--- a/build/tools/SetIds/SetIds.xml	Mon Feb 03 15:59:46 2025 +0000
+++ b/build/tools/SetIds/SetIds.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_SetIds" name="SetIds" version="2.0.0">
+<tool id="met4j_SetIds" name="SetIds" version="2.0.1">
   <description>Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new 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 attributes.SetIds#if str($colname) != 'nan':
  -cnew "$colname"
@@ -62,63 +62,117 @@
   </outputs>
   <tests>
     <test>
+            
       <param name="sbml" value="toy_model.xml"/>
+            
       <param name="tab" value="idMetabolites.tsv"/>
+            
       <param name="o" value="METABOLITE"/>
+            
       <output ftype="sbml" name="out">
+                
         <assert_contents>
+                    
           <is_valid_xml/>
+                    
           <has_line_matching expression=".*id=.metaboliteA.*" n="1"/>
+                    
           <has_line_matching expression=".*id=.metaboliteB.*" n="1"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="sbml" value="toy_model.xml"/>
+            
       <param name="tab" value="idReactions.tsv"/>
+            
       <output ftype="sbml" name="out">
+                
         <assert_contents>
+                    
           <is_valid_xml/>
+                    
           <has_line_matching expression=".*id=.reaction1.*" n="1"/>
+                    
           <has_line_matching expression=".*id=.reaction2.*" n="1"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="sbml" value="XF_network.sbml"/>
+            
       <param name="tab" value="idPathways.tsv"/>
+            
       <param name="o" value="PATHWAY"/>
+            
       <output ftype="sbml" name="out">
+                
         <assert_contents>
+                    
           <is_valid_xml/>
+                    
           <has_line_matching expression=".*groups:id=.CEB.*" n="1"/>
+                    
           <has_line_matching expression=".*groups:id=.NSP.*" n="1"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="sbml" value="XF_network.sbml"/>
+            
       <param name="tab" value="idGenes.tsv"/>
+            
       <param name="o" value="GENE"/>
+            
       <output ftype="sbml" name="out">
+                
         <assert_contents>
+                    
           <is_valid_xml/>
+                    
           <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>
+                    
           <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="sbml" value="XF_network.sbml"/>
+            
       <param name="tab" value="idCompartments.tsv"/>
+            
       <param name="o" value="COMPARTMENT"/>
+            
       <output ftype="sbml" name="out">
+                
         <assert_contents>
+                    
           <is_valid_xml/>
+                    
           <has_line_matching expression=".*id=.cytosol.*" n="1"/>
+                    
           <has_line_matching expression=".*id=.extra.*" n="1"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
   </tests>
   <help><![CDATA[Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids