--- a/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml	Wed Jul 26 15:33:45 2023 +0000
+++ b/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -1,16 +1,15 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="MET4J_VERSION_TEST">
-  <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="develop">
+  <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</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.ExtractSubReactionNetwork -i "$inputPath"
  -s "$sourcePath"
  $undirected
- $asTable
  -t "$targetPath"
  -sc "$sideCompoundFile"
 #if str($rExclude) != 'None':
@@ -23,13 +22,15 @@
  -k "$k"
 #end if
  $st
- -o "$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="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/>
     <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
-    <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
     <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/>
     <param argument="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/>
     <param argument="-re" format="txt" label="an optional file containing list of reactions to ignore" name="rExclude" optional="true" type="data" value=""/>
@@ -40,26 +41,70 @@
       </sanitizer>
     </param>
     <param argument="-st" checked="false" falsevalue="" label="Extract Steiner Tree" name="st" truevalue="-st" 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="outputPath"/>
+    <data format="txt" name="output"/>
   </outputs>
   <tests>
     <test>
+                        
+      
+      
       <param name="inputPath" value="toy_model.xml"/>
+                        
+      
+      
       <param name="sourcePath" value="seeds.txt"/>
+                        
+      
+      
       <param name="targetPath" value="targets.txt"/>
+                        
+      
+      
       <param name="sideCompoundFile" value="sides.txt"/>
-      <output ftype="gml" name="outputPath">
+                        
+      
+      
+      <param name="format" value="gml"/>
+                        
+      
+      
+      <output ftype="txt" name="output">
+                                
+        
+        
         <assert_contents>
+                                        
+          
+          
           <has_line_matching expression=".*node.*" n="3"/>
+                                        
+          
+          
           <has_line_matching expression=".*edge.*" n="2"/>
+                                      
+        
+        
         </assert_contents>
+                              
+      
+      
       </output>
+                      
+    
+    
     </test>
   </tests>
-  <help><![CDATA[Create a subnetwork from a GSMN in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.
-The subnetwork corresponds to part of the network that connects reactions from the first list to reactions from the second list.
+  <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.
+The subnetwork corresponds to the part of the network that connects reactions from the first list to reactions from the second list.
 Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, reaction graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds to ignore for linking reactions must be provided. An optional edge weight file, if available, can also be used.]]></help>
   <citations/>
 </tool>