Mercurial > repos > metexplore > met4j
comparison build/tools/PrecursorNetwork/PrecursorNetwork.xml @ 6:7a6f2380fc1d draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
| author | metexplore |
|---|---|
| date | Wed, 17 May 2023 13:26:37 +0000 |
| parents | |
| children | 1436e9cde9c9 |
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| 5:35c9abcd8934 | 6:7a6f2380fc1d |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | |
| 2 <tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="1.3.0"> | |
| 3 <description>Perform a network expansion from a set of compound targets to create a precursor 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:1.3.0</container> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath" | |
| 11 -t "$targetsFilePath" | |
| 12 #if str($sideCompoundFile) != 'None': | |
| 13 -sc "$sideCompoundFile" | |
| 14 #end if | |
| 15 #if str($reactionToIgnoreFile) != 'None': | |
| 16 -ir "$reactionToIgnoreFile" | |
| 17 #end if | |
| 18 $asTable | |
| 19 -o "$output" | |
| 20 ]]></command> | |
| 21 <inputs> | |
| 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=""/> | |
| 23 <param argument="-t" format="txt" label="input target file: tabulated file containing node of interest ids" name="targetsFilePath" optional="false" type="data" value=""/> | |
| 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=""/> | |
| 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=""/> | |
| 26 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data format="gml" name="output"/> | |
| 30 </outputs> | |
| 31 <tests> | |
| 32 <test> | |
| 33 <param name="sbmlFilePath" value="toy_model.xml"/> | |
| 34 <param name="targetsFilePath" value="targets.txt"/> | |
| 35 <output ftype="gml" name="output"> | |
| 36 <assert_contents> | |
| 37 <has_line_matching expression=".*node.*" n="13"/> | |
| 38 <has_line_matching expression=".*edge.*" n="15"/> | |
| 39 </assert_contents> | |
| 40 </output> | |
| 41 </test> | |
| 42 </tests> | |
| 43 <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network. | |
| 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> | |
| 45 <citations/> | |
| 46 </tool> |