Mercurial > repos > recetox > matchms

diff matchms_similarity_wrapper.py @ 13:cfa8b66fb106 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
author recetox
date Fri, 22 Jul 2022 16:46:28 +0000
parents ba9410f612bc
children 8af3f0718510
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--- a/matchms_similarity_wrapper.py	Tue Mar 22 16:02:16 2022 +0000
+++ b/matchms_similarity_wrapper.py	Fri Jul 22 16:46:28 2022 +0000
@@ -4,7 +4,7 @@
 import numpy as np
 from matchms import calculate_scores
 from matchms.importing import load_from_mgf, load_from_msp
-from matchms.similarity import CosineGreedy, CosineHungarian, MetadataMatch, ModifiedCosine
+from matchms.similarity import CosineGreedy, CosineHungarian, MetadataMatch, ModifiedCosine, NeutralLossesCosine
 from pandas import DataFrame
 
 
@@ -64,6 +64,10 @@
         similarity_metric = ModifiedCosine(args.tolerance, args.mz_power, args.intensity_power)
         reference_spectra = list(map(convert_precursor_mz, reference_spectra))
         queries_spectra = list(map(convert_precursor_mz, queries_spectra))
+    elif args.similarity_metric == 'NeutralLossesCosine':
+        similarity_metric = NeutralLossesCosine(args.tolerance, args.mz_power, args.intensity_power)
+        reference_spectra = list(map(convert_precursor_mz, reference_spectra))
+        queries_spectra = list(map(convert_precursor_mz, queries_spectra))
     else:
         return -1