Merge pull request RECETOX#436 from hechth/networking_fix

Update matchms molecular networking tool
wverastegui · Nov 19, 2023 · 13f4f7a · 13f4f7a
2 parents 14d9015 + cb5477c
commit 13f4f7a
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Showing 3 changed files with 19 additions and 3 deletions.
diff --git a/tools/matchms/matchms_networking.xml b/tools/matchms/matchms_networking.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>create similarity network graph from matchms similarity scores</description>
 
     <macros>
@@ -28,7 +28,7 @@
     <configfiles>
         <configfile name="matchms_networking_cli">
             python3 ${__tool_directory__}/matchms_networking_wrapper.py \
-            --score_name '${score_layer_name}_score' \
+            --score_name '${score_layer_name}' \
             --graph_format '$graph_format' \
             --identifier '$identifier_key' \
             --top_n '$top_n' \
@@ -191,6 +191,18 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="scores" value="networking/test9.json" ftype="json"/>
+            <param name="graph_format" value="graphml"/>
+            <param name="identifier_key" value="compound_name"/>
+            <param name="score_cutoff" value="0.4"/>
+            <param name="keep_unconnected_nodes" value="false"/>
+            <output name="similarity_network_file" ftype="graphml">
+                <assert_contents>
+                    <is_valid_xml />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
 
     <help>

diff --git a/tools/matchms/matchms_networking_wrapper.py b/tools/matchms/matchms_networking_wrapper.py
@@ -27,8 +27,11 @@ def main(argv):
                                 score_cutoff=args.score_cutoff,
                                 link_method=args.link_method,
                                 keep_unconnected_nodes=args.keep_unconnected_nodes)
+    score_name = next((s for s in scores.score_names if args.score_name in s and "score" in s), None)
+    if score_name is None:
+        raise ValueError(f"Could not find any score name containing '{args.score_name}'.")
 
-    network.create_network(scores, args.score_name)
+    network.create_network(scores, score_name)
     network.export_to_file(filename=args.output_filename, graph_format=args.graph_format)
 
     return 0