annotate tools/networkAnalysis/ChokePoint/ChokePoint.xml @ 0:3cdcfdae8bd2 draft default tip

"planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a58b6f8a6dde6ef64da64ee50395dc5bc848167a-dirty"

<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_ChokePoint" name="ChokePoint" version="0.11.0">
  <description>Compute the Choke points of a metabolic network.</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath"
#if str($sideCompoundFile) != 'None':
 -s "$sideCompoundFile"
#end if
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
    <param argument="-s" format="text" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
  </inputs>
  <outputs>
    <data format="tsv" name="outputPath"/>
  </outputs>
  <tests>
    <test>
      <param name="inputPath" value="XF_network.sbml"/>
      <output ftype="tsv" name="outputPath">
        <assert_contents>
          <has_n_lines n="202"/>
          <has_n_columns n="3"/>
          <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e &lt;==&gt; M_ade_p" n="1"/>
          <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --&gt; M_ru5p_L_c" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="XF_network.sbml"/>
      <param name="sideCompoundFile" value="sides.txt"/>
      <output ftype="tsv" name="outputPath">
        <assert_contents>
          <has_n_lines n="200"/>
          <has_n_columns n="3"/>
          <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e &lt;==&gt; M_ade_p" n="0"/>
          <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --&gt; M_ru5p_L_c" n="0"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Compute the Choke points of a metabolic network.
Load points constitute an indicator of lethality and can help identifying drug target Choke points are reactions that are required to consume or produce one compound. Targeting of choke point can lead to the accumulation or the loss of some metabolites, thus choke points constitute an indicator of lethality and can help identifying drug target 
See : Syed Asad Rahman, Dietmar Schomburg; Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinformatics 2006; 22 (14): 1767-1774. doi: 10.1093/bioinformatics/btl181]]></help>
</tool>