| Previous changeset 1:4aecfd6b319b (2021-03-17) Next changeset 3:72adeb3ca264 (2021-05-19) |
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Commit message:
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 557e6558b93e63fd0b70443164d2d624cc05c319" |
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modified:
matchms.xml matchms_wrapper.py |
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| diff -r 4aecfd6b319b -r a7c9fc186f8c matchms.xml --- a/matchms.xml Wed Mar 17 11:40:17 2021 +0000 +++ b/matchms.xml Mon Apr 19 08:31:42 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="matchms" name="matchMS" version="0.8.2+galaxy2"> +<tool id="matchms" name="matchMS" version="0.8.2+galaxy3"> <requirements> <requirement type="package" version="0.8.2">matchms</requirement> <requirement type="package" version="1.1.4">pandas</requirement> @@ -9,8 +9,8 @@ </environment_variables> <command detect_errors="exit_code"><![CDATA[ - python3 ${__tool_directory__}/matchms_wrapper.py "$references" "$queries" "$similarity_metric" "$similarity_scores" "$similarity_matches" - ]]> </command> + python3 ${__tool_directory__}/matchms_wrapper.py "$references" "$queries" "$similarity_metric" "$similarity_scores" "$similarity_matches" "$algorithm.tolerance" "$algorithm.mz_power" "$algorithm.intensity_power" + ]]> </command> <inputs> <param label="Reference spectra" name="references" type="data" format="msp" help="Reference mass spectra to match against as library." /> @@ -18,8 +18,13 @@ <param label="Similarity metric" name="similarity_metric" type="select" display="radio" help="Similarity metric to use for score computation."> <option value="CosineGreedy" selected="true">CosineGreedy</option> <option value="CosineHungarian">CosineHungarian</option> - <option value="IntersectMz">IntersectMz</option> </param> + + <section name="algorithm" title="Algorithm Parameters" expanded="true"> + <param label="tolerance" name="tolerance" type="float" value="0.1" help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm." /> + <param label="mz_power" name="mz_power" type="float" value="0.0" help="The power to raise mz to in the cosine function." /> + <param label="intensity_power" name="intensity_power" type="float" value="1.0" help="The power to raise intensity to in the cosine function." /> + </section> </inputs> <outputs> @@ -64,8 +69,6 @@ | RAMClustR | Mass spectra | msp | queries | +-----------+---------------+--------+-----------+ - RAMClustR outputs a collection of **msp** files which can be matched to a library (.msp) using a similarity score computed in matchMS. - Downstream Tools The **output** is a csv which contains the similarity score and second csv containing the number of matched peaks. ]]></help> |
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| diff -r 4aecfd6b319b -r a7c9fc186f8c matchms_wrapper.py --- a/matchms_wrapper.py Wed Mar 17 11:40:17 2021 +0000 +++ b/matchms_wrapper.py Mon Apr 19 08:31:42 2021 +0000 |
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| @@ -2,14 +2,12 @@ import sys from matchms import calculate_scores +from matchms.filtering import add_precursor_mz from matchms.importing import load_from_msp from matchms.similarity import ( CosineGreedy, CosineHungarian, - FingerprintSimilarity, - IntersectMz, ModifiedCosine, - ParentMassMatch ) from pandas import DataFrame @@ -23,30 +21,29 @@ parser.add_argument("similarity_metric", type=str, help='Metric to use for matching.') parser.add_argument("output_filename_scores", type=str, help="Path where to store the output .csv scores.") parser.add_argument("output_filename_matches", type=str, help="Path where to store the output .csv matches.") + parser.add_argument("tolerance", type=float, help="Tolerance to use for peak matching.") + parser.add_argument("mz_power", type=float, help="The power to raise mz to in the cosine function.") + parser.add_argument("intensity_power", type=float, help="The power to raise intensity to in the cosine function.") args = parser.parse_args() + reference_spectra = load_from_msp(args.references_filename) + queries_spectra = load_from_msp(args.queries_filename) + if args.similarity_metric == 'CosineGreedy': - similarity_metric = CosineGreedy() + similarity_metric = CosineGreedy(args.tolerance, args.mz_power, args.intensity_power) elif args.similarity_metric == 'CosineHungarian': - similarity_metric = CosineHungarian() - elif args.similarity_metric == 'FingerprintSimilarity': - similarity_metric = FingerprintSimilarity() - elif args.similarity_metric == 'IntersectMz': - similarity_metric = IntersectMz() + similarity_metric = CosineHungarian(args.tolerance, args.mz_power, args.intensity_power) elif args.similarity_metric == 'ModifiedCosine': - similarity_metric = ModifiedCosine() + similarity_metric = ModifiedCosine(args.tolerance, args.mz_power, args.intensity_power) + reference_spectra = map(add_precursor_mz, reference_spectra) + queries_spectra = map(add_precursor_mz, queries_spectra) else: - similarity_metric = ParentMassMatch() - - reference_spectra = [ - spectrum for spectrum in load_from_msp(args.references_filename) - ] - queries_spectra = [spectrum for spectrum in load_from_msp(args.queries_filename)] + return -1 scores = calculate_scores( - references=reference_spectra, - queries=queries_spectra, + references=list(reference_spectra), + queries=list(queries_spectra), similarity_function=similarity_metric, ) |