From 6f2776bb7d8d7ef3755fe3a01763e92ddf36f19b Mon Sep 17 00:00:00 2001 From: Zargham Ahmad Date: Mon, 25 Sep 2023 16:55:31 +0200 Subject: [PATCH] bump galaxy version --- tools/filter_compounds/macros.xml | 2 +- tools/matchms/matchms_filtering.xml | 2 +- tools/matchms/matchms_formatter.xml | 2 +- tools/matchms/matchms_metadata_export.xml | 2 +- tools/matchms/matchms_metadata_match.xml | 2 +- tools/matchms/matchms_networking.xml | 2 +- tools/matchms/matchms_similarity.xml | 2 +- tools/matchms/matchms_spectral_similarity.xml | 2 +- tools/msmetaenhancer/msmetaenhancer.xml | 2 +- tools/mzml_validator/mzml_validator.xml | 2 +- tools/ramclustr/ramclustr.xml | 2 +- tools/ramclustr/ramclustr_define_experiment.xml | 2 +- tools/recetox_aplcms/recetox_aplcms_align_features.xml | 2 +- tools/recetox_aplcms/recetox_aplcms_compute_clusters.xml | 2 +- tools/recetox_aplcms/recetox_aplcms_compute_template.xml | 2 +- tools/recetox_aplcms/recetox_aplcms_correct_time.xml | 2 +- tools/recetox_aplcms/recetox_aplcms_generate_feature_table.xml | 2 +- tools/recetox_aplcms/recetox_aplcms_merge_known_table.xml | 2 +- tools/recetox_aplcms/recetox_aplcms_recover_weaker_signals.xml | 2 +- tools/recetox_aplcms/recetox_aplcms_remove_noise.xml | 2 +- tools/riassigner/riassigner.xml | 2 +- tools/spec2vec/spec2vec_similarity.xml | 2 +- tools/spec2vec/spec2vec_training.xml | 2 +- 23 files changed, 23 insertions(+), 23 deletions(-) diff --git a/tools/filter_compounds/macros.xml b/tools/filter_compounds/macros.xml index 736a1c60..dc92bb4f 100644 --- a/tools/filter_compounds/macros.xml +++ b/tools/filter_compounds/macros.xml @@ -1,6 +1,6 @@ 3.1.1 - 1 + 2 + filter and normalize mass spectrometry data diff --git a/tools/matchms/matchms_formatter.xml b/tools/matchms/matchms_formatter.xml index bae8ab25..3ba3822d 100644 --- a/tools/matchms/matchms_formatter.xml +++ b/tools/matchms/matchms_formatter.xml @@ -1,4 +1,4 @@ - + reformat scores object of matchms to long format table diff --git a/tools/matchms/matchms_metadata_export.xml b/tools/matchms/matchms_metadata_export.xml index feba2226..43794c0f 100644 --- a/tools/matchms/matchms_metadata_export.xml +++ b/tools/matchms/matchms_metadata_export.xml @@ -1,4 +1,4 @@ - + extract all metadata from mass spectra file to tabular format macros.xml diff --git a/tools/matchms/matchms_metadata_match.xml b/tools/matchms/matchms_metadata_match.xml index 553d174e..20d84584 100644 --- a/tools/matchms/matchms_metadata_match.xml +++ b/tools/matchms/matchms_metadata_match.xml @@ -1,4 +1,4 @@ - + matchms metadata match calculation for numeric fields based on tolerance diff --git a/tools/matchms/matchms_networking.xml b/tools/matchms/matchms_networking.xml index b8c3b2d7..d0590fb6 100644 --- a/tools/matchms/matchms_networking.xml +++ b/tools/matchms/matchms_networking.xml @@ -1,4 +1,4 @@ - + create similarity network graph from matchms similarity scores diff --git a/tools/matchms/matchms_similarity.xml b/tools/matchms/matchms_similarity.xml index d196f0ff..a935f117 100644 --- a/tools/matchms/matchms_similarity.xml +++ b/tools/matchms/matchms_similarity.xml @@ -1,4 +1,4 @@ - + calculate the similarity score and matched peaks diff --git a/tools/matchms/matchms_spectral_similarity.xml b/tools/matchms/matchms_spectral_similarity.xml index d0d9c82e..bad57d74 100644 --- a/tools/matchms/matchms_spectral_similarity.xml +++ b/tools/matchms/matchms_spectral_similarity.xml @@ -1,4 +1,4 @@ - + matchms spectral similarity calculation diff --git a/tools/msmetaenhancer/msmetaenhancer.xml b/tools/msmetaenhancer/msmetaenhancer.xml index dbc39aa4..bd5a24ef 100644 --- a/tools/msmetaenhancer/msmetaenhancer.xml +++ b/tools/msmetaenhancer/msmetaenhancer.xml @@ -1,4 +1,4 @@ - + annotate MS data diff --git a/tools/mzml_validator/mzml_validator.xml b/tools/mzml_validator/mzml_validator.xml index c0118e2f..8638f0c2 100644 --- a/tools/mzml_validator/mzml_validator.xml +++ b/tools/mzml_validator/mzml_validator.xml @@ -1,4 +1,4 @@ - + validates mzML files against XML Schema Definition (XSD) + A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. macros.xml diff --git a/tools/ramclustr/ramclustr_define_experiment.xml