--- a/build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml	Tue Jul 04 10:21:26 2023 +0000
+++ b/build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml	Wed Jul 26 15:33:45 2023 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="1.4.0">
+<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="1.5.0">
   <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>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath"
  -s "$sourcePath"
@@ -13,6 +13,9 @@
  $asTable
  -t "$targetPath"
  -sc "$sideCompoundFile"
+#if str($rExclude) != 'None':
+ -re "$rExclude"
+#end if
 #if str($weightFile) != 'None':
  -cw "$weightFile"
 #end if
@@ -29,6 +32,7 @@
     <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=""/>
     <param argument="-cw" format="tsv" label="an optional file containing weights for reactions pairs" name="weightFile" optional="true" type="data" value=""/>
     <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1">
       <sanitizer invalid_char="_">