--- a/ExtractSubNetwork.xml	Tue Oct 28 14:20:25 2025 +0000
+++ b/ExtractSubNetwork.xml	Wed Jan 21 15:29:14 2026 +0000
@@ -48,37 +48,29 @@
       <option value="nodeList">nodeList</option>
       <option value="json">json</option>
       <option value="matrix">matrix</option>
+      <option value="jsonviz">jsonviz</option>
     </param>
   </inputs>
   <outputs>
     <data format="txt" name="output"/>
   </outputs>
-  <tests>
-    <test>
-      <param name="inputPath" value="toy_model.xml"/>
-      <param name="sourcePath" value="seeds.txt"/>
-      <param name="targetPath" value="targets.txt"/>
-      <param name="format" value="gml"/>
-      <output ftype="txt" name="output">
-        <assert_contents>
-          <has_line_matching expression=".*node.*" n="3"/>
-          <has_line_matching expression=".*edge.*" n="2"/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
+  <tests/>
   <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds of interests ids, one per row.
 The subnetwork corresponds to the part of the network that connects compounds from the first list to compounds from the second list.
 Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. The relevance of considered path can be increased by weighting the edges using degree squared, chemical similarity (require InChI or SMILES annotations) or any provided weighting.
 See previous works on subnetwork extraction for parameters recommendations.
 @ATTRIBUTION@]]></help>
   <citations>
+    <citation type="doi">10.1093/nar/gki437</citation>
+    <citation type="doi">10.1093/bioinformatics/btu760</citation>
+    <citation type="doi">10.1093/bib/bbv115</citation>
+    <citation type="doi">10.1016/j.biosystems.2011.05.004</citation>
+    <citation type="doi">10.1016/j.biosystems.2011.05.004</citation>
+    <citation type="doi">10.1093/nar/gki437</citation>
+    <citation type="doi">10.1016/j.jmb.2005.09.079</citation>
+    <citation type="doi">10.1093/bioinformatics/btg217</citation>
     <citation type="doi">10.1093/bib/bbv115</citation>
     <citation type="doi">10.1093/bioinformatics/bti116</citation>
-    <citation type="doi">10.1093/nar/gki437</citation>
-    <citation type="doi">10.1093/bioinformatics/btg217</citation>
-    <citation type="doi">10.1016/j.biosystems.2011.05.004</citation>
     <citation type="doi">10.1093/bioinformatics/btu760</citation>
-    <citation type="doi">10.1016/j.jmb.2005.09.079</citation>
   </citations>
 </tool>