diff --git a/usegalaxy.org/metabolomics.yml b/usegalaxy.org/metabolomics.yml new file mode 100644 index 00000000..78ccca7a --- /dev/null +++ b/usegalaxy.org/metabolomics.yml @@ -0,0 +1,162 @@ +tool_panel_section_label: Metabolomics +tools: + # RECETOX Tools + - name: assign_ri_from_comment + owner: recetox + - name: biotransformer + owner: recetox + - name: gc_derivatization + owner: recetox + - name: isolib + owner: recetox + - name: matchms_add_key + owner: recetox + - name: matchms_convert + owner: recetox + - name: matchms_filtering + owner: recetox + - name: matchms_fingerprint_similarity + owner: recetox + - name: matchms_formatter + owner: recetox + - name: matchms_metadata_export + owner: recetox + - name: matchms_metadata_match + owner: recetox + - name: matchms_metadata_merge + owner: recetox + - name: matchms_networking + owner: recetox + - name: matchms_remove_key + owner: recetox + - name: matchms_remove_spectra + owner: recetox + - name: matchms_similarity + owner: recetox + - name: matchms_spectral_similarity + owner: recetox + - name: matchms_split + owner: recetox + - name: matchms_subsetting + owner: recetox + - name: msmetaenhancer + owner: recetox + - name: qcxms_neutral_run + owner: recetox + - name: qcxms_production_run + owner: recetox + - name: qcxms_getres + owner: recetox + - name: ramclustr + owner: recetox + - name: ramclustr_define_experiment + owner: recetox + - name: recetox_aplcms_generate_feature_table + owner: recetox + - name: recetox_aplcms_recover_weaker_signals + owner: recetox + - name: recetox_aplcms_correct_time + owner: recetox + - name: recetox_aplcms_compute_clusters + owner: recetox + - name: recetox_aplcms_remove_noise + owner: recetox + - name: recetox_aplcms_merge_known_table + owner: recetox + - name: recetox_aplcms_compute_template + owner: recetox + - name: recetox_aplcms_align_features + owner: recetox + - name: recetox_msfinder + owner: recetox + - name: recetox_xmsannotator_advanced + owner: recetox + - name: rename_annotated_feature + owner: recetox + - name: rem_complex + owner: recetox + - name: riassigner + owner: recetox + - name: rmassbank + owner: recetox + - name: spec2vec_similarity + owner: recetox + - name: spec2vec_training + owner: recetox + - name: use_theoretical_mz_annotations + owner: recetox + - name: waveica + owner: recetox + - name: xcms_plot_raw + owner: workflow4metabolomics + - name: xcms_plot_eic + owner: workflow4metabolomics + - name: xtb_molecular_optimization + owner: recetox + + # W4M Tools + ## CAMERA + - name: camera_combinexsannos + owner: mmonsoor + - name: camera_annotate + owner: lecorguille + + ## XCMS Suite + - name: msnbase_readmsdata + owner: lecorguille + - name: xcms_export_samplemetadata + owner: lecorguille + - name: xcms_fillpeaks + owner: lecorguille + - name: xcms_group + owner: lecorguille + - name: xcms_merge + owner: lecorguille + - name: xcms_plot_chromatogram + owner: lecorguille + - name: xcms_refine + owner: workflow4metabolomics + - name: xcms_retcor + owner: lecorguille + - name: xcms_summary + owner: lecorguille + - name: xcms_xcmsset + owner: lecorguille + + ## Stats + - name: anova + owner: lecorguille + - name: batchcorrection + owner: melpetera + - name: corr_table + owner: melpetera + - name: checkformat + owner: ethevenot + - name: heatmap + owner: ethevenot + - name: generic_filter + owner: melpetera + - name: idchoice + owner: melpetera + - name: intensity_checks + owner: melpetera + - name: multivariate + owner: ethevenot + - name: qualitymetrics + owner: ethevenot + - name: tablemerge + owner: melpetera + - name: transformation + owner: ethevenot + - name: withinvariation + owner: yguitton + - name: w4mclassfilter + owner: eschen42 + - name: w4mcorcov + owner: eschen42 + + # Other + - name: msconvert + owner: galaxyp + - name: thermo_raw_file_converter + owner: galaxyp \ No newline at end of file diff --git a/usegalaxy.org/metabolomics.yml.lock b/usegalaxy.org/metabolomics.yml.lock new file mode 100644 index 00000000..edbc50f1 --- /dev/null +++ b/usegalaxy.org/metabolomics.yml.lock @@ -0,0 +1,455 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Metabolomics +tools: +- name: assign_ri_from_comment + owner: recetox + revisions: + - 97ccdb1ba47c + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: biotransformer + owner: recetox + revisions: + - e5fcba090b10 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: gc_derivatization + owner: recetox + revisions: + - 600b391827e3 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: isolib + owner: recetox + revisions: + - 6b0fef8a77c0 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_add_key + owner: recetox + revisions: + - 1d10d32fa3b3 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_convert + owner: recetox + revisions: + - c990df6afc24 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_filtering + owner: recetox + revisions: + - 00e66c401366 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_fingerprint_similarity + owner: recetox + revisions: + - d7b517f2c5fe + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_formatter + owner: recetox + revisions: + - 9e3c83d2afc3 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_metadata_export + owner: recetox + revisions: + - b576ed720711 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_metadata_match + owner: recetox + revisions: + - 1d443ed476a1 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_metadata_merge + owner: recetox + revisions: + - 84ead993862c + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_networking + owner: recetox + revisions: + - 1d74ae228df3 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_remove_key + owner: recetox + revisions: + - 9d1b01d3fedd + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_remove_spectra + owner: recetox + revisions: + - fbe335d27d25 