Repository 'matchms'
hg clone https://toolshed.g2.bx.psu.edu/repos/recetox/matchms

Changeset 2:67ed0d4f3724 (2022-09-08)
Previous changeset 1:f680068b7863 (2022-07-22) Next changeset 3:9f8532c99845 (2022-09-21)
Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b974ff354fa375975050026482e1b6ded8005682
modified:
matchms_similarity.xml
matchms_similarity_wrapper.py
test-data/similarity/scores_test6_out.tsv
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diff -r f680068b7863 -r 67ed0d4f3724 matchms_similarity.xml
--- a/matchms_similarity.xml Fri Jul 22 16:48:21 2022 +0000
+++ b/matchms_similarity.xml Thu Sep 08 14:48:21 2022 +0000
b
@@ -1,4 +1,4 @@
-<tool id="matchms" name="matchMS similarity" version="@TOOL_VERSION@+galaxy0" python_template_version="3.8">
+<tool id="matchms" name="matchMS similarity" version="@TOOL_VERSION@+galaxy1" python_template_version="3.8">
     <description>calculate the similarity score and matched peaks</description>
 
     <macros>
@@ -131,8 +131,10 @@
         <test>
             <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
             <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
-            <param name="ri_filtering.is_true" value="TRUE" />
-            <param name="ri_filtering.tolerance" value="60.0" />
+            <conditional name="ri_filtering">
+                <param name="is_true" value="True"></param>
+                <param name="tolerance" value="60.0" />
+            </conditional>
             <param name="similarity_metric" value="CosineGreedy"/>
             <output name="similarity_scores" file="similarity/scores_test6_out.tsv" ftype="tsv"/>
             <output name="similarity_matches" file="similarity/matches_test6_out.tsv" ftype="tsv"/>
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diff -r f680068b7863 -r 67ed0d4f3724 matchms_similarity_wrapper.py
--- a/matchms_similarity_wrapper.py Fri Jul 22 16:48:21 2022 +0000
+++ b/matchms_similarity_wrapper.py Thu Sep 08 14:48:21 2022 +0000
[
@@ -82,7 +82,7 @@
     if args.ri_tolerance is not None:
         print("RI filtering with tolerance ", args.ri_tolerance)
         ri_matches = calculate_scores(reference_spectra, queries_spectra, MetadataMatch("retention_index", "difference", args.ri_tolerance)).scores
-        scores.scores["score"] = np.where(ri_matches, scores.scores["score"], 0.0)
+        scores._scores["score"] = np.where(ri_matches, scores.scores["score"], 0.0)
 
     write_outputs(args, scores)
     return 0
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diff -r f680068b7863 -r 67ed0d4f3724 test-data/similarity/scores_test6_out.tsv
--- a/test-data/similarity/scores_test6_out.tsv Fri Jul 22 16:48:21 2022 +0000
+++ b/test-data/similarity/scores_test6_out.tsv Thu Sep 08 14:48:21 2022 +0000
b
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