--- a/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml	Mon Jun 27 13:41:08 2022 +0000
+++ b/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml	Tue Jul 19 14:20:07 2022 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="0.12.0">
+<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="1.0.1">
   <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds and/or 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:0.12.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath"
  -s "$sourcePath"
@@ -27,12 +27,12 @@
 ]]></command>
   <inputs>
     <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
-    <param argument="-s" format="text" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/>
-    <param argument="-t" format="text" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/>
+    <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/>
+    <param argument="-t" format="txt" label="input targets txt file" name="targetPath" 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="-sc" format="text" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/>
-    <param argument="-br" format="text" label="a file containing list of blocked reactions to ignore" name="blkdReactionFile" optional="true" 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="-br" format="txt" label="a file containing list of blocked reactions to ignore" name="blkdReactionFile" 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="_">
@@ -45,7 +45,7 @@
     <data format="gml" name="outputPath"/>
   </outputs>
   <tests>
-      <test>
+    <test>
         <param name="inputPath" value="toy_model.xml"/>
         <param name="sourcePath" value="seeds.txt"/>
         <param name="targetPath" value="targets.txt"/>
@@ -57,7 +57,6 @@
           </assert_contents>
         </output>
       </test>
-
   </tests>
   <help><![CDATA[Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds and/or 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 and compounds from the first list to reactions and compounds from the second list.