Mercurial > repos > recetox > matchms_filtering
comparison 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 |
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date | Mon, 15 Jul 2024 08:00:24 +0000 |
parents | 86d265d2a334 |
children |
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21:07cac38cbd29 | 22:00e66c401366 |
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1 import argparse | 1 import argparse |
2 import sys | 2 import sys |
3 | 3 |
4 from matchms.exporting import save_as_mgf, save_as_msp | 4 from matchms.exporting import save_as_mgf, save_as_msp |
5 from matchms.filtering import add_compound_name, add_fingerprint, add_losses, add_parent_mass, add_precursor_mz, \ | 5 from matchms.filtering import add_compound_name, add_fingerprint, add_parent_mass, add_precursor_mz, \ |
6 add_retention_index, add_retention_time, clean_compound_name | 6 add_retention_index, add_retention_time, clean_compound_name |
7 from matchms.filtering import default_filters, normalize_intensities, reduce_to_number_of_peaks, select_by_mz, \ | 7 from matchms.filtering import default_filters, normalize_intensities, reduce_to_number_of_peaks, select_by_mz, \ |
8 select_by_relative_intensity | 8 select_by_relative_intensity |
9 from matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass import derive_precursor_mz_from_parent_mass | 9 from matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass import derive_precursor_mz_from_parent_mass |
10 from matchms.importing import load_from_mgf, load_from_msp | 10 from matchms.importing import load_from_mgf, load_from_msp |
14 parser = argparse.ArgumentParser(description="Compute MSP similarity scores") | 14 parser = argparse.ArgumentParser(description="Compute MSP similarity scores") |
15 parser.add_argument("--spectra", type=str, required=True, help="Mass spectra file to be filtered.") | 15 parser.add_argument("--spectra", type=str, required=True, help="Mass spectra file to be filtered.") |
16 parser.add_argument("--spectra_format", type=str, required=True, help="Format of spectra file.") | 16 parser.add_argument("--spectra_format", type=str, required=True, help="Format of spectra file.") |
17 parser.add_argument("--output", type=str, required=True, help="Filtered mass spectra file.") | 17 parser.add_argument("--output", type=str, required=True, help="Filtered mass spectra file.") |
18 parser.add_argument("-normalise_intensities", action='store_true', | 18 parser.add_argument("-normalise_intensities", action='store_true', |
19 help="Normalize intensities of peaks (and losses) to unit height.") | 19 help="Normalize intensities of peaks to unit height.") |
20 parser.add_argument("-default_filters", action='store_true', | 20 parser.add_argument("-default_filters", action='store_true', |
21 help="Collection of filters that are considered default and that do no require any (factory) arguments.") | 21 help="Collection of filters that are considered default and that do no require any (factory) arguments.") |
22 parser.add_argument("-clean_metadata", action='store_true', | 22 parser.add_argument("-clean_metadata", action='store_true', |
23 help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata.") | 23 help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata.") |
24 parser.add_argument("-relative_intensity", action='store_true', | 24 parser.add_argument("-relative_intensity", action='store_true', |
60 | 60 |
61 if args.default_filters: | 61 if args.default_filters: |
62 spectrum = default_filters(spectrum) | 62 spectrum = default_filters(spectrum) |
63 | 63 |
64 if args.clean_metadata: | 64 if args.clean_metadata: |
65 filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_losses, add_parent_mass, | 65 filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_parent_mass, |
66 add_retention_index, add_retention_time, clean_compound_name] | 66 add_retention_index, add_retention_time, clean_compound_name] |
67 for metadata_filter in filters: | 67 for metadata_filter in filters: |
68 spectrum = metadata_filter(spectrum) | 68 spectrum = metadata_filter(spectrum) |
69 | 69 |
70 if args.relative_intensity: | 70 if args.relative_intensity: |