--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build/tools/ScopeNetwork/ScopeNetwork.xml	Wed May 17 13:26:37 2023 +0000
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.3.0">
+  <description>Perform a network expansion from a set of compound seeds to create a scope network</description>
+  <xrefs>
+    <xref type="bio.tools">met4j</xref>
+  </xrefs>
+  <requirements>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath"
+ -s "$seedsFilePath"
+#if str($sideCompoundFile) != 'None':
+ -sc "$sideCompoundFile"
+#end if
+ $includeSides
+#if str($reactionToIgnoreFile) != 'None':
+ -ir "$reactionToIgnoreFile"
+#end if
+ $trace
+ $asTable
+ -o "$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="-s" format="txt" label="input seeds file: tabulated file containing node of interest ids" name="seedsFilePath" optional="false" type="data" value=""/>
+    <param argument="-sc" format="txt" label="an optional file containing list of ubiquitous side compounds to be considered available by default but ignored during expansion" name="sideCompoundFile" optional="true" type="data" value=""/>
+    <param argument="-ssc" checked="false" falsevalue="" label="show side compounds in output network" name="includeSides" truevalue="-ssc" type="boolean" value="false"/>
+    <param argument="-ir" format="txt" label="an optional file containing list of reaction to ignore (forbid inclusion in scope" name="reactionToIgnoreFile" optional="true" type="data" value=""/>
+    <param argument="-t" checked="false" falsevalue="" label="trace inclusion step index for each node in output" name="trace" truevalue="-t" 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"/>
+  </inputs>
+  <outputs>
+    <data format="gml" name="output"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="sbmlFilePath" value="toy_model.xml"/>
+      <param name="seedsFilePath" value="seeds.txt"/>
+      <param name="sideCompoundFile" value="sides.txt"/>
+      <output ftype="gml" name="output">
+        <assert_contents>
+          <has_line_matching expression=".*node.*" n="9"/>
+          <has_line_matching expression=".*edge.*" n="11"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network
+The scope of a set of compounds (seed) refer to the maximal metabolic network that can be extended from them,where the extension process consist of adding a reaction to the network if and only if all of its substrates are either a seed or a product of a previously added reaction
+For more information, see Handorf, Ebenhöh and Heinrich (2005). *Expanding metabolic networks: scopes of compounds, robustness, and evolution.* Journal of molecular evolution, 61(4), 498-512. (https://doi.org/10.1007/s00239-005-0027-1)]]></help>
+  <citations/>
+</tool>