Mercurial > repos > metexplore > met4j

annotate build/tools/NetworkSummary/NetworkSummary.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
parents 1274e2a62479
children 6a112eaf8f38
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_NetworkSummary" name="NetworkSummary" version="develop">
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3 <description>Create a report summarizing several graph measures characterising the structure of a metabolic network.</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath"
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11 #if str($sideCompoundFile) != 'None':
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12 -s "$sideCompoundFile"
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13 #end if
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14 $skipdist
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15 $directed
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16 -o "$outputPath"
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17 ]]></command>
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18 <inputs>
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19 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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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=""/>
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21 <param argument="-sd" checked="false" falsevalue="" label="skip full distance matrix computation (quick summary)" name="skipdist" truevalue="-sd" type="boolean" value="false"/>
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22 <param argument="-d" checked="false" falsevalue="" label="use reaction direction for distances" name="directed" truevalue="-d" type="boolean" value="false"/>
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23 </inputs>
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24 <outputs>
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25 <data format="txt" name="outputPath"/>
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26 </outputs>
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27 <tests>
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28 <test>
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40 <param name="inputPath" value="toy_model.xml"/>
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52 <output name="outputPath">
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64 <assert_contents>
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76 <has_n_lines min="1"/>
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88 </assert_contents>
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100 </output>
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112 </test>
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113 </tests>
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114 <help><![CDATA[Create a report summarizing several graph measures characterising the structure of a metabolic network.
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115 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>
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116 <citations/>
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117 </tool>