Mercurial > repos > recetox > matchms_fingerprint_similarity
annotate matchms_filtering_wrapper.py @ 7:cbfd7c35e0a4 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
author | recetox |
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date | Mon, 04 Dec 2023 19:15:40 +0000 |
parents | df85b26201d1 |
children | f87b1c271012 |
rev | line source |
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84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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1 import argparse |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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2 import sys |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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3 |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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4 from matchms.exporting import save_as_mgf, save_as_msp |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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5 from matchms.filtering import add_compound_name, add_fingerprint, add_losses, add_parent_mass, add_precursor_mz,\ |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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6 add_retention_index, add_retention_time, clean_compound_name |
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df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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7 from matchms.filtering import default_filters, normalize_intensities, reduce_to_number_of_peaks, select_by_mz, \ |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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8 select_by_relative_intensity |
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84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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9 from matchms.importing import load_from_mgf, load_from_msp |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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10 |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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11 |
1
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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12 def require_key(spectrum, key): |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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13 if spectrum.get(key): |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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14 return spectrum |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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15 |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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16 return None |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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17 |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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18 |
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84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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19 def main(argv): |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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20 parser = argparse.ArgumentParser(description="Compute MSP similarity scores") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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21 parser.add_argument("--spectra", type=str, required=True, help="Mass spectra file to be filtered.") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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22 parser.add_argument("--spectra_format", type=str, required=True, help="Format of spectra file.") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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23 parser.add_argument("--output", type=str, required=True, help="Filtered mass spectra file.") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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24 parser.add_argument("-normalise_intensities", action='store_true', |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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25 help="Normalize intensities of peaks (and losses) to unit height.") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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26 parser.add_argument("-default_filters", action='store_true', |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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27 help="Collection of filters that are considered default and that do no require any (factory) arguments.") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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28 parser.add_argument("-clean_metadata", action='store_true', |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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29 help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata.") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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30 parser.add_argument("-relative_intensity", action='store_true', |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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31 help="Keep only peaks within set relative intensity range (keep if to_intensity >= intensity >= from_intensity).") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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32 parser.add_argument("--from_intensity", type=float, help="Lower bound for intensity filter") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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33 parser.add_argument("--to_intensity", type=float, help="Upper bound for intensity filter") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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34 parser.add_argument("-mz_range", action='store_true', |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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35 help="Keep only peaks between set m/z range (keep if to_mz >= m/z >= from_mz).") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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36 parser.add_argument("--from_mz", type=float, help="Lower bound for m/z filter") |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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37 parser.add_argument("--to_mz", type=float, help="Upper bound for m/z filter") |
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df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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38 parser.add_argument("-require_smiles", action='store_true', |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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39 help="Remove spectra that does not contain SMILES.") |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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40 parser.add_argument("-require_inchi", action='store_true', |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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41 help="Remove spectra that does not contain INCHI.") |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
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42 parser.add_argument("-reduce_to_top_n_peaks", action='store_true', |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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43 help="reduce to top n peaks filter.") |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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44 parser.add_argument("--n_max", type=int, help="Maximum number of peaks. Remove peaks if more peaks are found.") |
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84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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45 args = parser.parse_args() |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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46 |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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47 if not (args.normalise_intensities |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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48 or args.default_filters |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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49 or args.clean_metadata |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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50 or args.relative_intensity |
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df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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51 or args.mz_range |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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52 or args.require_smiles |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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53 or args.require_inchi |
df85b26201d1
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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54 or args.reduce_to_top_n_peaks): |
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84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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55 raise ValueError('No filter selected.') |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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56 |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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57 if args.spectra_format == 'msp': |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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58 spectra = list(load_from_msp(args.spectra)) |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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59 elif args.queries_format == 'mgf': |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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60 spectra = list(load_from_mgf(args.spectra)) |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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61 else: |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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62 raise ValueError(f'File format {args.spectra_format} not supported for mass spectra file.') |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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63 |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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64 filtered_spectra = [] |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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65 for spectrum in spectra: |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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66 if args.normalise_intensities: |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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67 spectrum = normalize_intensities(spectrum) |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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68 |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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69 if args.default_filters: |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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70 spectrum = default_filters(spectrum) |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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71 |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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72 if args.clean_metadata: |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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73 filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_losses, add_parent_mass, |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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74 add_retention_index, add_retention_time, clean_compound_name] |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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75 for metadata_filter in filters: |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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76 spectrum = metadata_filter(spectrum) |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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77 |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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78 if args.relative_intensity: |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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79 spectrum = select_by_relative_intensity(spectrum, args.from_intensity, args.to_intensity) |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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80 |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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81 if args.mz_range: |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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82 spectrum = select_by_mz(spectrum, args.from_mz, args.to_mz) |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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83 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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84 if args.reduce_to_top_n_peaks: |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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85 spectrum = reduce_to_number_of_peaks(spectrum_in=spectrum, n_max=args.n_max) |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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86 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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87 if args.require_smiles and spectrum is not None: |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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88 spectrum = require_key(spectrum, "smiles") |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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89 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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90 if args.require_inchi and spectrum is not None: |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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91 spectrum = require_key(spectrum, "inchi") |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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92 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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93 if spectrum is not None: |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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94 filtered_spectra.append(spectrum) |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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95 |
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96 if args.spectra_format == 'msp': |
84af792d3a78
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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97 save_as_msp(filtered_spectra, args.output) |
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98 else: |
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99 save_as_mgf(filtered_spectra, args.output) |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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100 |
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101 return 0 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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102 |
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103 |
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104 if __name__ == "__main__": |
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105 main(argv=sys.argv[1:]) |