<tool id="gff3_to_fasta" name="Extract proteins from gff3" version="1.1.1">
    <description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description>
    <requirements>
        <container type="docker">iracooke/protk-1.4.3</container>
        <requirement type="package" version="1.4.3">protk</requirement>
   </requirements>
    <stdio>
        <exit_code range="1:"   level="fatal"   description="Failure" />
    </stdio>
    <command>
        augustus_to_proteindb.rb $gff_file -o $output $coords
    </command>
    <inputs>
        <param name="gff_file" type="data" format="gff3" label="Augustus Generated gff3 File" />
        <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--info" falsevalue="" />
    </inputs>
    <outputs>
        <data format="fasta" name="output" />
    </outputs>
    <tests>
      <!-- Just test that the tool runs and produces vaguely correct output -->
      <test>
          <param name="gff_file" value="augustus_sample.gff" format="gff3"/>
          <output name="output" file="augustus_sample.fasta" format="fasta"/>
      </test>
    </tests>
  <help>

**What it does**

Extract proteins from gff3 and encode genomic coordinates in the fasta header.
Currently this only works with gff3 generated using the Augustus gene finder

  </help>
</tool>