--- a/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml	Mon Feb 03 15:59:46 2025 +0000
+++ b/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml	Thu Feb 13 15:08:22 2025 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="2.0.0">
+<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="2.0.1">
   <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath"
  -s "$sourcePath"
@@ -54,17 +54,29 @@
   </outputs>
   <tests>
     <test>
+            
       <param name="inputPath" value="toy_model.xml"/>
+            
       <param name="sourcePath" value="seeds.txt"/>
+            
       <param name="targetPath" value="targets.txt"/>
+            
       <param name="sideCompoundFile" value="sc.txt"/>
+            
       <param name="format" value="gml"/>
+            
       <output ftype="txt" name="output">
+                
         <assert_contents>
+                    
           <has_line_matching expression=".*node.*" n="5"/>
+                    
           <has_line_matching expression=".*edge.*" n="4"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
   </tests>
   <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.