view ChokePoint.xml @ 2:d8bd2b838d9e draft default tip

planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 538e93b3d7804d3e2d6a8d83aea3853279d37de3

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_ChokePoint" name="ChokePoint" version="@TOOL_VERSION@">
  <description>Compute the Choke points of a metabolic network.</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[met4j networkAnalysis.ChokePoint -i "$inputPath"
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" 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="695"/>
          <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_AGDC_r.*R_AGDC_r.*M_acgam6p_c \+ M_h2o_c --&gt; M_ac_c \+ M_gam6p_c" n="1"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Compute the Choke points of a metabolic network.
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.
@ATTRIBUTION@]]></help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/btl181</citation>
  </citations>
</tool>