diff ScopeNetwork.xml @ 0:36d03cbd172d draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e28ca123295d50b85ba872e5a4720fd72697ecc3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ScopeNetwork.xml	Thu Mar 13 15:50:26 2025 +0000
@@ -0,0 +1,62 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="@TOOL_VERSION@">
+  <description>Perform a network expansion from a set of compound seeds to create a scope network</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="bio_tools"/>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[met4j fr.inrae.toulouse.metexplore.met4j_toolbox.networkAnalysis.ScopeNetwork -i "$sbmlFilePath"
+ -s "$seedsFilePath"
+#if str($sideCompoundFile) != 'None':
+ -sc "$sideCompoundFile"
+#end if
+ $includeSides
+#if str($reactionToIgnoreFile) != 'None':
+ -ir "$reactionToIgnoreFile"
+#end if
+ $trace
+#if str($format):
+ -f "$format"
+#end if
+ -o "$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="-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="-f" label="Format of the exported graphTabulated edge list by default (source id &#9; edge type &#9; target id). Other options include GML, JsonGraph, and tabulated node list (label &#9; node id &#9; node type)." name="format" optional="true" type="select" value="tab">
+      <option value="gml">gml</option>
+      <option selected="true" value="tab">tab</option>
+      <option value="nodeList">nodeList</option>
+      <option value="json">json</option>
+      <option value="matrix">matrix</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="sbmlFilePath" value="toy_model.xml"/>
+      <param name="seedsFilePath" value="seeds.txt"/>
+      <param name="sideCompoundFile" value="sides.txt"/>
+      <param name="format" value="gml"/>
+      <output ftype="txt" 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
+@ATTRIBUTION@]]></help>
+  <citations>
+    <citation type="doi">10.1007/s00239-005-0027-1</citation>
+  </citations>
+</tool>