annotate Sbml2Tab.xml @ 1:be58dd7c74ee draft

planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 6bb33ff0ff022029543e5e5ace7d16418715aa1c

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="@TOOL_VERSION@">
  <description>Create a tabulated file listing reaction attributes from a SBML file</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[met4j convert.Sbml2Tab#if str($i):
 -irr "$i"
#end if
#if str($r):
 -rev "$r"
#end if
 -i "$in"
 -o "$out"
]]></command>
  <inputs>
    <param argument="-irr" label="[--&gt;] String for irreversible reaction" name="i" optional="true" type="text" value="--&gt;">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-rev" label="[&lt;==&gt;] String for reversible reaction" name="r" optional="true" type="text" value="&lt;==&gt;">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-i" format="sbml" label="Sbml file" name="in" optional="false" type="data" value=""/>
  </inputs>
  <outputs>
    <data format="tsv" name="out"/>
  </outputs>
  <tests>
    <test>
      <param name="in" value="toy_model.xml"/>
      <output ftype="tsv" name="out">
        <assert_contents>
          <has_n_lines n="8"/>
          <has_n_columns n="9"/>
          <has_text text="2.0 E[c] --&gt; D[c]"/>
          <has_text text="A[c] &lt;==&gt; B[c]"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="in" value="toy_model.xml"/>
      <param name="i" value="-&gt;"/>
      <param name="r" value="="/>
      <output ftype="tsv" name="out">
        <assert_contents>
          <has_n_lines n="8"/>
          <has_n_columns n="9"/>
          <has_text text="2.0 E[c] -&gt; D[c]"/>
          <has_text text="A[c] = B[c]"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file
@ATTRIBUTION@]]></help>
  <citations/>
</tool>