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annotate tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml @ 8:1274e2a62479 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
author metexplore
date Wed, 26 Jul 2023 15:33:45 +0000
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dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="MET4J_VERSION_TEST">
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3 <description>Perform a network expansion from a set of compound targets to create a precursor 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:MET4J_VERSION_TEST</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath"
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11 -t "$targetsFilePath"
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12 #if str($sideCompoundFile) != 'None':
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13 -sc "$sideCompoundFile"
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14 #end if
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15 #if str($reactionToIgnoreFile) != 'None':
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16 -ir "$reactionToIgnoreFile"
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17 #end if
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18 $asTable
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19 -o "$output"
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20 ]]></command>
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21 <inputs>
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22 <param argument="-i" format="sbml" label="input SBML file: path to network used for computing scope, in sbml format." name="sbmlFilePath" optional="false" type="data" value=""/>
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23 <param argument="-t" format="txt" label="input target file: tabulated file containing node of interest ids" name="targetsFilePath" optional="false" type="data" value=""/>
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24 <param argument="-sc" format="txt" label="an optional file containing list of ubiquitous compounds to be considered already available" name="sideCompoundFile" optional="true" type="data" value=""/>
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25 <param argument="-ir" format="txt" label="an optional file containing list of reaction to ignore (forbid inclusion in scope)" name="reactionToIgnoreFile" optional="true" type="data" value=""/>
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26 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
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27 </inputs>
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28 <outputs>
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29 <data format="gml" name="output"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="sbmlFilePath" value="toy_model.xml"/>
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34 <param name="targetsFilePath" value="targets.txt"/>
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35 <output ftype="gml" name="output">
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36 <assert_contents>
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37 <has_line_matching expression=".*node.*" n="13"/>
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38 <has_line_matching expression=".*edge.*" n="15"/>
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39 </assert_contents>
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40 </output>
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41 </test>
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42 </tests>
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43 <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network.
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44 The precursor network of a set of compounds (targets) refer to the sub-part of a metabolic network from which a target can be reachedThe network expansion process consist of adding a reaction to the network if any of its products are either a targets or a substrate of a previously added reaction]]></help>
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45 <citations/>
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46 </tool>