comparison tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml @ 2:e69a78624877 draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit cb957f5d5540a48293fe8487c0cfad78ab439d7c

1:9b162ee6ff8e

<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="0.12.0">
  <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>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath"
 -s "$sourcePath"
 $undirected
 $asTable

 $st
 -o "$outputPath"
]]></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="-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="-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="_">
        <valid initial="string.printable"/>
      </sanitizer>

2:e69a78624877

<?xml version="1.0" encoding="UTF-8"?>
<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:1.0.1</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath"
 -s "$sourcePath"
 $undirected
 $asTable

 $st
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" 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="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="_">
        <valid initial="string.printable"/>
      </sanitizer>