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<?xml version="1.0"?>
<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>
		<import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <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>