--- a/build/tools/MetaboRank/MetaboRank.xml	Wed Jul 26 15:33:45 2023 +0000
+++ b/build/tools/MetaboRank/MetaboRank.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -1,11 +1,11 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_MetaboRank" name="MetaboRank" version="1.5.0">
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_MetaboRank" name="MetaboRank" version="develop">
   <description>Compute the MetaboRank, a custom personalized PageRank for metabolic network.</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.MetaboRank -i "$sbmlFilePath"
  -s "$seedsFilePath"
@@ -44,15 +44,125 @@
   </outputs>
   <tests>
     <test>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="sbmlFilePath" value="XF_network.sbml"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="seedsFilePath" value="XF_network_C_Seed.tab"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="inputSide" value="XF_network_C_Side.tab"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <output name="output">
-	<assert_contents>
-		<has_n_lines n="1100"/>
-		<has_n_columns n="11"/>
+                                                                                        	
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        <assert_contents>
+                                                                                                              		
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_n_lines n="1100"/>
+                                                                                                              		
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_n_columns n="11"/>
+                                                                                                                      
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
         </assert_contents>
+                                                                                              
+      
+      
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+      
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+      
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+      
+      
       </output>
+                                                                      
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
     </test>
   </tests>
   <help><![CDATA[Compute the MetaboRank, a custom personalized PageRank for metabolic network.
@@ -60,6 +170,8 @@
 The MetaboRank can, from metabolomics results, be used to fuel a recommender system highlighting interesting compounds to investigate, retrieve missing identification and drive literature mining.
 It is a two dimensional centrality computed from personalized PageRank and CheiRank, with special transition probability and normalization to handle the specificities of metabolic networks.
 For convenience, a one dimensional centrality rank is also computed from the highest rank from PageRank or CheiRank, and using lowest rank as tie-breaker.
-See publication for more information: Frainay et al. MetaboRank: network-based recommendation system to interpret and enrich metabolomics results, Bioinformatics (35-2), https://doi.org/10.1093/bioinformatics/bty577]]></help>
-  <citations/>
+See publication for more information.]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/bty577</citation>
+  </citations>
 </tool>