--- a/tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml	Thu Jan 12 13:45:13 2023 +0000
+++ b/tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml	Wed May 17 13:26:37 2023 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="1.2.1">
+<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="MET4J_VERSION_TEST">
   <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CarbonSkeletonNet -s "$inputPath"
  -g "$inputAAM"
@@ -16,6 +16,7 @@
  $undirected
  $computeWeight
  $asMatrix
+ $main
  $fromIndexes
  -o "$outputPath"
 ]]></command>
@@ -29,6 +30,7 @@
     <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>
     <param argument="-tp" checked="false" falsevalue="" label="set transition probability as weight" name="computeWeight" truevalue="-tp" type="boolean" value="false"/>
     <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/>
+    <param argument="-main" checked="false" falsevalue="" label="Compute RPAIRS-like tags and keep only main transitions for each reaction" name="main" truevalue="-main" type="boolean" value="false"/>
     <param argument="-i" checked="false" falsevalue="" label="Use GSAM output with carbon indexes" name="fromIndexes" truevalue="-i" type="boolean" value="false"/>
   </inputs>
   <outputs>