--- a/build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml	Wed Jul 26 15:33:45 2023 +0000
+++ b/build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -1,11 +1,11 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="1.5.0">
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="develop">
   <description>Create a reaction to reaction distance matrix.</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 networkAnalysis.ReactionDistanceMatrix -i "$inputPath"
 #if str($sideCompoundFile) != 'None':
@@ -38,91 +38,982 @@
   </outputs>
   <tests>
     <test>
+                                                                        
+      
+      
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       <param name="inputPath" value="toy_model.xml"/>
+                                                                        
+      
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+      
       <output ftype="csv" name="outputPath">
+                                                                                                
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         <assert_contents>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_n_lines n="8"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,Infinity,Infinity" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac2,Infinity,0.0,1.0,1.0,2.0,Infinity,Infinity" n="1"/>
+                                                                                                                      
+        
+        
+        
+        
+        
+        
+        
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+        
         </assert_contents>
+                                                                                              
+      
+      
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+      
+      
+      
       </output>
+                                                                      
+    
+    
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+    
     </test>
     <test>
+                                                                        
+      
+      
+      
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+      
       <param name="inputPath" value="toy_model.xml"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="undirected" value="true"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <output ftype="csv" name="outputPath">
+                                                                                                
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         <assert_contents>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_n_lines n="8"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0,4.0,3.0" n="1"/>
+                                                                                                                      
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         </assert_contents>
+                                                                                              
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       </output>
+                                                                      
+    
+    
+    
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+    
+    
+    
+    
     </test>
     <test>
+                                                                        
+      
+      
+      
+      
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+      
+      
+      
+      
+      
       <param name="inputPath" value="toy_model.xml"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="undirected" value="true"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="sideCompoundFile" value="sides.txt"/>
+                                                                        
+      
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+      
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+      
       <output ftype="csv" name="outputPath">
+                                                                                                
+        
+        
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+        
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+        
+        
+        
+        
+        
         <assert_contents>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_n_lines n="8"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
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+          
+          
+          
+          
           <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
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+          
+          
+          
+          
           <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0,4.0,3.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0,3.0,2.0" n="1"/>
+                                                                                                                      
+        
+        
+        
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+        
         </assert_contents>
+                                                                                              
+      
+      
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+      
       </output>
+                                                                      
+    
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+    
     </test>
     <test>
+                                                                        
+      
+      
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       <param name="inputPath" value="toy_model.xml"/>
+                                                                        
+      
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       <param name="undirected" value="true"/>
+                                                                        
+      
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       <param name="rExclude" value="rexclude.txt"/>
+                                                                        
+      
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       <output ftype="csv" name="outputPath">
+                                                                                                
+        
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+        
         <assert_contents>
+                                                                                                                        
+          
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           <has_n_lines n="6"/>
+                                                                                                                        
+          
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+          
+          
+          
+          
           <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
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+          
+          
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           <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
+                                                                                                                        
+          
+          
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+          
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           <has_line_matching expression="reac4,2.0,1.0,1.0,0.0,1.0" n="1"/>
+                                                                                                                        
+          
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+          
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           <has_line_matching expression="reac5,3.0,2.0,2.0,1.0,0.0" n="1"/>
+                                                                                                                      
+        
+        
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         </assert_contents>
+                                                                                              
+      
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       </output>
+                                                                      
+    
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     </test>
     <test>
+                                                                        
+      
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       <param name="inputPath" value="toy_model.xml"/>
+                                                                        
+      
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       <param name="undirected" value="true"/>
+                                                                        
+      
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       <param name="sideCompoundFile" value="sides.txt"/>
+                                                                        
+      
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       <param name="rExclude" value="rexclude.txt"/>
+                                                                        
+      
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       <output ftype="csv" name="outputPath">
+                                                                                                
+        
+        
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+        
+        
+        
+        
+        
+        
         <assert_contents>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_n_lines n="6"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
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+          
+          
+          
+          
           <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0" n="1"/>
+                                                                                                                        
+          
+          
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+          
+          
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+          
+          
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+          
           <has_line_matching expression="reac5,3.0,3.0,2.0,1.0,0.0" n="1"/>
+                                                                                                                      
+        
+        
+        
+        
+        
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+        
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+        
         </assert_contents>
+                                                                                              
+      
+      
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+      
       </output>
+                                                                      
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
     </test>
     <test>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
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+      
       <param name="inputPath" value="toy_model.xml"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
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+      
       <param name="sideCompoundFile" value="sides.txt"/>
+                                                                        
+      
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       <param name="rExclude" value="rexclude.txt"/>
+                                                                        
+      
+      
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+      
+      
       <output ftype="csv" name="outputPath">
+                                                                                                
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         <assert_contents>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_n_lines n="6"/>
+                                                                                                                        
+          
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+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
+                                                                                                                        
+          
+          
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+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac2,Infinity,0.0,1.0,2.0,3.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac3,Infinity,Infinity,0.0,1.0,2.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac4,Infinity,Infinity,Infinity,0.0,1.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="reac5,Infinity,Infinity,Infinity,Infinity,0.0" n="1"/>
+                                                                                                                      
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         </assert_contents>
+                                                                                              
+      
+      
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+      
+      
+      
       </output>
+                                                                      
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
     </test>
   </tests>
   <help><![CDATA[Create a reaction to reaction distance matrix.