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_similarity + owner: recetox + revisions: + - 872d8040f713 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_spectral_similarity + owner: recetox + revisions: + - 7627b40601f6 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_split + owner: recetox + revisions: + - 500f473df7e4 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: matchms_subsetting + owner: recetox + revisions: + - 6d2f2c565431 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: msmetaenhancer + owner: recetox + revisions: + - b5467dead5b1 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: qcxms_neutral_run + owner: recetox + revisions: + - 8f465c0c3b6c + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: qcxms_production_run + owner: recetox + revisions: + - e97bfe7ac906 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: qcxms_getres + owner: recetox + revisions: + - 53dce0e49af7 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: ramclustr + owner: recetox + revisions: + - da7722f665f4 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: ramclustr_define_experiment + owner: recetox + revisions: + - f2c1d0bbb074 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: recetox_aplcms_generate_feature_table + owner: recetox + revisions: + - b3413f335327 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: recetox_aplcms_recover_weaker_signals + owner: recetox + revisions: + - d7f5878a98c3 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: recetox_aplcms_correct_time + owner: recetox + revisions: + - 9064aecc78a7 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: recetox_aplcms_compute_clusters + owner: recetox + revisions: + - f3a18e020cdd + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: recetox_aplcms_remove_noise + owner: recetox + revisions: + - ffbabefbd2e2 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: recetox_aplcms_merge_known_table + owner: recetox + revisions: + - 17a48d0a80f4 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: recetox_aplcms_compute_template + owner: recetox + revisions: + - dfebc82ba1f0 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: recetox_aplcms_align_features + owner: recetox + revisions: + - 79ad928a0dae + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: recetox_msfinder + owner: recetox + revisions: + - e7eff0c9baa3 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: recetox_xmsannotator_advanced + owner: recetox + revisions: + - 6b5dec818827 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: rename_annotated_feature + owner: recetox + revisions: + - 268fcec93d9c + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: rem_complex + owner: recetox + revisions: + - 60db8070a5c3 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: riassigner + owner: recetox + revisions: + - af25aa61c611 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: rmassbank + owner: recetox + revisions: + - 5a6bb93ec656 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: spec2vec_similarity + owner: recetox + revisions: + - 721a4e666191 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: spec2vec_training + owner: recetox + revisions: + - 9d917de87cca + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: use_theoretical_mz_annotations + owner: recetox + revisions: + - e0cac9994a72 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: waveica + owner: recetox + revisions: + - bf32ae95a06f + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_plot_raw + owner: workflow4metabolomics + revisions: + - 520448a32548 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_plot_eic + owner: workflow4metabolomics + revisions: + - 51015f22fcb7 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xtb_molecular_optimization + owner: recetox + revisions: + - 6e1ef071fffc + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: camera_combinexsannos + owner: mmonsoor + revisions: + - 961089e21ae2 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: camera_annotate + owner: lecorguille + revisions: + - 4b9ab71be05e + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: msnbase_readmsdata + owner: lecorguille + revisions: + - 6de175c1f6ef + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_export_samplemetadata + owner: lecorguille + revisions: + - 4ea32e46b2d6 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_fillpeaks + owner: lecorguille + revisions: + - ec9aebabc1d2 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_group + owner: lecorguille + revisions: + - 71572faf938e + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_merge + owner: lecorguille + revisions: + - 6d475a389abc + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_plot_chromatogram + owner: lecorguille + revisions: + - c8bef8f6a1cb + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_refine + owner: workflow4metabolomics + revisions: + - 090b33a9981c + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_retcor + owner: lecorguille + revisions: + - d2b82d89f848 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_summary + owner: lecorguille + revisions: + - 444e3ed135e3 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_xcmsset + owner: lecorguille + revisions: + - 6550698fe60f + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: anova + owner: lecorguille + revisions: + - 102049093b7d + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: batchcorrection + owner: melpetera + revisions: + - 23314e1192d4 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: corr_table + owner: melpetera + revisions: + - 2173ad5e7750 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: checkformat + owner: ethevenot + revisions: + - e7c5811ec12f + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: heatmap + owner: ethevenot + revisions: + - b1667c118127 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: generic_filter + owner: melpetera + revisions: + - cfd7c4aa5c26 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: idchoice + owner: melpetera + revisions: + - bb19b1d15732 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: intensity_checks + owner: melpetera + revisions: + - ec75de7f1e08 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: multivariate + owner: ethevenot + revisions: + - 5526f8258e8a + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: qualitymetrics + owner: ethevenot + revisions: + - acdf51018708 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: tablemerge + owner: melpetera + revisions: + - e44c5246247a + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: transformation + owner: ethevenot + revisions: + - cc0e9eff0de2 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: withinvariation + owner: yguitton + revisions: + - 5086ad0c0992 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: w4mclassfilter + owner: eschen42 + revisions: + - aae9fa9a7d4d + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: w4mcorcov + owner: eschen42 + revisions: + - 90708fdbc22d + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: msconvert + owner: galaxyp + revisions: + - 545054b15d7c + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: thermo_raw_file_converter + owner: galaxyp + revisions: + - 19e45916daf9 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics diff --git a/usegalaxy.org/training_metabolomics.yml b/usegalaxy.org/training_metabolomics.yml deleted file mode 100644 index ee7283a6..00000000 --- a/usegalaxy.org/training_metabolomics.yml +++ /dev/null @@ -1,42 +0,0 @@ -tool_panel_section_label: Metabolomics -tools: -- name: msconvert - owner: galaxyp -- name: msnbase_readmsdata - owner: lecorguille -- name: xcms_fillpeaks - owner: lecorguille -- name: xcms_group - owner: lecorguille -- name: xcms_merge - owner: lecorguille -- name: xcms_retcor - owner: lecorguille -- name: xcms_xcmsset - owner: lecorguille -- name: matchms - owner: recetox -- name: matchms_filtering - owner: recetox -- name: matchms_formatter - owner: recetox -- name: ramclustr - owner: recetox -- name: ramclustr_define_experiment - owner: recetox -- name: riassigner - owner: recetox -- name: waveica - owner: recetox -- name: camera_annotate - owner: lecorguille -- name: xcms_export_samplemetadata - owner: lecorguille -- name: xcms_plot_chromatogram - owner: lecorguille -- name: xcms_summary - owner: lecorguille -- name: idchoice - owner: melpetera -- name: intensity_checks - owner: melpetera \ No newline at end of file diff --git a/usegalaxy.org/training_metabolomics.yml.lock b/usegalaxy.org/training_metabolomics.yml.lock deleted file mode 100644 index 0978cf29..00000000 --- a/usegalaxy.org/training_metabolomics.yml.lock +++ /dev/null @@ -1,155 +0,0 @@ -install_repository_dependencies: true -install_resolver_dependencies: false -install_tool_dependencies: false -tools: -- name: msconvert - owner: galaxyp - revisions: - - 545054b15d7c - - 6153e8ada1ee - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: msnbase_readmsdata - owner: lecorguille - revisions: - - 11ab2081bd4a - - 12def6edac2f - - 6de175c1f6ef - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: xcms_fillpeaks - owner: lecorguille - revisions: - - 26d77e9ceb49 - - bb9ee352fce0 - - ec9aebabc1d2 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: xcms_group - owner: lecorguille - revisions: - - 2b676d5eb848 - - 71572faf938e - - d45a786cbc40 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: xcms_merge - owner: lecorguille - revisions: - - 58b5a4b6e1da - - 5bd125a3f3b0 - - 6d475a389abc - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: xcms_retcor - owner: lecorguille - revisions: - - 8242376d9f35 - - aa252eec9229 - - d2b82d89f848 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: xcms_xcmsset - owner: lecorguille - revisions: - - 6550698fe60f - - b02d1992a43a - - f5d51091cf84 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: matchms - owner: recetox - revisions: - - 4015f250a5a1 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: matchms_filtering - owner: recetox - revisions: - - 00e66c401366 - - 07cac38cbd29 - - 357df6c47d92 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: matchms_formatter - owner: recetox - revisions: - - 6501d0287dcd - - 715fe77be601 - - 9e3c83d2afc3 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: ramclustr - owner: recetox - revisions: - - 2ec9253a647e - - da7722f665f4 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: ramclustr_define_experiment - owner: recetox - revisions: - - 25625114618e - - f2c1d0bbb074 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: riassigner - owner: recetox - revisions: - - af25aa61c611 - - c702620c22b1 - - f6bf8f1f3224 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: waveica - owner: recetox - revisions: - - 071a424241ec - - 1a2aeb8137bf - - b77023c41c76 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: camera_annotate - owner: lecorguille - revisions: - - 4b9ab71be05e - - 512c2b701d96 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: xcms_export_samplemetadata - owner: lecorguille - revisions: - - 4ea32e46b2d6 - - 94eb263cfab4 - - cdab04a1d1d7 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: xcms_plot_chromatogram - owner: lecorguille - revisions: - - 024974037c4e - - 8846a03995d3 - - c8bef8f6a1cb - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: xcms_summary - owner: lecorguille - revisions: - - 018a9771de28 - - 2a2850fdf29e - - 444e3ed135e3 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: idchoice - owner: melpetera - revisions: - - bb19b1d15732 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics -- name: intensity_checks - owner: melpetera - revisions: - - a31f3f802b2b - - ec75de7f1e08 - tool_panel_section_id: metabolomics - tool_panel_section_label: Metabolomics