Mercurial > repos > metexplore > met4j
comparison tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.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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| 1:9b162ee6ff8e | 2:e69a78624877 |
|---|---|
| 1 <?xml version="1.0" encoding="UTF-8"?> | 1 <?xml version="1.0" encoding="UTF-8"?> |
| 2 <tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="0.12.0"> | 2 <tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="1.0.1"> |
| 3 <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds of interests ids, one per row.</description> | 3 <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds of interests ids, one per row.</description> |
| 4 <xrefs> | 4 <xrefs> |
| 5 <xref type="bio.tools">met4j</xref> | 5 <xref type="bio.tools">met4j</xref> |
| 6 </xrefs> | 6 </xrefs> |
| 7 <requirements> | 7 <requirements> |
| 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container> | 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container> |
| 9 </requirements> | 9 </requirements> |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubNetwork -i "$inputPath" | 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubNetwork -i "$inputPath" |
| 11 -s "$sourcePath" | 11 -s "$sourcePath" |
| 12 -t "$targetPath" | 12 -t "$targetPath" |
| 13 #if str($sideCompoundFile) != 'None': | 13 #if str($sideCompoundFile) != 'None': |
| 26 $st | 26 $st |
| 27 -o "$outputPath" | 27 -o "$outputPath" |
| 28 ]]></command> | 28 ]]></command> |
| 29 <inputs> | 29 <inputs> |
| 30 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> | 30 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> |
| 31 <param argument="-s" format="text" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/> | 31 <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/> |
| 32 <param argument="-t" format="text" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/> | 32 <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/> |
| 33 <param argument="-sc" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/> | 33 <param argument="-sc" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/> |
| 34 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/> | 34 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting" name="degree" truevalue="-dw" type="boolean" value="false"/> |
| 35 <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/> | 35 <param argument="-cw" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/> |
| 36 <param argument="-sw" checked="false" falsevalue="" label="penalize traversal of non-relevant edges by using chemical similarity weighting" name="chemicalSim" truevalue="-sw" type="boolean" value="false"/> | 36 <param argument="-sw" checked="false" falsevalue="" label="penalize traversal of non-relevant edges by using chemical similarity weighting" name="chemicalSim" truevalue="-sw" type="boolean" value="false"/> |
| 37 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> | 37 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> |
| 38 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> | 38 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> |