--- a/build/tools/Sbml2Graph/Sbml2Graph.xml	Wed Jul 26 15:33:45 2023 +0000
+++ b/build/tools/Sbml2Graph/Sbml2Graph.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -1,62 +1,172 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="1.5.0">
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="develop">
   <description>Create a graph representation of a SBML file content, and export it in graph file format.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</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 convert.Sbml2Graph -i "$inputPath"
  $bipartite
  $compound
  $reaction
- $tab
- $gml
- -o "$outputPath"
+#if str($format):
+ -f "$format"
+#end if
+ -o "$output"
 ]]></command>
   <inputs>
     <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
     <param argument="-b" checked="false" falsevalue="" label="create bipartite graph" name="bipartite" truevalue="-b" type="boolean" value="false"/>
     <param argument="-c" checked="true" falsevalue="" label="create compound graph" name="compound" truevalue="-c" type="boolean" value="true"/>
     <param argument="-r" checked="false" falsevalue="" label="create reaction graph" name="reaction" truevalue="-r" type="boolean" value="false"/>
-    <param argument="-tab" checked="false" falsevalue="" label="export in tabulated file" name="tab" truevalue="-tab" type="boolean" value="false"/>
-    <param argument="-gml" checked="true" falsevalue="" label="export in GML file" name="gml" truevalue="-gml" type="boolean" value="true"/>
+    <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id &#9; edge type &#9; target id). Other options include GML, JsonGraph, and tabulated node list (label &#9; node id &#9; node type)." name="format" optional="true" type="select" value="tab">
+      <option value="gml">gml</option>
+      <option selected="true" value="tab">tab</option>
+      <option value="nodeList">nodeList</option>
+      <option value="json">json</option>
+      <option value="matrix">matrix</option>
+    </param>
   </inputs>
   <outputs>
-    <data format="txt" name="outputPath"/>
+    <data format="txt" name="output"/>
   </outputs>
   <tests>
     <test>
+                        
+      
+      
       <param name="inputPath" value="toy_model.xml"/>
-      <output name="outputPath">
+                        
+      
+      
+      <param name="format" value="gml"/>
+                        
+      
+      
+      <output name="output">
+                                
+        
+        
         <assert_contents>
-          <has_n_lines n="101"/>
+                                        
+          
+          
+          <has_line_matching expression=".*node.*" n="8"/>
+                                        
+          
+          
+          <has_line_matching expression=".*edge.*" n="9"/>
+                                      
+        
+        
         </assert_contents>
+                              
+      
+      
       </output>
+                      
+    
+    
     </test>
     <test>
+                        
+      
+      
       <param name="inputPath" value="toy_model.xml"/>
+                        
+      
+      
       <param name="bipartite" value="true"/>
+                        
+      
+      
       <param name="compound" value="false"/>
-      <output name="outputPath">
+                        
+      
+      
+      <param name="format" value="gml"/>
+                        
+      
+      
+      <output name="output">
+                                
+        
+        
         <assert_contents>
-          <has_n_lines n="184"/>
+                                        
+          
+          
+          <has_line_matching expression=".*node.*" n="15"/>
+                                        
+          
+          
+          <has_line_matching expression=".*edge.*" n="17"/>
+                                      
+        
+        
         </assert_contents>
+                              
+      
+      
       </output>
+                      
+    
+    
     </test>
     <test>
+                        
+      
+      
       <param name="inputPath" value="toy_model.xml"/>
+                        
+      
+      
       <param name="reaction" value="true"/>
+                        
+      
+      
       <param name="compound" value="false"/>
-      <output name="outputPath">
+                        
+      
+      
+      <param name="format" value="gml"/>
+                        
+      
+      
+      <output name="output">
+                                
+        
+        
         <assert_contents>
-          <has_n_lines n="90"/>
+                                                                     
+          
+          
+          
+          <has_line_matching expression=".*node.*" n="7"/>
+                                        
+          
+          
+          <has_line_matching expression=".*edge.*" n="8"/>
+                                    
+        
+        
+        
         </assert_contents>
+                                  
+      
+      
+      
       </output>
+                   
+    
+    
     </test>
   </tests>
   <help><![CDATA[Create a graph representation of a SBML file content, and export it in graph file format.
-The graph can be either a compound graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help>
-  <citations/>
+The graph can be either a compound graph, a reaction graph or a bipartite graph, and can be exported in gml or tabulated file format.]]></help>
+  <citations>
+    <citation type="doi">10.1109/tcbb.2008.79</citation>
+  </citations>
 </tool>