<tool id="snap" name="SNAP" profile="16.04" version="@VERSION@">
    <description>gene prediction</description>
    <xrefs>
        <xref type="bio.tools">snap</xref>
    </xrefs>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
        snap
            -gff
            $lcmask
            #if $strand == 'forward'
                -plus
            #else if $strand == 'backward'
                -minus
            #end if
            -aa '${output_aa}'
            -tx '${output_tx}'
            '${model}'
            '${input_genome}'
        > '${output_gff}'
]]>
    </command>
    <inputs>
        <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>

        <param name="model" type="data" format="snaphmm" label="Prediction model" help="File created with 'Train SNAP' tool"/>

        <param argument="-lcmask" type="boolean"
            label="Treat lowercase as N"
            truevalue="-lcmask" falsevalue="" checked="false" />

        <param name="strand" type="select"
            label="Predict genes on specific strands">
            <option value="both">both</option>
            <option value="forward">forward</option>
            <option value="backward">backward</option>
        </param>
    </inputs>
    <outputs>
        <data format="gff" name="output_gff" label="${tool.name} on ${on_string}: GFF"/>
        <data format="fasta" name="output_aa" label="${tool.name} on ${on_string}: Protein sequence"/>
        <data format="fasta" name="output_tx" label="${tool.name} on ${on_string}: Coding sequence"/>
    </outputs>
    <tests>
        <test>
            <param name="input_genome" value="human.fa" ftype="fasta" />
            <param name="model" value="snap.hmm" />
            <!-- FIXME ftype temporarily removed because the not yet existing snaphmm type breaks travis tests -->
            <!--param name="model" value="snap.hmm" ftype="snaphmm" /-->
            <output name="output_gff" file="snap_annot.gff" ftype="gff"/>
            <output name="output_aa" file="annot_aa.fasta" ftype="fasta"/>
            <output name="output_tx" file="annot_tx.fasta" ftype="fasta"/>
        </test>
    </tests>
    <help>
<![CDATA[
    SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.
]]>
    </help>
    <expand macro="citations"/>
</tool>