--- a/build/tools/DistanceMatrix/DistanceMatrix.xml	Wed Jul 26 15:33:45 2023 +0000
+++ b/build/tools/DistanceMatrix/DistanceMatrix.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -1,11 +1,11 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="1.5.0">
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="develop">
   <description>Create a compound to compound 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.DistanceMatrix -i "$inputPath"
 #if str($sideCompoundFile) != 'None':
@@ -34,30 +34,294 @@
   </outputs>
   <tests>
     <test>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="inputPath" value="toy_model.xml"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <output ftype="csv" name="outputPath">
+                                                                                                
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         <assert_contents>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_n_lines n="9"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="id,A,A_ext,B,C,D,D_ext,E,E_ext" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="B,1.0,Infinity,0.0,2.0,1.0,2.0,Infinity,Infinity" n="1"/>
+                                                                                                                      
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         </assert_contents>
+                                                                                              
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       </output>
+                                                                      
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
     </test>
     <test>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="inputPath" value="toy_model.xml"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="sideCompoundFile" value="sides.txt"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="degree" value="true"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="undirected" value="true"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <output ftype="csv" name="outputPath">
+                                                                                                
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         <assert_contents>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_n_lines n="8"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="id,A,B,C,D,D_ext,E,E_ext" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="A,0.0,4.0,4.0,20.0,21.0,24.0,25.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="B,4.0,0.0,8.0,16.0,17.0,20.0,21.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="C,4.0,8.0,0.0,16.0,17.0,20.0,21.0" n="1"/>
+                                                                                                                        
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
           <has_line_matching expression="D,8.0,4.0,4.0,0.0,1.0,4.0,5.0" n="1"/>
+                                                                                                                      
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         </assert_contents>
+                                                                                              
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       </output>
+                                                                      
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
     </test>
   </tests>
   <help><![CDATA[Create a compound to compound distance matrix.