--- a/tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml	Wed Jul 26 15:33:45 2023 +0000
+++ b/tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -1,11 +1,11 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="MET4J_VERSION_TEST">
-  <description>Get reactants lists from a list of reactions and a GSMN.</description>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="develop">
+  <description>Get reactant lists from a list of reactions and a SBML file.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetReactantsFromReactions -i "$sbml"
  -r "$reactionFile"
@@ -38,38 +38,357 @@
   </outputs>
   <tests>
     <test>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="sbml" value="XF_network.sbml"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="reactionFile" value="XF_network_R_Seed.tab"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <output ftype="tsv" name="outputFile">
+                                                                                                
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         <assert_contents>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_text_matching expression="R_GLUN" n="4"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_text_matching expression="R_ACGS" n="5"/>
+                                                                                                                      
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         </assert_contents>
+                                                                                              
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       </output>
+                                                                      
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
     </test>
     <test>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="sbml" value="XF_network.sbml"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="reactionFile" value="XF_network_R_Seed.tab"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="printSubstrates" value="true"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <output ftype="tsv" name="outputFile">
+                                                                                                
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         <assert_contents>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_text_matching expression="R_GLUN" n="2"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_text_matching expression="R_ACGS" n="5"/>
+                                                                                                                      
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         </assert_contents>
+                                                                                              
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       </output>
+                                                                      
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
     </test>
     <test>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="sbml" value="XF_network.sbml"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="reactionFile" value="XF_network_R_Seed.tab"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="printProducts" value="true"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <output ftype="tsv" name="outputFile">
+                                                                                                
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         <assert_contents>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_text_matching expression="R_GLUN" n="2"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_text_matching expression="R_ACGS" n="5"/>
+                                                                                                                      
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         </assert_contents>
+                                                                                              
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       </output>
+                                                                      
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
     </test>
   </tests>
-  <help><![CDATA[Get reactants lists from a list of reactions and a GSMN. Output a tab-separated file with one row per reactant, reaction identifiers in first column, reactant identifiers in second column. It can provides substrates, products, or both (by default). In the case of reversible reactions, all reactants are considered both substrates and products]]></help>
+  <help><![CDATA[Get reactant lists from a list of reactions and a Sbml file. Output a tab-separated file with one row per reactant, reaction identifiers in first column, reactant identifiers in second column. It can provides substrates, products, or both (by default). In the case of reversible reactions, all reactants are considered as both substrates and products]]></help>
   <citations/>
 </tool>