added filtering option for matchms & spec2vec

RECETOX · Oct 18, 2023 · 6209a03 · 6209a03
1 parent 1a1b590
commit 6209a03
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Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/tools/matchms/matchms_spectral_similarity.xml b/tools/matchms/matchms_spectral_similarity.xml
@@ -53,7 +53,9 @@ scores._scores = similarity.matrix(
 scores._scores.data.dtype.names = [name+"_scores", name+"_matches"]
 #end if
 
+#if $filter_zero == "TRUE"
 scores.filter_by_range(name=name+"_matches", low=0)
+#end if
 scores.to_json("$similarity_scores")
 </configfile>
 </configfiles>
@@ -64,6 +66,8 @@ scores.to_json("$similarity_scores")
             <expand macro="similarity_metrics"/>
         </param>
         <expand macro="similarity_algorithm_params"/>
+        <param label="Filter zero scores" name="filter_zero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
+            help="Filter out zero scores from the output."/>
     </inputs>
 
     <outputs>

diff --git a/tools/spec2vec/spec2vec_similarity.xml b/tools/spec2vec/spec2vec_similarity.xml
@@ -1,4 +1,4 @@
-<tool id="spec2vec_similarity" name="spec2vec similarity" version="@TOOL_VERSION@+galaxy2" profile="21.09">
+<tool id="spec2vec_similarity" name="spec2vec similarity" version="@TOOL_VERSION@+galaxy3" profile="21.09">
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -39,8 +39,10 @@ layer = similarity.sparse_array(
     is_symmetric=False)
 
 scores._scores.add_sparse_data(scores._scores.row, scores._scores.col, layer, name)
-
+#if $filter_zero == "TRUE"
 scores.filter_by_range(inplace=True, name=name, low=0)
+#end if
+
 scores.to_json("$similarity_scores")
 </configfile>
 </configfiles>
@@ -56,6 +58,8 @@ scores.to_json("$similarity_scores")
             The default is 0, which means that no weighing will be done."/>
         <param label="Maximum share of new peaks" name="allow_missing_percentage"  type="float" value="0.1" max="1.0" min="0.0"
             help="Maximum allowed share of the peaks that are new to the model in relation to the whole peak corpus."/>
+        <param label="Filter zero scores" name="filter_zero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
+            help="Filter out zero scores from the output."/>
     </inputs>
     <outputs>
         <data label="Spec2Vec scores of ${on_string}" name="similarity_scores" format="json"/>