Mercurial > repos > recetox > matchms
diff matchms_wrapper.py @ 4:57959596262d draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 3c7f3cf3f925215a23b2f6665432c32b5ebdc2aa"
| author | recetox |
|---|---|
| date | Tue, 08 Jun 2021 11:28:40 +0000 |
| parents | a7c9fc186f8c |
| children | 672c22d7f004 |
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--- a/matchms_wrapper.py Wed May 19 11:45:29 2021 +0000 +++ b/matchms_wrapper.py Tue Jun 08 11:28:40 2021 +0000 @@ -15,7 +15,7 @@ def main(argv): parser = argparse.ArgumentParser(description="Compute MSP similarity scores") parser.add_argument( - "references_filename", type=str, help="Path to reference MSP library." + "--ref", type=str, dest="references_filename", help="Path to reference MSP library." ) parser.add_argument("queries_filename", type=str, help="Path to query spectra.") parser.add_argument("similarity_metric", type=str, help='Metric to use for matching.') @@ -27,8 +27,13 @@ args = parser.parse_args() - reference_spectra = load_from_msp(args.references_filename) - queries_spectra = load_from_msp(args.queries_filename) + queries_spectra = list(load_from_msp(args.queries_filename)) + if(args.references_filename): + reference_spectra = list(load_from_msp(args.references_filename)) + symmetric = False + else: + reference_spectra = queries_spectra.copy() + symmetric = True if args.similarity_metric == 'CosineGreedy': similarity_metric = CosineGreedy(args.tolerance, args.mz_power, args.intensity_power) @@ -45,6 +50,7 @@ references=list(reference_spectra), queries=list(queries_spectra), similarity_function=similarity_metric, + is_symmetric=symmetric ) query_names = [spectra.metadata['name'] for spectra in scores.queries]