b/tools/ramclustr/ramclustr_define_experiment.xml index 4c345d63..741029c8 100644 --- a/tools/ramclustr/ramclustr_define_experiment.xml +++ b/tools/ramclustr/ramclustr_define_experiment.xml @@ -1,4 +1,4 @@ - + Definition of experimental design used for record keeping and writing spectra data. macros.xml diff --git a/tools/recetox_aplcms/recetox_aplcms_align_features.xml b/tools/recetox_aplcms/recetox_aplcms_align_features.xml index 07facb4e..0b413e64 100644 --- a/tools/recetox_aplcms/recetox_aplcms_align_features.xml +++ b/tools/recetox_aplcms/recetox_aplcms_align_features.xml @@ -1,4 +1,4 @@ - + align peaks across samples macros.xml diff --git a/tools/recetox_aplcms/recetox_aplcms_compute_clusters.xml b/tools/recetox_aplcms/recetox_aplcms_compute_clusters.xml index 04592824..58d5d511 100644 --- a/tools/recetox_aplcms/recetox_aplcms_compute_clusters.xml +++ b/tools/recetox_aplcms/recetox_aplcms_compute_clusters.xml @@ -1,4 +1,4 @@ - + compute clusters of mz and rt across samples and assign cluster IDs to individual features macros.xml diff --git a/tools/recetox_aplcms/recetox_aplcms_compute_template.xml b/tools/recetox_aplcms/recetox_aplcms_compute_template.xml index 96882ddd..b9defd3c 100644 --- a/tools/recetox_aplcms/recetox_aplcms_compute_template.xml +++ b/tools/recetox_aplcms/recetox_aplcms_compute_template.xml @@ -1,4 +1,4 @@ - + compute retention time correction template feature table macros.xml diff --git a/tools/recetox_aplcms/recetox_aplcms_correct_time.xml b/tools/recetox_aplcms/recetox_aplcms_correct_time.xml index b9d0ef80..af187e52 100644 --- a/tools/recetox_aplcms/recetox_aplcms_correct_time.xml +++ b/tools/recetox_aplcms/recetox_aplcms_correct_time.xml @@ -1,4 +1,4 @@ - + correct retention time across samples for peak alignment macros.xml diff --git a/tools/recetox_aplcms/recetox_aplcms_generate_feature_table.xml b/tools/recetox_aplcms/recetox_aplcms_generate_feature_table.xml index 1345ff27..8cdbf2dc 100644 --- a/tools/recetox_aplcms/recetox_aplcms_generate_feature_table.xml +++ b/tools/recetox_aplcms/recetox_aplcms_generate_feature_table.xml @@ -1,4 +1,4 @@ - + generate feature table from noise-removed HRMS profile data macros.xml diff --git a/tools/recetox_aplcms/recetox_aplcms_merge_known_table.xml b/tools/recetox_aplcms/recetox_aplcms_merge_known_table.xml index 839da029..c6b026d5 100644 --- a/tools/recetox_aplcms/recetox_aplcms_merge_known_table.xml +++ b/tools/recetox_aplcms/recetox_aplcms_merge_known_table.xml @@ -1,4 +1,4 @@ - + join knowledge from aligned features and known table. macros.xml diff --git a/tools/recetox_aplcms/recetox_aplcms_recover_weaker_signals.xml b/tools/recetox_aplcms/recetox_aplcms_recover_weaker_signals.xml index 99e03f21..84342fb5 100644 --- a/tools/recetox_aplcms/recetox_aplcms_recover_weaker_signals.xml +++ b/tools/recetox_aplcms/recetox_aplcms_recover_weaker_signals.xml @@ -1,4 +1,4 @@ - + recover weaker signals from raw data using an aligned feature table macros.xml diff --git a/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml b/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml index f4e35414..1e8a01c3 100644 --- a/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml +++ b/tools/recetox_aplcms/recetox_aplcms_remove_noise.xml @@ -1,4 +1,4 @@ - + filter noise and detect peaks in high resolution mass spectrometry (HRMS) profile data macros.xml diff --git a/tools/riassigner/riassigner.xml b/tools/riassigner/riassigner.xml index d75c0884..ff00b08d 100644 --- a/tools/riassigner/riassigner.xml +++ b/tools/riassigner/riassigner.xml @@ -1,4 +1,4 @@ - + compute retention indices macros.xml diff --git a/tools/spec2vec/spec2vec_similarity.xml b/tools/spec2vec/spec2vec_similarity.xml index 3ae6607b..8965ff9d 100644 --- a/tools/spec2vec/spec2vec_similarity.xml +++ b/tools/spec2vec/spec2vec_similarity.xml @@ -1,4 +1,4 @@ - + macros.xml diff --git a/tools/spec2vec/spec2vec_training.xml b/tools/spec2vec/spec2vec_training.xml index b80cc09f..d38c6007 100644 --- a/tools/spec2vec/spec2vec_training.xml +++ b/tools/spec2vec/spec2vec_training.xml @@ -1,4 +1,4 @@ - + Train a Spec2Vec model for mass spectra similarity scoring