<tool id="gff3_to_fasta" name="Extract proteins from gff3" version="1.1.0">
	<requirements>
        <container type="docker">iracooke/protk-1.4.1</container>		
	    <requirement type="package" version="1.4">protk</requirement>
   </requirements>

	<description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description>

	<command>
		augustus_to_proteindb.rb $gff_file -o $output $coords
	</command>




	<stdio>
		<exit_code range="1:"   level="fatal"   description="Failure" />
	</stdio>

	<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

----

**References**


  </help>

</tool>