--- a/tools/attributes/SetCharges/SetCharges.xml	Mon Feb 03 15:59:46 2025 +0000
+++ b/tools/attributes/SetCharges/SetCharges.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_SetCharges" name="SetCharges" version="2.0.0">
+<tool id="met4j_SetCharges" name="SetCharges" version="2.0.1">
   <description>Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges</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.SetCharges#if str($colcharge) != 'nan':
  -cc "$colcharge"
@@ -50,63 +50,117 @@
   </outputs>
   <tests>
     <test>
+            
       <param name="sbml" value="toy_model.xml"/>
+            
       <param name="tab" value="charges.tsv"/>
+            
       <output ftype="sbml" name="out">
+                
         <assert_contents>
+                    
           <is_valid_xml/>
+                    
           <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
+                    
           <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="sbml" value="toy_model.xml"/>
+            
       <param name="tab" value="chargesWithComment.tsv"/>
+            
       <output ftype="sbml" name="out">
+                
         <assert_contents>
+                    
           <is_valid_xml/>
+                    
           <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
+                    
           <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="sbml" value="toy_model.xml"/>
+            
       <param name="tab" value="charges.tsv"/>
+            
       <param name="nSkip" value="1"/>
+            
       <output ftype="sbml" name="out">
+                
         <assert_contents>
+                    
           <is_valid_xml/>
+                    
           <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
+                    
           <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="sbml" value="toy_model.xml"/>
+            
       <param name="tab" value="charges.tsv"/>
+            
       <param name="ci" value="2"/>
+            
       <param name="cc" value="3"/>
+            
       <output ftype="sbml" name="out">
+                
         <assert_contents>
+                    
           <is_valid_xml/>
+                    
           <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
+                    
           <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="sbml" value="XF_network.sbml"/>
+            
       <param name="tab" value="chargesXF.tsv"/>
+            
       <param name="p" value="true"/>
+            
       <param name="s" value="true"/>
+            
       <output ftype="sbml" name="out">
+                
         <assert_contents>
+                    
           <is_valid_xml/>
+                    
           <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
   </tests>
   <help><![CDATA[Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges