--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml	Fri Jun 10 10:31:34 2022 +0000
@@ -0,0 +1,43 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="0.11.0">
+  <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:0.11.0</container>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath"
+ -t "$targetsFilePath"
+#if str($sideCompoundFile) != 'None':
+ -sc "$sideCompoundFile"
+#end if
+#if str($reactionToIgnoreFile) != 'None':
+ -ir "$reactionToIgnoreFile"
+#end if
+ -o "$output"
+]]>  </command>
+  <inputs>
+    <param argument="-i" format="sbml" label="input SBML file: path to network used for computing scope, in sbml format." name="sbmlFilePath" optional="false" type="data" value=""/>
+    <param argument="-t" format="" label="input target file: tabulated file containing node of interest ids" name="targetsFilePath" optional="false" type="data" value=""/>
+    <param argument="-sc" format="" 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="" label="an optional file containing list of reaction to ignore (forbid inclusion in scope)" name="reactionToIgnoreFile" optional="true" type="data" value=""/>
+  </inputs>
+  <outputs>
+    <data format="gml" name="output"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="sbmlFilePath" value="toy_model.xml"/>
+      <param name="targetsFilePath" value="targets.txt"/>
+      <output ftype="gml" 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.
+The precursor network of a set of compounds (targets) refer to the sub-part of a metabolic network from which a target can be reachedThe network expansion process consist of adding a reaction to the network if any of its products are either a targets or a substrate of a previously added reaction]]></help>
+</tool>