<tool id="graphmap_align" name="Mapper" version="@VERSION@">
    <description>for long, error-prone reads, like Nanopore ONT and PacBio</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs" />
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[
        ln -s '$r' ref.${r.ext} && 
        ln -s '$d' reads.${d.ext} && 

        graphmap align  
        -r ref.${r.ext} 
        -d reads.${d.ext}
        #if $preset:
            -x $preset
        #end if
        -t \${GALAXY_SLOTS:-4} |
        samtools view -b -u | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam -
    ]]></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 to increase sensitivity for different sequencing technologies. (-x)">
            <option value="illumina">illumina preset</option>
            <option value="overlap">overlap preset</option>
            <option value="sensitive">sensitive preset</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="bam" from_work_dir="output.bam" />
    </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="bam" file="result1_map.bam" lines_diff="2"/>
        </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="illumina"/>
            <output name="output" ftype="bam" file="result2_map.bam" lines_diff="2"/>
        </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="sensitive"/>
            <output name="output" ftype="bam" file="result3_map.bam" lines_diff="2"/>
        </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>