diff Sbml2PathwayNet.xml @ 0:a59d87b81ddf 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/Sbml2PathwayNet.xml	Thu Mar 13 15:49:43 2025 +0000
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_Sbml2PathwayNet" name="Sbml2PathwayNet" version="@TOOL_VERSION@">
+  <description>Creation of a Pathway Network representation of a SBML file content</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.convert.Sbml2PathwayNet -i "$inputPath"
+#if str($inputSide) != 'None':
+ -sc "$inputSide"
+#end if
+ $removeIsolated
+ $onlySourcesAndSinks
+#if str($weightFile) != 'None':
+ -cw "$weightFile"
+#end if
+ $connectors
+#if str($format):
+ -f "$format"
+#end if
+ -o "$outputPath"
+]]></command>
+  <inputs>
+    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
+    <param argument="-sc" format="txt" label="input Side compound file (recommended)" name="inputSide" optional="true" type="data" value=""/>
+    <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/>
+    <param argument="-oss" checked="false" falsevalue="" label="consider only metabolites that are source or sink in the pathway (i.e non-intermediary compounds)" name="onlySourcesAndSinks" truevalue="-oss" type="boolean" value="false"/>
+    <param argument="-cw" format="tsv" label="an optional file containing weights for pathway pairs" name="weightFile" optional="true" type="data" value=""/>
+    <param argument="-ncw" checked="false" falsevalue="" label="set number of connecting compounds as weight" name="connectors" truevalue="-ncw" 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="outputPath"/>
+  </outputs>
+  <tests/>
+  <help><![CDATA[Creation of a Pathway Network representation of a SBML file content
+Genome-scale metabolic networks are often partitioned into metabolic pathways. Pathways are frequently considered independently despite frequent coupling in their activity due to shared metabolites. In order to decipher the interconnections linking overlapping pathways, this app proposes the creation of "Pathway Network", where two pathways are linked if they share compounds.
+@ATTRIBUTION@]]></help>
+  <citations/>
+</tool>