Mercurial > repos > recetox > matchms_remove_spectra
comparison matchms_remove_spectra.xml @ 1:c24ebd41dd53 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 2abca9206b76bf42e6322d751ed3a31a6cc003a4
| author | recetox |
|---|---|
| date | Tue, 04 Jun 2024 07:10:48 +0000 |
| parents | 80df426e7e47 |
| children | fbe335d27d25 |
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| 0:80df426e7e47 | 1:c24ebd41dd53 |
|---|---|
| 1 <tool id="matchms_remove_spectra" name="matchms remove spectra" version="@TOOL_VERSION@+galaxy0" profile="21.09"> | 1 <tool id="matchms_remove_spectra" name="matchms remove spectra" version="@TOOL_VERSION@+galaxy1" profile="21.09"> |
| 2 <description>Filters spectra based on metadata presence</description> | 2 <description>Filters spectra based on metadata presence</description> |
| 3 | 3 |
| 4 <macros> | 4 <macros> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 26 from matchms.filtering.filter_utils.smile_inchi_inchikey_conversions import is_valid_inchi, is_valid_smiles, is_valid_inchikey | 26 from matchms.filtering.filter_utils.smile_inchi_inchikey_conversions import is_valid_inchi, is_valid_smiles, is_valid_inchikey |
| 27 from matchms.filtering import require_compound_name, require_formula, require_precursor_mz, \ | 27 from matchms.filtering import require_compound_name, require_formula, require_precursor_mz, \ |
| 28 require_retention_time, require_retention_index, require_valid_annotation | 28 require_retention_time, require_retention_index, require_valid_annotation |
| 29 from matchms.importing import load_from_mgf, load_from_msp | 29 from matchms.importing import load_from_mgf, load_from_msp |
| 30 | 30 |
| 31 #set metadata_fields = str("', '").join([str($f) for $f in $metadata_fields]) | 31 #set metadata_fields = [str($f) for $f in $metadata_fields] |
| 32 required_metadata = "$metadata_fields" | 32 required_metadata = [x for x in $metadata_fields] |
| 33 | |
| 34 if "$spectra.ext" == "msp": | 33 if "$spectra.ext" == "msp": |
| 35 spectra = list(load_from_msp("${spectra}")) | 34 spectra = list(load_from_msp("${spectra}")) |
| 36 elif "$spectra.ext" == 'mgf': | 35 elif "$spectra.ext" == 'mgf': |
| 37 spectra = list(load_from_mgf("${spectra}")) | 36 spectra = list(load_from_mgf("${spectra}")) |
| 38 else: | 37 else: |
| 39 raise ValueError(f'File format {$spectra.ext} not supported for mass spectra file.') | 38 raise ValueError(f'File format {$spectra.ext} not supported for mass spectra file.') |
| 40 | 39 |
| 41 filtered_spectra = [] | 40 filtered_spectra = [] |
| 42 removed_spectra = [] | 41 removed_spectra = [] |
| 43 keep = False | |
| 44 | 42 |
| 45 for spectrum in spectra: | 43 for spectrum in spectra: |
| 44 keep = True | |
| 45 | |
| 46 if 'smiles' in required_metadata: | 46 if 'smiles' in required_metadata: |
| 47 keep = is_valid_smiles(spectrum.get('smiles')) | 47 keep = keep and is_valid_smiles(spectrum.get('smiles', '').strip()) |
| 48 | 48 |
| 49 if 'inchi' in required_metadata: | 49 if 'inchi' in required_metadata: |
| 50 keep = is_valid_inchi(spectrum.get('inchi')) | 50 keep = keep and is_valid_inchi(spectrum.get('inchi', '').strip()) |
| 51 | 51 |
| 52 if 'inchikey' in required_metadata: | 52 if 'inchikey' in required_metadata: |
| 53 keep = is_valid_inchikey(spectrum.get('inchikey')) | 53 inchikey = spectrum.get('inchikey', '') |
| 54 keep = keep and is_valid_inchikey(inchikey.strip()) | |
| 54 | 55 |
| 55 if 'precursor_mz' in required_metadata: | 56 if 'precursor_mz' in required_metadata: |
| 56 result = require_precursor_mz(spectrum) | 57 result = require_precursor_mz(spectrum) |
| 57 if result is not None: | 58 keep = keep and result is not None |
| 58 keep = True | |
| 59 else: | |
| 60 keep = False | |
| 61 | 59 |
| 62 if 'valid_annotation' in required_metadata: | 60 if 'valid_annotation' in required_metadata: |
| 63 result = require_valid_annotation(spectrum) | 61 result = require_valid_annotation(spectrum) |
| 64 if result is not None: | 62 keep = keep and result is not None |
| 65 keep = True | 63 |
| 66 else: | |
| 67 keep = False | |
| 68 | |
| 69 if 'formula' in required_metadata: | 64 if 'formula' in required_metadata: |
| 70 result = require_formula(spectrum) | 65 result = require_formula(spectrum) |
| 71 if result is not None: | 66 keep = keep and result is not None |
| 72 keep = True | |
| 73 else: | |
| 74 keep = False | |
| 75 | 67 |
| 76 if 'compound_name' in required_metadata: | 68 if 'compound_name' in required_metadata: |
| 77 result = require_compound_name(spectrum) | 69 result = require_compound_name(spectrum) |
| 78 if result is not None: | 70 keep = keep and result is not None |
| 79 keep = True | 71 |
| 80 else: | |
| 81 keep = False | |
| 82 | |
| 83 if 'retention_time' in required_metadata: | 72 if 'retention_time' in required_metadata: |
| 84 result = require_retention_time(spectrum) | 73 result = require_retention_time(spectrum) |
| 85 if result is not None: | 74 keep = keep and result is not None |
| 86 keep = True | |
| 87 else: | |
| 88 keep = False | |
| 89 | 75 |
| 90 if 'retention_index' in required_metadata: | 76 if 'retention_index' in required_metadata: |
| 91 result = require_retention_index(spectrum) | 77 result = require_retention_index(spectrum) |
| 92 if result is not None: | 78 if result is not None: |
| 93 keep = True | 79 keep = keep and float(result.get('retention_index', 0)) > 0 |
| 94 else: | 80 else: |
| 95 keep = False | 81 keep = False |
| 96 | 82 |
| 97 if keep: | 83 if keep: |
| 98 filtered_spectra.append(spectrum) | 84 filtered_spectra.append(spectrum) |