Mercurial > repos > metexplore > met4j
diff tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml @ 2:e69a78624877 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit cb957f5d5540a48293fe8487c0cfad78ab439d7c
author | metexplore |
---|---|
date | Tue, 19 Jul 2022 14:20:07 +0000 |
parents | 9b162ee6ff8e |
children | 6bd9aad9626d |
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--- a/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Mon Jun 27 13:41:08 2022 +0000 +++ b/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Tue Jul 19 14:20:07 2022 +0000 @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="0.12.0"> +<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="1.0.1"> <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath" -s "$sourcePath" @@ -24,11 +24,11 @@ ]]></command> <inputs> <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> - <param argument="-s" format="text" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/> + <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/> <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> - <param argument="-t" format="text" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/> - <param argument="-sc" format="text" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/> + <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/> + <param argument="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/> <param argument="-cw" format="tsv" label="an optional file containing weights for reactions pairs" name="weightFile" optional="true" type="data" value=""/> <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1"> <sanitizer invalid_char="_">