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comparison tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml @ 6:7a6f2380fc1d draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
parents 35c9abcd8934
children
comparison
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5:35c9abcd8934 6:7a6f2380fc1d
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="1.2.1"> 2 <tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="MET4J_VERSION_TEST">
3 <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</description> 3 <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</description>
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">met4j</xref> 5 <xref type="bio.tools">met4j</xref>
6 </xrefs> 6 </xrefs>
7 <requirements> 7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CarbonSkeletonNet -s "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CarbonSkeletonNet -s "$inputPath"
11 -g "$inputAAM" 11 -g "$inputAAM"
12 $keepSingleCarbon 12 $keepSingleCarbon
13 $mergeComp 13 $mergeComp
14 $mergeEdges 14 $mergeEdges
15 $removeIsolated 15 $removeIsolated
16 $undirected 16 $undirected
17 $computeWeight 17 $computeWeight
18 $asMatrix 18 $asMatrix
19 $main
19 $fromIndexes 20 $fromIndexes
20 -o "$outputPath" 21 -o "$outputPath"
21 ]]></command> 22 ]]></command>
22 <inputs> 23 <inputs>
23 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> 24 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
27 <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/> 28 <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/>
28 <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/> 29 <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/>
29 <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/> 30 <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>
30 <param argument="-tp" checked="false" falsevalue="" label="set transition probability as weight" name="computeWeight" truevalue="-tp" type="boolean" value="false"/> 31 <param argument="-tp" checked="false" falsevalue="" label="set transition probability as weight" name="computeWeight" truevalue="-tp" type="boolean" value="false"/>
31 <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/> 32 <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/>
33 <param argument="-main" checked="false" falsevalue="" label="Compute RPAIRS-like tags and keep only main transitions for each reaction" name="main" truevalue="-main" type="boolean" value="false"/>
32 <param argument="-i" checked="false" falsevalue="" label="Use GSAM output with carbon indexes" name="fromIndexes" truevalue="-i" type="boolean" value="false"/> 34 <param argument="-i" checked="false" falsevalue="" label="Use GSAM output with carbon indexes" name="fromIndexes" truevalue="-i" type="boolean" value="false"/>
33 </inputs> 35 </inputs>
34 <outputs> 36 <outputs>
35 <data format="gml" name="outputPath"/> 37 <data format="gml" name="outputPath"/>
36 </outputs> 38 </outputs>