<tool id="sixframe_translate" name="Generate 6-frame translation" version="1.1.0">
	<requirements>
        <container type="docker">iracooke/protk-1.4.1</container>		
	    <requirement type="package" version="1.4">protk</requirement>
   </requirements>

	<description>Translates DNA/RNA to protein</description>

	<command>
		sixframe.rb $fasta_file -o $output $strip_header $coords
	</command>




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

	<inputs>	
		<param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
		<param name="strip_header" type="boolean" label="Strip header info" help="" truevalue="--strip-header" falsevalue="" />
		<param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--coords" falsevalue="" />
	</inputs>

	<outputs>
		<data format="fasta" name="output" />
	</outputs>

	<tests>
	  <test>
	      <param name="fasta_file" value="small_genome.fasta" format="fasta"/>
	      <output name="output" format="fasta">
	          <assert_contents>
	              <has_text text="SVQHWFYRFQAGHPRVFCPKNGPRRLW" />
	          </assert_contents>
	      </output>
	  </test>
	</tests>


  <help>

**What it does**

Generates 6 frame translations suitable for proteogenomics workflows

----

**References**


  </help>

</tool>