view ExtractSubReactionNetwork.xml @ 3:6acc432dc801 draft default tip

planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="@TOOL_VERSION@">
  <description>Create a subnetwork from a metabolic network 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>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[met4j networkAnalysis.ExtractSubReactionNetwork -i "$inputPath"
 -s "$sourcePath"
 $undirected
 -t "$targetPath"
 -sc "$sideCompoundFile"
#if str($rExclude) != 'None':
 -re "$rExclude"
#end if
#if str($weightFile) != 'None':
 -cw "$weightFile"
#end if
#if str($k):
 -k "$k"
#end if
 $st
#if str($format):
 -f "$format"
#end if
 -o "$output"
]]></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="-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="-re" format="txt" label="an optional file containing list of reactions to ignore" name="rExclude" optional="true" 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>
    </param>
    <param argument="-st" checked="false" falsevalue="" label="Extract Steiner Tree" name="st" truevalue="-st" type="boolean" value="false"/>
    <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id &#9; edge type &#9; target id). Other options include GML, JsonGraph, and tabulated node list (label &#9; node id &#9; node type)." name="format" optional="true" type="select" value="tab">
      <option value="gml">gml</option>
      <option selected="true" value="tab">tab</option>
      <option value="nodeList">nodeList</option>
      <option value="json">json</option>
      <option value="matrix">matrix</option>
      <option value="jsonviz">jsonviz</option>
    </param>
  </inputs>
  <outputs>
    <data format="txt" name="output"/>
  </outputs>
  <tests/>
  <help><![CDATA[Create a subnetwork from a metabolic network 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.
The subnetwork corresponds to the part of the network that connects reactions from the first list to reactions from the second list.
Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, reaction graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds to ignore for linking reactions must be provided. An optional edge weight file, if available, can also be used.
@ATTRIBUTION@]]></help>
  <citations/>
</tool>