Mercurial > repos > metexplore > met4j
diff build/tools/PrecursorNetwork/PrecursorNetwork.xml @ 6:7a6f2380fc1d draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author | metexplore |
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date | Wed, 17 May 2023 13:26:37 +0000 |
parents | |
children | 1436e9cde9c9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/tools/PrecursorNetwork/PrecursorNetwork.xml Wed May 17 13:26:37 2023 +0000 @@ -0,0 +1,46 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="1.3.0"> + <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:1.3.0</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 + $asTable + -o "$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="txt" label="input target file: tabulated file containing node of interest ids" name="targetsFilePath" optional="false" type="data" value=""/> + <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=""/> + <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=""/> + <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> + </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> + <citations/> +</tool>