annotate tools/convert/Sbml2Tab/Sbml2Tab.xml.bak @ 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_Sbml2Tab" name="Sbml2Tab" version="0.9.1">
  <description>Create a tabulated file from a SBML file</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.9.1-SNAPSHOT</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i):
 -i "$i"
#end if
#if str($r):
 -r "$r"
#end if
 -in "$in"
 -out "$out"
]]></command>
  <inputs>
    <param argument="-i" label="[--&gt;] String for irreversible reaction" name="i" optional="true" type="text">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-r" label="[&lt;==&gt;] String for reversible reaction" name="r" optional="true" type="text">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-in" format="format" label="Sbml file" name="in" optional="false" type="data"/>
  </inputs>
  <outputs>
    <data format="tsv" name="out"/>
  </outputs>
  <help><![CDATA[Create a tabulated file from a SBML file]]></help>
  <tests>
    <test>
      <param name="in" value="toy_model.xml" />
      <output name="out" ftype="tsv" >
      <assert_contents>
        <has_n_lines n="8"></has_n_lines>
        <has_n_columns n="9"></has_n_columns>
        <has_text text="2.0 E[c] --&gt; D[c]"></has_text>
        <has_text text="A[c] &lt;==&gt; B[c]"></has_text>
      </assert_contents>
    </output>
    </test>
    <test>
      <param name="in" value="toy_model.xml" />
      <param name="i" value="-&gt;" />
      <param name="r" value="=" />
      <output name="out" ftype="tsv" >
      <assert_contents>
        <has_n_lines n="8"></has_n_lines>
        <has_n_columns n="9"></has_n_columns>
        <has_text text="2.0 E[c] -&gt; D[c]"></has_text>
        <has_text text="A[c] = B[c]"></has_text>
      </assert_contents>
    </output>
    </test>
  </tests>
</tool>