--- a/build/tools/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml	Mon Feb 03 15:59:46 2025 +0000
+++ b/build/tools/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.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_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="2.0.0">
+<tool id="met4j_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="2.0.1">
   <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</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 convert.Sbml2CarbonSkeletonNet -i "$inputPath"
  -g "$inputAAM"
@@ -46,90 +46,168 @@
   </outputs>
   <tests>
     <test>
+            
       <param name="inputPath" value="Human-GEM_pathways.xml"/>
+            
       <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
+            
       <param name="format" value="gml"/>
+            
       <output name="output">
+                
         <assert_contents>
+                    
           <has_n_lines n="2602"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="inputPath" value="Human-GEM_pathways.xml"/>
+            
       <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
+            
       <param name="keepSingleCarbon" value="true"/>
+            
       <param name="format" value="gml"/>
+            
       <output name="output">
+                
         <assert_contents>
+                    
           <has_n_lines n="2629"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="inputPath" value="Human-GEM_pathways.xml"/>
+            
       <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
+            
       <param name="mergeComp" value="true"/>
+            
       <param name="format" value="gml"/>
+            
       <output name="output">
+                
         <assert_contents>
+                    
           <has_n_lines n="2406"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="inputPath" value="Human-GEM_pathways.xml"/>
+            
       <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
+            
       <param name="mergeEdges" value="true"/>
+            
       <param name="format" value="gml"/>
+            
       <output name="output">
+                
         <assert_contents>
+                    
           <has_n_lines n="2071"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="inputPath" value="Human-GEM_pathways.xml"/>
+            
       <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
+            
       <param name="removeIsolated" value="true"/>
+            
       <param name="format" value="gml"/>
+            
       <output name="output">
+                
         <assert_contents>
+                    
           <has_n_lines n="2490"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="inputPath" value="Human-GEM_pathways.xml"/>
+            
       <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
+            
       <param name="undirected" value="true"/>
+            
       <param name="format" value="gml"/>
+            
       <output name="output">
+                
         <assert_contents>
+                    
           <has_n_lines n="3214"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="inputPath" value="Human-GEM_pathways.xml"/>
+            
       <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
+            
       <param name="format" value="matrix"/>
+            
       <output name="output">
+                
         <assert_contents>
+                    
           <has_n_lines n="112"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="inputPath" value="Human-GEM_pathways.xml"/>
+            
       <param name="inputAAM" value="Human-GEM_pathways-transitions2.tab"/>
+            
       <param name="fromIndexes" value="true"/>
+            
       <param name="format" value="gml"/>
+            
       <output name="output">
+                
         <assert_contents>
+                    
           <has_n_lines n="2611"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
   </tests>
   <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produces a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) performs atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.]]></help>