<tool id="sixframe_translate" name="Generate 6-frame translation" version="1.1.1">
    <description>Translates DNA/RNA to protein</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>
        sixframe.rb
        $fasta_file
        -o $output
        $strip_header
        $coords
        $peptideshaker
        --min-len $minlen

        #if $gffoutput:
            --gff
        #end if
    </command>
    <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="gffoutput" type="boolean" label="Produce gff instead of fasta" help="" truevalue="true" falsevalue="false" />
        <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--coords" falsevalue="" />
        <param name="peptideshaker" type="boolean" label="Format fasta entries for PeptideShaker" help="" truevalue="--peptideshaker" falsevalue="" />
        <param name="minlen" type="integer" value="20" min="1" label="Minimum Peptide Length"/>
    </inputs>
    <outputs>
        <data format="fasta" name="output">
            <change_format>
                <when input="gffoutput" value="true" format="gff3" />
            </change_format>
        </data>
    </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

    </help>
</tool>