diff matchms_spectral_similarity.xml @ 1:3f96c93f8566 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a

--- a/matchms_spectral_similarity.xml	Tue Jun 27 14:28:07 2023 +0000
+++ b/matchms_spectral_similarity.xml	Thu Oct 12 13:29:49 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="matchms_spectral_similarity" name="matchms spectral similarity" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_spectral_similarity" name="matchms spectral similarity" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>matchms spectral similarity calculation</description>
 
     <macros>
@@ -12,14 +12,14 @@
         <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
     </requirements>
 
+    <command detect_errors="exit_code"><![CDATA[
+        python3 ${python_wrapper}
+    ]]> </command>
+
     <environment_variables>
         <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
     </environment_variables>
 
-    <command detect_errors="exit_code"><![CDATA[
-        python3 ${python_wrapper}
-    ]]> </command>
-
 <configfiles>
 <configfile name="python_wrapper">
 @init_logger@
@@ -36,16 +36,24 @@
 
 @init_scores@
 
+#if $scores.use_scores == "True"
 layer = similarity.sparse_array(
     references=scores.references,
     queries=scores.queries,
     idx_row = scores._scores.row,
     idx_col = scores._scores.col,
     is_symmetric=False)
+scores._scores.add_sparse_data(scores._scores.row, scores._scores.col, layer, name)
+#else
+scores._scores = similarity.matrix(
+    references=scores.references,
+    queries=scores.queries,
+    array_type="sparse",
+    is_symmetric=False)
+scores._scores.data.dtype.names = [name+"_scores", name+"_matches"]
+#end if
 
-scores._scores.add_sparse_data(scores._scores.row, scores._scores.col, layer, name)
-
-scores.filter_by_range(inplace=True, name=name+"_matches", low=0)
+scores.filter_by_range(name=name+"_matches", low=0)
 scores.to_json("$similarity_scores")
 </configfile>
 </configfiles>