From 12dcb61060152f7eabdae2ac968b39ed7a084653 Mon Sep 17 00:00:00 2001 From: hechth Date: Wed, 16 Jul 2025 14:52:21 +0200 Subject: [PATCH 1/3] added new tools and ran updates --- galaxy-umsa.grid.cesnet.cz/ipapy2.yml | 18 +++++++ galaxy-umsa.grid.cesnet.cz/ipapy2.yml.lock | 51 +++++++++++++++++++ galaxy-umsa.grid.cesnet.cz/matchms.yml.lock | 15 ++++++ galaxy-umsa.grid.cesnet.cz/pre_processing.yml | 2 + galaxy-umsa.grid.cesnet.cz/recetox.yml | 10 ++++ galaxy-umsa.grid.cesnet.cz/recetox.yml.lock | 7 +++ .../statistics.yml.lock | 1 + .../text_manipulation.yml.lock | 3 ++ .../visualization.yml.lock | 7 +++ galaxy-umsa.grid.cesnet.cz/w4m.yml.lock | 1 + 10 files changed, 115 insertions(+) create mode 100644 galaxy-umsa.grid.cesnet.cz/ipapy2.yml create mode 100644 galaxy-umsa.grid.cesnet.cz/ipapy2.yml.lock diff --git a/galaxy-umsa.grid.cesnet.cz/ipapy2.yml b/galaxy-umsa.grid.cesnet.cz/ipapy2.yml new file mode 100644 index 0000000..3c7f842 --- /dev/null +++ b/galaxy-umsa.grid.cesnet.cz/ipapy2.yml @@ -0,0 +1,18 @@ +tool_panel_section_label: ipapy2 +tools: +- name: ipapy2_clustering + owner: recetox +- name: ipapy2_compute_all_adducts + owner: recetox +- name: ipapy2_compute_bio + owner: recetox +- name: ipapy2_gibbs_sampler_add + owner: recetox +- name: ipapy2_gibbs_sampler + owner: recetox +- name: ipapy2_map_isotope_patterns + owner: recetox +- name: ipapy2_MS1_annotation + owner: recetox +- name: ipapy2_MS2_annotation + owner: recetox \ No newline at end of file diff --git a/galaxy-umsa.grid.cesnet.cz/ipapy2.yml.lock b/galaxy-umsa.grid.cesnet.cz/ipapy2.yml.lock new file mode 100644 index 0000000..0e30dfa --- /dev/null +++ b/galaxy-umsa.grid.cesnet.cz/ipapy2.yml.lock @@ -0,0 +1,51 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: ipapy2 +tools: +- name: ipapy2_clustering + owner: recetox + revisions: + - cb18b8fcb441 + tool_panel_section_id: ipapy2 + tool_panel_section_label: ipapy2 +- name: ipapy2_compute_all_adducts + owner: recetox + revisions: + - f85a6d4e44b0 + tool_panel_section_id: ipapy2 + tool_panel_section_label: ipapy2 +- name: ipapy2_compute_bio + owner: recetox + revisions: + - ca72f5330bc9 + tool_panel_section_id: ipapy2 + tool_panel_section_label: ipapy2 +- name: ipapy2_gibbs_sampler_add + owner: recetox + revisions: + - 428abc41a101 + tool_panel_section_id: ipapy2 + tool_panel_section_label: ipapy2 +- name: ipapy2_gibbs_sampler + owner: recetox + revisions: + - b2253cf7db76 + tool_panel_section_id: ipapy2 + tool_panel_section_label: ipapy2 +- name: ipapy2_map_isotope_patterns + owner: recetox + revisions: + - 774152f21f29 + tool_panel_section_id: ipapy2 + tool_panel_section_label: ipapy2 +- name: ipapy2_MS1_annotation + owner: recetox + revisions: [] + tool_panel_section_id: ipapy2 + tool_panel_section_label: ipapy2 +- name: ipapy2_MS2_annotation + owner: recetox + revisions: [] + tool_panel_section_id: ipapy2 + tool_panel_section_label: ipapy2 diff --git a/galaxy-umsa.grid.cesnet.cz/matchms.yml.lock b/galaxy-umsa.grid.cesnet.cz/matchms.yml.lock index 8a5b32f..72ead27 100644 --- a/galaxy-umsa.grid.cesnet.cz/matchms.yml.lock +++ b/galaxy-umsa.grid.cesnet.cz/matchms.yml.lock @@ -6,6 +6,7 @@ tools: owner: recetox revisions: - 5bbd1a8404f5 + - 