<?xml version="1.0"?>
<tool id="edu.tamu.cpt.gff3.prepForApollo" name="Prep GFF3 Input for Apollo" version="20.8.0.0">
  <description>by ensuring that CDS features have a wrapping exon feature</description>
  <macros>
    <import>macros.xml</import>
    <import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
$__tool_directory__/gff3_prep_for_apollo.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="ApolloPrep_In.gff3" />
			<output name="output" value="ApolloPrep_Out.gff3" />
		</test>
  </tests>
  <help><![CDATA[
**What it does**

This tool updates the gene model in a GFF3 so that it can be added into Apollo
and be used to promote annotations with the correct CDS calculation. It finds any
CDS feature who's direct parent is a gene feature, and creates an exon feature 
that is the child of the gene feature and the parent of the CDS. If a gene has 
multiple CDS features, they will be wrapped under the same exon feature. 

All other features present in the GFF under the gene will be kept the same. 

Warning: Use this tool only when it is absolutely necessary to fix a gene model. 

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