Mercurial > repos > recetox > matchms_filtering
diff matchms_filtering_wrapper.py @ 22:00e66c401366 draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8db07edd3b0d2ff778036dec410027ad58365488
author | recetox |
---|---|
date | Mon, 15 Jul 2024 08:00:24 +0000 |
parents | 86d265d2a334 |
children |
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--- a/matchms_filtering_wrapper.py Tue Jun 04 07:11:49 2024 +0000 +++ b/matchms_filtering_wrapper.py Mon Jul 15 08:00:24 2024 +0000 @@ -2,7 +2,7 @@ import sys from matchms.exporting import save_as_mgf, save_as_msp -from matchms.filtering import add_compound_name, add_fingerprint, add_losses, add_parent_mass, add_precursor_mz, \ +from matchms.filtering import add_compound_name, add_fingerprint, add_parent_mass, add_precursor_mz, \ add_retention_index, add_retention_time, clean_compound_name from matchms.filtering import default_filters, normalize_intensities, reduce_to_number_of_peaks, select_by_mz, \ select_by_relative_intensity @@ -16,7 +16,7 @@ parser.add_argument("--spectra_format", type=str, required=True, help="Format of spectra file.") parser.add_argument("--output", type=str, required=True, help="Filtered mass spectra file.") parser.add_argument("-normalise_intensities", action='store_true', - help="Normalize intensities of peaks (and losses) to unit height.") + help="Normalize intensities of peaks to unit height.") parser.add_argument("-default_filters", action='store_true', help="Collection of filters that are considered default and that do no require any (factory) arguments.") parser.add_argument("-clean_metadata", action='store_true', @@ -62,7 +62,7 @@ spectrum = default_filters(spectrum) if args.clean_metadata: - filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_losses, add_parent_mass, + filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_parent_mass, add_retention_index, add_retention_time, clean_compound_name] for metadata_filter in filters: spectrum = metadata_filter(spectrum)