6ac4a790adad - a598091029ad - cab0e4dcf372 tool_panel_section_id: matchms @@ -14,6 +15,7 @@ tools: owner: recetox revisions: - 1fd950c5586a + - e23c14cee5a9 - ec25de0f0c58 - fc1a698a71e8 tool_panel_section_id: matchms @@ -21,6 +23,7 @@ tools: - name: matchms_add_key owner: recetox revisions: + - 081390a8e739 - 51da674b945d - 7c5b86026e57 - a5d41764722d @@ -29,6 +32,7 @@ tools: - name: matchms_networking owner: recetox revisions: + - 131baa30af82 - 3cd1cf3034d1 - ab8a33c370f5 - f04b378325e5 @@ -40,6 +44,7 @@ tools: - 05a7fc94e66c - 330b0dfae8da - 844d32c59314 + - c86d265f6f5e tool_panel_section_id: matchms tool_panel_section_label: matchms - name: matchms_spectral_similarity @@ -47,12 +52,14 @@ tools: revisions: - 26c92af1bd28 - 44e7027714d7 + - 77d6425daa07 - 7ba589b01dbc tool_panel_section_id: matchms tool_panel_section_label: matchms - name: matchms_metadata_export owner: recetox revisions: + - 51205379251d - 8832425b1ff6 - cbadbec49b5d - dd49ef90297c @@ -64,11 +71,13 @@ tools: - 1d3ee4f9f63d - ad9d2d1b2b8d - fd890f162ce6 + - fe9f3cd0b8dd tool_panel_section_id: matchms tool_panel_section_label: matchms - name: matchms_convert owner: recetox revisions: + - 50836782d36f - 692471e62c68 - 9e83636da9d3 - bff7bfcf975e @@ -79,6 +88,7 @@ tools: revisions: - 07cac38cbd29 - 83c4b4359ac4 + - a6583110825c - da15e8ea3b28 tool_panel_section_id: matchms tool_panel_section_label: matchms @@ -86,6 +96,7 @@ tools: owner: recetox revisions: - 446fddefcee7 + - 6864944b00fd - ea6c5636c0cf - fc1bc38ede0b tool_panel_section_id: matchms @@ -94,6 +105,7 @@ tools: owner: recetox revisions: - 0a64e2bcce96 + - 10908b5bb7c8 - 19367db5cf3c - fbdb2ae524df tool_panel_section_id: matchms @@ -101,6 +113,7 @@ tools: - name: matchms_formatter owner: recetox revisions: + - 604131c54f97 - 6501d0287dcd - a5a5b147da70 - f76a397afbe1 @@ -109,6 +122,7 @@ tools: - name: matchms_remove_spectra owner: recetox revisions: + - 6fa0150f6172 - 80df426e7e47 - c24ebd41dd53 - d50ce2f51fc0 @@ -117,6 +131,7 @@ tools: - name: matchms_matchms_export_skyline_transition_list owner: recetox revisions: + - 535eadf882a3 - 8aa0014a5ad4 tool_panel_section_id: matchms tool_panel_section_label: matchms diff --git a/galaxy-umsa.grid.cesnet.cz/pre_processing.yml b/galaxy-umsa.grid.cesnet.cz/pre_processing.yml index 23bb020..59a89c1 100644 --- a/galaxy-umsa.grid.cesnet.cz/pre_processing.yml +++ b/galaxy-umsa.grid.cesnet.cz/pre_processing.yml @@ -5,4 +5,6 @@ tools: - name: bioconductor_msnbase_smooth_chromatogram owner: recetox - name: bioconductor_msnbase_smooth_mz + owner: receto +- name: bioconductor_mzr owner: recetox diff --git a/galaxy-umsa.grid.cesnet.cz/recetox.yml b/galaxy-umsa.grid.cesnet.cz/recetox.yml index 4217593..e170b4f 100644 --- a/galaxy-umsa.grid.cesnet.cz/recetox.yml +++ b/galaxy-umsa.grid.cesnet.cz/recetox.yml @@ -46,3 +46,13 @@ tools: owner: recetox - name: isolib owner: recetox +- name: wtv + owner: recetox +- name: mzspeclib_convert + owner: recetox +- name: mzspeclib_describe + owner: recetox +- name: mzspeclib_validate + owner: recetox +- name: mztabm_validate + owner: recetox \ No newline at end of file diff --git a/galaxy-umsa.grid.cesnet.cz/recetox.yml.lock b/galaxy-umsa.grid.cesnet.cz/recetox.yml.lock