<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="2.0.0">
  <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or 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:2.0.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath"
 -s "$sourcePath"
 -t "$targetPath"
 $undirected
 -sc "$sideCompoundFile"
#if str($blkdReactionFile) != 'None':
 -br "$blkdReactionFile"
#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="-t" format="txt" label="input targets txt file" name="targetPath" 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="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/>
    <param argument="-br" format="txt" label="a file containing list of blocked reactions to ignore" name="blkdReactionFile" 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>
    </param>
  </inputs>
  <outputs>
    <data format="txt" name="output"/>
  </outputs>
  <tests>
    <test>
      <param name="inputPath" value="toy_model.xml"/>
      <param name="sourcePath" value="seeds.txt"/>
      <param name="targetPath" value="targets.txt"/>
      <param name="sideCompoundFile" value="sc.txt"/>
      <param name="format" value="gml"/>
      <output ftype="txt" name="output">
        <assert_contents>
          <has_line_matching expression=".*node.*" n="5"/>
          <has_line_matching expression=".*edge.*" n="4"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of compounds and/or 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 and compounds from the first list to reactions and compounds 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, bipartite graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds and blocked reactions to ignore during path build must be provided. An optional edge weight file, if available, can also be used.]]></help>
  <citations/>
</tool>
