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comparison build/tools/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml @ 8:1274e2a62479 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
author metexplore
date Wed, 26 Jul 2023 15:33:45 +0000
parents 1436e9cde9c9
children
comparison
equal deleted inserted replaced
7:1436e9cde9c9 8:1274e2a62479
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="1.4.0"> 2 <tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="1.5.0">
3 <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> 3 <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>
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:1.4.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath"
11 -s "$sourcePath" 11 -s "$sourcePath"
12 $undirected 12 $undirected
13 $asTable 13 $asTable
14 -t "$targetPath" 14 -t "$targetPath"
15 -sc "$sideCompoundFile" 15 -sc "$sideCompoundFile"
16 #if str($rExclude) != 'None':
17 -re "$rExclude"
18 #end if
16 #if str($weightFile) != 'None': 19 #if str($weightFile) != 'None':
17 -cw "$weightFile" 20 -cw "$weightFile"
18 #end if 21 #end if
19 #if str($k): 22 #if str($k):
20 -k "$k" 23 -k "$k"
27 <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/> 30 <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/>
28 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> 31 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
29 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/> 32 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
30 <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/> 33 <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/>
31 <param argument="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/> 34 <param argument="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/>
35 <param argument="-re" format="txt" label="an optional file containing list of reactions to ignore" name="rExclude" optional="true" type="data" value=""/>
32 <param argument="-cw" format="tsv" label="an optional file containing weights for reactions pairs" name="weightFile" optional="true" type="data" value=""/> 36 <param argument="-cw" format="tsv" label="an optional file containing weights for reactions pairs" name="weightFile" optional="true" type="data" value=""/>
33 <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1"> 37 <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1">
34 <sanitizer invalid_char="_"> 38 <sanitizer invalid_char="_">
35 <valid initial="string.printable"/> 39 <valid initial="string.printable"/>
36 </sanitizer> 40 </sanitizer>