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view tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.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 |
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children | 9b162ee6ff8e |
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<?xml version="1.0" encoding="UTF-8"?> <tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="0.11.0"> <description>Perform a network expansion from a set of compound targets to create a precursor network.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath" -t "$targetsFilePath" #if str($sideCompoundFile) != 'None': -sc "$sideCompoundFile" #end if #if str($reactionToIgnoreFile) != 'None': -ir "$reactionToIgnoreFile" #end if -o "$output" ]]> </command> <inputs> <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=""/> <param argument="-t" format="" label="input target file: tabulated file containing node of interest ids" name="targetsFilePath" optional="false" type="data" value=""/> <param argument="-sc" format="" label="an optional file containing list of ubiquitous compounds to be considered already available" name="sideCompoundFile" optional="true" type="data" value=""/> <param argument="-ir" format="" label="an optional file containing list of reaction to ignore (forbid inclusion in scope)" name="reactionToIgnoreFile" optional="true" type="data" value=""/> </inputs> <outputs> <data format="gml" name="output"/> </outputs> <tests> <test> <param name="sbmlFilePath" value="toy_model.xml"/> <param name="targetsFilePath" value="targets.txt"/> <output ftype="gml" name="output"> <assert_contents> <has_line_matching expression=".*node.*" n="13"/> <has_line_matching expression=".*edge.*" n="15"/> </assert_contents> </output> </test> </tests> <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network. 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> </tool>