--- a/build/tools/PrecursorNetwork/PrecursorNetwork.xml	Wed Jul 26 15:33:45 2023 +0000
+++ b/build/tools/PrecursorNetwork/PrecursorNetwork.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -1,11 +1,11 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="1.5.0">
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="develop">
   <description>Perform a network expansion from a set of compound targets to create a precursor 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.PrecursorNetwork -i "$sbmlFilePath"
  -t "$targetsFilePath"
@@ -15,7 +15,9 @@
 #if str($reactionToIgnoreFile) != 'None':
  -ir "$reactionToIgnoreFile"
 #end if
- $asTable
+#if str($format):
+ -f "$format"
+#end if
  -o "$output"
 ]]></command>
   <inputs>
@@ -23,21 +25,58 @@
     <param argument="-t" format="txt" label="input target file: tabulated file containing node of interest ids" name="targetsFilePath" optional="false" type="data" value=""/>
     <param argument="-sc" format="txt" label="an optional file containing list of ubiquitous compounds to be considered already available" name="sideCompoundFile" optional="true" type="data" value=""/>
     <param argument="-ir" format="txt" label="an optional file containing list of reaction to ignore (forbid inclusion in scope)" name="reactionToIgnoreFile" optional="true" type="data" value=""/>
-    <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
+    <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="gml" name="output"/>
+    <data format="txt" name="output"/>
   </outputs>
   <tests>
     <test>
+                        
+      
+      
       <param name="sbmlFilePath" value="toy_model.xml"/>
+                        
+      
+      
       <param name="targetsFilePath" value="targets.txt"/>
-      <output ftype="gml" name="output">
+                        
+      
+      
+      <param name="format" value="gml"/>
+                        
+      
+      
+      <output ftype="txt" name="output">
+                                
+        
+        
         <assert_contents>
+                                        
+          
+          
           <has_line_matching expression=".*node.*" n="13"/>
+                                        
+          
+          
           <has_line_matching expression=".*edge.*" n="15"/>
+                                      
+        
+        
         </assert_contents>
+                              
+      
+      
       </output>
+                      
+    
+    
     </test>
   </tests>
   <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network.