Mercurial > repos > metexplore > met4j
comparison tools/networkAnalysis/NetworkSummary/NetworkSummary.xml @ 0:dcd16521b969 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
author | metexplore |
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date | Fri, 10 Jun 2022 10:31:34 +0000 |
parents | |
children | 9b162ee6ff8e |
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1 <?xml version="1.0" encoding="UTF-8"?> | |
2 <tool id="met4j_NetworkSummary" name="NetworkSummary" version="0.11.0"> | |
3 <description>Create a report summarizing several graph measures characterising the structure of the network.</description> | |
4 <xrefs> | |
5 <xref type="bio.tools">met4j</xref> | |
6 </xrefs> | |
7 <requirements> | |
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container> | |
9 </requirements> | |
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath" | |
11 #if str($sideCompoundFile) != 'None': | |
12 -s "$sideCompoundFile" | |
13 #end if | |
14 $skipdist | |
15 $directed | |
16 -o "$outputPath" | |
17 ]]></command> | |
18 <inputs> | |
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=""/> | |
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"/> | |
23 </inputs> | |
24 <outputs> | |
25 <data format="" name="outputPath"/> | |
26 </outputs> | |
27 <tests> | |
28 <test> | |
29 <param name="inputPath" value="toy_model.xml"/> | |
30 <output name="outputPath"> | |
31 </output> | |
32 </test> | |
33 </tests> | |
34 <help><![CDATA[Use a metabolic network in SBML file and an optional list of side compounds, and produce a report summarizing several graph measures characterising the structure of the network.This includes (non-exhaustive list): size and order, connectivity, density, degree distribution, shortest paths length, top centrality nodes...]]></help> | |
35 </tool> |