<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="1.0.1">
  <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</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.CarbonSkeletonNet -s "$inputPath"
 -g "$inputAAM"
 $keepSingleCarbon
 $mergeComp
 $mergeEdges
 $removeIsolated
 $undirected
 $computeWeight
 $asMatrix
 $fromIndexes
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
    <param argument="-g" format="gsam" label="input GSAM file" name="inputAAM" optional="false" type="data" value=""/>
    <param argument="-ks" checked="false" falsevalue="" label="keep edges involving single-carbon compounds, such as CO2 (requires formulas in SBML)" name="keepSingleCarbon" truevalue="-ks" type="boolean" value="false"/>
    <param argument="-mc" checked="false" falsevalue="" label="merge compartments (requires unique compound names that are consistent across compartments)" name="mergeComp" truevalue="-mc" type="boolean" value="false"/>
    <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="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" 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 transition probability as weight" name="computeWeight" truevalue="-tp" type="boolean" value="false"/>
    <param argument="-am" checked="false" falsevalue="" label="export as matrix (implies simple graph conversion). Default export as GML file" name="asMatrix" truevalue="-am" type="boolean" value="false"/>
    <param argument="-i" checked="false" falsevalue="" label="Use GSAM output with carbon indexes" name="fromIndexes" truevalue="-i" type="boolean" value="false"/>
  </inputs>
  <outputs>
    <data format="gml" name="outputPath"/>
  </outputs>
  <tests>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
      <output name="outputPath">
        <assert_contents>
          <has_n_lines n="2602"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
      <param name="keepSingleCarbon" value="true"/>
      <output name="outputPath">
        <assert_contents>
          <has_n_lines n="2629"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
      <param name="mergeComp" value="true"/>
      <output name="outputPath">
        <assert_contents>
          <has_n_lines n="2406"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
      <param name="mergeEdges" value="true"/>
      <output name="outputPath">
        <assert_contents>
          <has_n_lines n="2071"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
      <param name="removeIsolated" value="true"/>
      <output name="outputPath">
        <assert_contents>
          <has_n_lines n="2490"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
      <param name="undirected" value="true"/>
      <output name="outputPath">
        <assert_contents>
          <has_n_lines n="3214"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
      <param name="asMatrix" value="true"/>
      <output name="outputPath">
        <assert_contents>
          <has_n_lines n="112"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="inputAAM" value="Human-GEM_pathways-transitions2.tab"/>
      <param name="fromIndexes" value="true"/>
      <output name="outputPath">
        <assert_contents>
          <has_n_lines n="2611"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produce a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) perform atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.]]></help>
  <citations/>
</tool>