<tool id="graphmap_overlap" name="Owler" version="@VERSION@">
    <description>fast, trimmed overlap pipeline without aligning</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[
        ln -s '$r' ref.${r.ext} && 
        ln -s '$d' reads.${d.ext} && 

        graphmap owler
        -r ref.${r.ext} 
        -d reads.${d.ext}
        -o output.mhap 
        #if $preset:
            -x $preset
        #end if
        -t \${GALAXY_SLOTS:-4} 
    ]]></command>
    <inputs>
        <param argument="-r" type="data"  format="fasta,fastq" label="reference sequence" />
        <param argument="-d" type="data"  format="fasta,fastq" label="reads" />
        <param name="preset" type="select" optional="True" label="Pre-set parameters (-x)">
            <option value="no-filters">Disable filters</option>
        </param>
<!-- 
        <param type="data" name="reference" format="fasta,fastq" label="Sequences"/>
        <param type="data" name="reads" format="fasta,fastq" label="Sequences"/>
        <param type="data" name="overlaps" format="sam,tabular" label="Overlaps"/>
        <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> -->

    </inputs>
    <outputs>
        <data name="output" format="txt" from_work_dir="output.mhap" />
    </outputs>
    <tests>
        <test>
            <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
            <param name="d" value="E.coli_contigs.fasta"/>
            <output name="output" ftype="txt" file="result1_owler.mhap"/>
        </test>
        <test>
            <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
            <param name="d" value="E.coli_contigs.fasta"/>
            <param name="preset" value="no-filters"/>
            <output name="output" ftype="txt" file="result2_owler.mhap"/>
        </test></tests>
    <help><![CDATA[
        GraphMap - A very accurate and sensitive long-read, high error-rate sequence mapper
        GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan Nagarajan
        GraphMap is licensed under The MIT License.
    ]]></help>
    <expand macro="citations" />
</tool>