index 14a7c35..041a98e 100644 --- a/galaxy-umsa.grid.cesnet.cz/recetox.yml.lock +++ b/galaxy-umsa.grid.cesnet.cz/recetox.yml.lock @@ -21,6 +21,7 @@ tools: owner: recetox revisions: - 3e2cb0bc6959 + - 646ef66527da - b5467dead5b1 tool_panel_section_id: recetox tool_panel_section_label: RECETOX @@ -45,6 +46,7 @@ tools: - 071a424241ec - 1a2aeb8137bf - 6480c6d5fa36 + - 821062fc5782 - bf32ae95a06f tool_panel_section_id: recetox tool_panel_section_label: RECETOX @@ -53,6 +55,7 @@ tools: revisions: - 050cfef6ba65 - da7722f665f4 + - f52181a205d3 tool_panel_section_id: recetox tool_panel_section_label: RECETOX - name: rmassbank @@ -89,6 +92,7 @@ tools: owner: recetox revisions: - 25625114618e + - ef3cbcdf5f5d - f2c1d0bbb074 tool_panel_section_id: recetox tool_panel_section_label: RECETOX @@ -103,6 +107,7 @@ tools: owner: galaxyp revisions: - 19e45916daf9 + - 5c04f9decc01 tool_panel_section_id: recetox tool_panel_section_label: RECETOX - name: assign_ri_from_comment @@ -129,6 +134,7 @@ tools: owner: recetox revisions: - 54401f9d1a30 + - 9b4b624c4d60 tool_panel_section_id: recetox tool_panel_section_label: RECETOX - name: ms2deepscore_config_generator @@ -159,6 +165,7 @@ tools: - name: isolib owner: recetox revisions: + - 06f2d0d6d107 - 2b1118bce0b1 tool_panel_section_id: recetox tool_panel_section_label: RECETOX diff --git a/galaxy-umsa.grid.cesnet.cz/statistics.yml.lock b/galaxy-umsa.grid.cesnet.cz/statistics.yml.lock index 2a64411..bd9984e 100644 --- a/galaxy-umsa.grid.cesnet.cz/statistics.yml.lock +++ b/galaxy-umsa.grid.cesnet.cz/statistics.yml.lock @@ -5,6 +5,7 @@ tools: - name: intensity_checks owner: melpetera revisions: + - 2e580585782e - ec75de7f1e08 tool_panel_section_id: statistics tool_panel_section_label: Statistics diff --git a/galaxy-umsa.grid.cesnet.cz/text_manipulation.yml.lock b/galaxy-umsa.grid.cesnet.cz/text_manipulation.yml.lock index 86422ea..bfee01b 100644 --- a/galaxy-umsa.grid.cesnet.cz/text_manipulation.yml.lock +++ b/galaxy-umsa.grid.cesnet.cz/text_manipulation.yml.lock @@ -6,6 +6,7 @@ tools: owner: iuc revisions: - 22c2a1ac7ae3 + - a2667f8d23de - a513e3fbb4c5 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation @@ -23,6 +24,7 @@ tools: revisions: - 6073bb457ec0 - 86755160afbf + - c41d78ae5fee - ddf54b12c295 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation @@ -31,5 +33,6 @@ tools: revisions: - 3bf5661c0280 - 56a8da1f2243 + - cd36d6e45e29 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation diff --git a/galaxy-umsa.grid.cesnet.cz/visualization.yml.lock b/galaxy-umsa.grid.cesnet.cz/visualization.yml.lock index ddf58fa..264049e 100644 --- a/galaxy-umsa.grid.cesnet.cz/visualization.yml.lock +++ b/galaxy-umsa.grid.cesnet.cz/visualization.yml.lock @@ -13,6 +13,7 @@ tools: revisions: - 0e7290688b50 - 17b666467c32 + - 63d211052ffb - dfd5d981b5a4 tool_panel_section_id: visualization tool_panel_section_label: Visualization @@ -20,6 +21,7 @@ tools: owner: iuc revisions: - 10515715c940 + - 15cebddc6dba - 1a72f938213e - 391a4cc45fea tool_panel_section_id: visualization @@ -27,6 +29,7 @@ tools: - name: ggplot2_pca owner: iuc revisions: + - 1df3b30325dd - 7e616a1bdb07 - ae344ccf9d62 - b1268b7544d3 @@ -36,6 +39,7 @@ tools: owner: