view ontologizer.xml @ 21:452159eb3cd5

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<tool id="ontologizer" name="ontologizer" version="0.0.14">
  <description>from http://compbio.charite.de/contao/</description>
  <requirements>
    <requirement type="set_environment">ONTOLOGIZER_JAR_PATH</requirement>
    <requirement type="package" version="0.0.1">ontologizer-jar</requirement>
  </requirements>
  <command>java -Xmx2G -jar $ONTOLOGIZER_JAR --go $go --association $gaf --population $pop --studyset $study --dot 0.05 > $output</command>
  <inputs>
    <param name="go" type="text" label="Gene ontology" />
    <param name="gaf" type="text" label="Gene association file" />
    <param name="pop" type="text" label="population gene set" />
    <param name="study" type="text" label="study gene set" />
  </inputs>
  <outputs>
    <!-- need to figure out how to handle multiple outputs -->
    <data type="text" name="output" />
  </outputs>
  <tests>
    <!-- see http://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests -->
    <test>
     <param name="go" file="ontologizer/test.obo" />
     <param name="gaf" file="ontologizer/test.gaf" />
     <param name="pop" file="ontologizer/test.gs" />
     <param name="study" file="ontologizer/test.gs" />
     <output name="output" file="test.output"/>
    </test>
  </tests>


  <help>
    see http://compbio.charite.de/contao/index.php/ontologizer2.html
  </help>

</tool>