tool_panel_section_label: ChemicalToolBox - name: mdanalysis_dihedral owner: chemteam revisions: + - 976cfd44b921 - aaa130695a2b tool_panel_section_label: ChemicalToolBox - name: mdanalysis_rdf owner: chemteam revisions: - 1a220575ad7a + - 49076afc90b1 tool_panel_section_label: ChemicalToolBox - name: mdanalysis_angle owner: chemteam revisions: + - 567f8c5d4680 - a0d210b9d287 tool_panel_section_label: ChemicalToolBox - name: packmol @@ -443,6 +512,7 @@ tools: - name: ctb_rdkit_descriptors owner: bgruening revisions: + - 0993ac4f4a23 - cf725c82c865 tool_panel_section_label: ChemicalToolBox - name: alchemical_analysis @@ -453,26 +523,31 @@ tools: - name: gmx_editconf owner: chemteam revisions: + - 88076940fa94 - bfb65cb551d8 tool_panel_section_label: ChemicalToolBox - name: gmx_makendx owner: chemteam revisions: - d9eb276dfa32 + - e3e536aa2633 tool_panel_section_label: ChemicalToolBox - name: gmx_restraints owner: chemteam revisions: + - 509aa136d4e3 - ca6a4740114e tool_panel_section_label: ChemicalToolBox - name: gmx_energy owner: chemteam revisions: - c8d2c0162b6e + - f26afd1b7104 tool_panel_section_label: ChemicalToolBox - name: gmx_trj owner: chemteam revisions: + - 32052c6c3310 - 9363254ef848 tool_panel_section_label: ChemicalToolBox - name: gmx_fep @@ -484,10 +559,12 @@ tools: owner: chemteam revisions: - a97dcfc23b4b + - c0c9a5024177 tool_panel_section_label: ChemicalToolBox - name: gmx_merge_topology_files owner: chemteam revisions: + - bc31d02be922 - ced8ec975548 tool_panel_section_label: ChemicalToolBox - name: gmx_nvt @@ -504,21 +581,25 @@ tools: owner: chemteam revisions: - 27ea4e1a3f95 + - c4fbab8e03c5 tool_panel_section_label: ChemicalToolBox - name: gmx_em owner: chemteam revisions: - 55918daa5651 + - b46d4b4d995c tool_panel_section_label: ChemicalToolBox - name: gmx_setup owner: chemteam revisions: + - 070e3ecc3fda - 4da9ee404eab tool_panel_section_label: ChemicalToolBox - name: md_converter owner: chemteam revisions: - 79e8ab8f1e81 + - d7ec25187599 tool_panel_section_label: ChemicalToolBox - name: gmx_npt owner: chemteam @@ -529,31 +610,37 @@ tools: owner: bgruening revisions: - 30c673b5b061 + - a84bcb007b09 tool_panel_section_label: ChemicalToolBox - name: qed owner: bgruening revisions: + - 52a8d34dd08f - fc45bf8b6e01 tool_panel_section_label: ChemicalToolBox - name: sucos_docking_scoring owner: bgruening revisions: + - 4f1896782f7c - fe318c648502 tool_panel_section_label: ChemicalToolBox - name: sucos_clustering owner: bgruening revisions: - 12725d4b90f3 + - b8725fec8c7b tool_panel_section_label: ChemicalToolBox - name: sucos_max_score owner: bgruening revisions: - 55ac04db36aa + - 9b48456a96fe tool_panel_section_label: ChemicalToolBox - name: openbabel_structure_distance_finder owner: bgruening revisions: - 4c9d6b47045c + - 8302ab092300 tool_panel_section_label: ChemicalToolBox - name: ctb_frankenstein_ligand owner: bgruening @@ -598,6 +685,7 @@ tools: - name: mmpbsa_mmgbsa owner: chemteam revisions: + - 608098b3668d - d09f116dfca5 tool_panel_section_label: ChemicalToolBox - name: ctb_im_pbf_ev @@ -669,51 +757,61 @@ tools: owner: lecorguille revisions: - 11ab2081bd4a + - 6de175c1f6ef tool_panel_section_label: XCMS - name: xcms_xcmsset owner: lecorguille revisions: + - 6550698fe60f - b02d1992a43a tool_panel_section_label: XCMS - name: xcms_summary owner: lecorguille revisions: - 018a9771de28 + - 444e3ed135e3 tool_panel_section_label: XCMS - name: xcms_retcor owner: lecorguille revisions: - aa252eec9229 + - d2b82d89f848 tool_panel_section_label: XCMS - name: xcms_plot_chromatogram owner: lecorguille revisions: - 024974037c4e + - c8bef8f6a1cb tool_panel_section_label: XCMS - name: xcms_merge owner: lecorguille revisions: - 5bd125a3f3b0 + - 6d475a389abc tool_panel_section_label: XCMS - name: xcms_group owner: lecorguille revisions: + - 71572faf938e - d45a786cbc40 tool_panel_section_label: XCMS - name: xcms_fillpeaks owner: lecorguille revisions: - 26d77e9ceb49 + - ec9aebabc1d2 tool_panel_section_label: XCMS - name: xcms_export_samplemetadata owner: lecorguille revisions: + - 4ea32e46b2d6 - 94eb263cfab4 tool_panel_section_label: XCMS - name: secimtools owner: malex revisions: - 2e7d47c0b027 + - caba07f41453 tool_panel_section_label: SECIMTools - name: metams_plot owner: workflow4metabolomics @@ -728,6 +826,7 @@ tools: - name: xcms_refine owner: workflow4metabolomics revisions: + - 090b33a9981c - 20f8ebc3a391 tool_panel_section_label: W4M - name: qualitymetrics @@ -763,57 +862,68 @@ tools: - name: mspurity_frag4feature owner: computational-metabolomics revisions: + - 174a523cb1da - e9fbb65451f6 tool_panel_section_label: msPurity - name: mspurity_spectralmatching owner: computational-metabolomics revisions: - 20f4fdaf36bb + - c33b92eeb1fb tool_panel_section_label: msPurity - name: mspurity_filterfragspectra owner: computational-metabolomics revisions: - 2e10c13085c9 + - a8842e5e75a7 tool_panel_section_label: msPurity - name: mspurity_puritya owner: computational-metabolomics revisions: + - 10e56e53668c - 55f1691db108 tool_panel_section_label: msPurity - name: mspurity_dimspredictpuritysingle owner: computational-metabolomics revisions: - 2ce66d2f6a24 + - 548fed2ef792 tool_panel_section_label: msPurity - name: mspurity_combineannotations owner: computational-metabolomics revisions: - d7104112fac6 + - f11c129a4227 tool_panel_section_label: msPurity - name: mspurity_purityx owner: computational-metabolomics revisions: + - 374022b7b469 - 942e676515fe tool_panel_section_label: msPurity - name: mspurity_createmsp owner: computational-metabolomics revisions: + - 3d92b95cf6c0 - 8512923bdd37 tool_panel_section_label: msPurity - name: mspurity_createdatabase owner: computational-metabolomics revisions: - 0cc6b67dccb8 + - 751b7378a683 tool_panel_section_label: msPurity - name: mspurity_averagefragspectra owner: computational-metabolomics revisions: - 94eb1fcfde88 + - ac284b969836 tool_panel_section_label: msPurity - name: mspurity_flagremove owner: computational-metabolomics revisions: - 69ed543767b2 + - da36e8bbcfbd tool_panel_section_label: msPurity - name: frag_hires_mass owner: ljocha @@ -849,11 +959,13 @@ tools: owner: galaxyp revisions: - 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