iuc revisions: - 398e5104f8a2 + - 6b9816a913de - 6fc8bab811da - b0d96516e6a5 tool_panel_section_id: visualization @@ -54,6 +58,7 @@ tools: revisions: - 5298e06f14f9 - e3a675da7fd0 + - f87634b12749 tool_panel_section_id: visualization tool_panel_section_label: Visualization - name: rcx_boxplot @@ -72,11 +77,13 @@ tools: owner: workflow4metabolomics revisions: - 51015f22fcb7 + - cbedca3ba6e1 tool_panel_section_id: visualization tool_panel_section_label: Visualization - name: xcms_plot_raw owner: workflow4metabolomics revisions: - 520448a32548 + - 8b8d360316c3 tool_panel_section_id: visualization tool_panel_section_label: Visualization diff --git a/galaxy-umsa.grid.cesnet.cz/w4m.yml.lock b/galaxy-umsa.grid.cesnet.cz/w4m.yml.lock index cc07b98..6298f9b 100644 --- a/galaxy-umsa.grid.cesnet.cz/w4m.yml.lock +++ b/galaxy-umsa.grid.cesnet.cz/w4m.yml.lock @@ -12,6 +12,7 @@ tools: - name: qualitymetrics owner: ethevenot revisions: + - 25c9349d1be9 - acdf51018708 tool_panel_section_id: w4m tool_panel_section_label: W4M From ade7d69c295c3b70cd7e8ed4bed9f8519901f316 Mon Sep 17 00:00:00 2001 From: hechth Date: Wed, 16 Jul 2025 15:09:38 +0200 Subject: [PATCH 2/3] fix --- galaxy-umsa.grid.cesnet.cz/pre_processing.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/galaxy-umsa.grid.cesnet.cz/pre_processing.yml b/galaxy-umsa.grid.cesnet.cz/pre_processing.yml index 59a89c1..9921650 100644 --- a/galaxy-umsa.grid.cesnet.cz/pre_processing.yml +++ b/galaxy-umsa.grid.cesnet.cz/pre_processing.yml @@ -5,6 +5,6 @@ tools: - name: bioconductor_msnbase_smooth_chromatogram owner: recetox - name: bioconductor_msnbase_smooth_mz - owner: receto + owner: recetox - name: bioconductor_mzr owner: recetox From 0ce43a52e8d76c15b1bbbeda8e30765b06f5dd68 Mon Sep 17 00:00:00 2001 From: hechth Date: Wed, 16 Jul 2025 15:21:56 +0200 Subject: [PATCH 3/3] fixed the ipapy2 annotation tools --- galaxy-umsa.grid.cesnet.cz/ipapy2.yml | 4 ++-- galaxy-umsa.grid.cesnet.cz/ipapy2.yml.lock | 10 ++++++---- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/galaxy-umsa.grid.cesnet.cz/ipapy2.yml b/galaxy-umsa.grid.cesnet.cz/ipapy2.yml index 3c7f842..251ca5e 100644 --- a/galaxy-umsa.grid.cesnet.cz/ipapy2.yml +++ b/galaxy-umsa.grid.cesnet.cz/ipapy2.yml @@ -12,7 +12,7 @@ tools: owner: recetox - name: ipapy2_map_isotope_patterns owner: recetox -- name: ipapy2_MS1_annotation +- name: ipapy2_ms1_annotation owner: recetox -- name: ipapy2_MS2_annotation +- name: ipapy2_ms2_annotation owner: recetox \ No newline at end of file diff --git a/galaxy-umsa.grid.cesnet.cz/ipapy2.yml.lock b/galaxy-umsa.grid.cesnet.cz/ipapy2.yml.lock index 0e30dfa..181fe5a 100644 --- a/galaxy-umsa.grid.cesnet.cz/ipapy2.yml.lock +++ b/galaxy-umsa.grid.cesnet.cz/ipapy2.yml.lock @@ -39,13 +39,15 @@ tools: - 774152f21f29 tool_panel_section_id: ipapy2 tool_panel_section_label: ipapy2 -- name: ipapy2_MS1_annotation +- name: ipapy2_ms1_annotation owner: recetox - revisions: [] + revisions: + - 7f84a8a5edde tool_panel_section_id: ipapy2 tool_panel_section_label: ipapy2 -- name: ipapy2_MS2_annotation +- name: ipapy2_ms2_annotation owner: recetox - revisions: [] + revisions: + - 6a23970e8093 tool_panel_section_id: ipapy2 tool_panel_section_label: ipapy2