<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_DegreeWeighting" name="DegreeWeighting" version="1.2.1">
  <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:1.2.1</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. See Croes et al. 2006 (https://doi.org/10.1016/j.jmb.2005.09.079) and Croes et al. 2005 (https://doi.org/10.1093/nar/gki437)]]></help>
  <citations/>
</tool>