<tool id="edu.tamu.cpt.gff3.require_phage_start" name="GFF3 Filter: Require Phage Start" version="19.1.0.0">
  <description>ensures start is ATG, TTG, or GTG</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[
@GENOME_SELECTOR_PRE@

python '$__tool_directory__/gff3_require_phage_start.py'

@GENOME_SELECTOR@
'$gff3_data'

> '$stdout'

]]></command>
  <inputs>
    <expand macro="genome_selector"/>
    <expand macro="gff3_input"/>
  </inputs>
  <outputs>
    <data format="gff3" name="stdout" label="$gff3_data.name filtered for start codon"/>
  </outputs>
  <tests>
    <test>
      <param name="reference_genome_source" value="history"/>
      <param name="genome_fasta" value="T7_ReqPhageIn.fasta"/>
      <param name="gff3_data" value="T7_ReqPhageIn.gff3"/>
      <output name="stdout" file="T7_ReqPhageOut.gff3"/>
    </test>
    <test>
      <param name="reference_genome_source" value="history"/>
      <param name="genome_fasta" value="Miro_ReqPhageIn.fa"/>
      <param name="gff3_data" value="Miro_ReqPhageIn.gff3"/>
      <output name="stdout" file="Miro_ReqPhageOut.gff3"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Removes any CDS from the GFF3 whose start codon is **not** ATG, TTG, or GTG.

.. class:: warningmark

The tool only retains *gene* and *CDS* features that pass this filter. 
      ]]></help>
  <expand macro="citations"/>
</tool>