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comparison tools/networkAnalysis/NetworkSummary/NetworkSummary.xml @ 5:35c9abcd8934 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
author metexplore
date Thu, 12 Jan 2023 13:45:13 +0000
parents ae4c301919c4
children 7a6f2380fc1d
comparison
equal deleted inserted replaced
4:ae4c301919c4 5:35c9abcd8934
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_NetworkSummary" name="NetworkSummary" version="1.2.0"> 2 <tool id="met4j_NetworkSummary" name="NetworkSummary" version="1.2.1">
3 <description>Create a report summarizing several graph measures characterising the structure of the network.</description> 3 <description>Create a report summarizing several graph measures characterising the structure of the network.</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:1.2.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath"
11 #if str($sideCompoundFile) != 'None': 11 #if str($sideCompoundFile) != 'None':
12 -s "$sideCompoundFile" 12 -s "$sideCompoundFile"
13 #end if 13 #end if
15 $directed 15 $directed
16 -o "$outputPath" 16 -o "$outputPath"
17 ]]></command> 17 ]]></command>
18 <inputs> 18 <inputs>
19 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> 19 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
20 <param argument="-s" format="" label="an optional file containing list of side compounds to ignore (recommended)" name="sideCompoundFile" optional="true" type="data" value=""/> 20 <param argument="-s" format="txt" label="an optional file containing list of side compounds to ignore (recommended)" name="sideCompoundFile" optional="true" type="data" value=""/>
21 <param argument="-sd" checked="false" falsevalue="" label="skip full distance matrix computation (quick summary)" name="skipdist" truevalue="-sd" type="boolean" value="false"/> 21 <param argument="-sd" checked="false" falsevalue="" label="skip full distance matrix computation (quick summary)" name="skipdist" truevalue="-sd" type="boolean" value="false"/>
22 <param argument="-d" checked="false" falsevalue="" label="use reaction direction for distances" name="directed" truevalue="-d" type="boolean" value="false"/> 22 <param argument="-d" checked="false" falsevalue="" label="use reaction direction for distances" name="directed" truevalue="-d" type="boolean" value="false"/>
23 </inputs> 23 </inputs>
24 <outputs> 24 <outputs>
25 <data format="" name="outputPath"/> 25 <data format="txt" name="outputPath"/>
26 </outputs> 26 </outputs>
27 <tests> 27 <tests>
28 <test> 28 <test>
29 <param name="inputPath" value="toy_model.xml"/> 29 <param name="inputPath" value="toy_model.xml"/>
30 <output name="outputPath"> 30 <output name="outputPath">