<tool id="edu.tamu.cpt.external.aragorn-gff3" name="Fix tRNA model" version="19.1.0.0">
  <description/>
  <macros>
    <import>macros.xml</import>
    <import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
'$__tool_directory__/fix-aragorn-gff3.py'
@INPUT_GFF@
> '$default']]></command>
  <inputs>
    <expand macro="gff3_input"/>
  </inputs>
  <outputs>
    <data format="gff3" name="default"/>
  </outputs>
  <tests>
    <test>
      <param name="gff3_data" value="FixAra_In.gff3"/>
      <output name="default" file="FixAra_Out.gff3"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

For an input GFF3 file with tRNAs from the Aragorn or converted from the tRNAscan-SE tools, this tool modifies 
the gene model to reflect a gene-tRNA-exon hierarchy. That change is needed 
to allow for creation of proper tRNA features in Apollo.
      ]]></help>
  <expand macro="citations"/>
</tool>