<tool id="edu.tamu.cpt.gff3.fixsixpack" name="GFF3 Add Gene to CDS for Sixpack" version="19.1.0.0">
  <description>Properly formats naive ORF caller output for Apollo</description>
  <macros>
    <import>macros.xml</import>

  </macros>
  <expand macro="requirements">
    <requirement type="package" version="3.9.16">python</requirement>
    <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
    <requirement type="package" version="1.81">biopython</requirement>
  </expand>
  <command detect_errors="aggressive"><![CDATA[
'$__tool_directory__/gff3_fix_sixpack.py'
@INPUT_GFF@
> '$output']]></command>
  <inputs>
    <expand macro="gff3_input"/>
  </inputs>
  <outputs>
    <data format="gff3" name="output"/>
  </outputs>
  <tests>
    <test>
      <param name="gff3_data" value="miro.gff3"/>
      <output name="output" file="miro.6pfix.gff3"/>
    </test>
    <test>
      <param name="gff3_data" value="miro.cds.gff3"/>
      <output name="output" file="miro.cds6pfix.gff3"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

This tool **strips ALL the mRNA features** in a GFF3 file. It specifically formats 
the output of the naïve ORF call Sixpack such that it will be compatible with 
Apollo via JBrowse.

      ]]></help>
  <expand macro="citations"/>
</tool>