<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_DegreeWeighting" name="DegreeWeighting" version="2.0.0">
  <description>Provides tabulated compound graph edge list, with one column with target's degree.</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.DegreeWeighting#if str($pow):
 -pow "$pow"
#end if
 -s "$inputPath"
#if str($inputSide) != 'None':
 -sc "$inputSide"
#end if
#if str($mergingStrat):
 -mc "$mergingStrat"
#end if
 $mergeEdges
 $undirected
 $computeWeight
 $removeNaN
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-pow" label="set weights as the degree raised to the power of number in parameter." name="pow" optional="true" type="text" value="1">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
    <param argument="-sc" format="txt" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
    <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form &quot;xxx_y&quot; with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">
      <option selected="true" value="no">no</option>
      <option value="by_name">by_name</option>
      <option value="by_id">by_id</option>
    </param>
    <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/>
    <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>
    <param argument="-tp" checked="false" falsevalue="" label="set weight as random walk transition probability, normalized by reaction" name="computeWeight" truevalue="-tp" type="boolean" value="false"/>
    <param argument="-nan" checked="false" falsevalue="" label="do not output edges with undefined weight" name="removeNaN" truevalue="-nan" type="boolean" value="false"/>
  </inputs>
  <outputs>
    <data format="tsv" name="outputPath"/>
  </outputs>
  <tests/>
  <help><![CDATA[Provides tabulated compound graph edge list, with one column with target's degree.Degree has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search.]]></help>
  <citations>
    <citation type="doi">10.1016/j.jmb.2005.09.079</citation>
  </citations>
</tool>
