<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">0.8.5</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">delly</requirement>
            <requirement type="package" version="1.10.2">bcftools</requirement>
        </requirements>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[delly -v 2>&1 | grep 'Delly version' | cut -f 3 -d ' ']]></version_command>
    </xml>
	<xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/bts378</citation>
        </citations>
    </xml>
	
    <!--
        command 
    -->

    <token name="@BAM@"><![CDATA[
#for $i, $current in enumerate($samples)
    ln -s '${current}' 'sample_${i}.bam' &&
    ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' &&
#end for
    ]]></token>
    <token name="@DUMP@"><![CDATA[
#if 'dump' in $oo.out
    && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
#end if
    ]]></token>
    <token name="@LOG@"><![CDATA[
#if 'log' in $oo.out
    |& tee '$out_log'
#end if
    ]]></token>
    <token name="@VCF@"><![CDATA[
#if 'vcf' in $oo.out
    && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
#end if
    ]]></token>

    <!--
        input 
    -->

    <xml name="exclude">
        <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
    </xml>
    <xml name="genome">
        <param argument="--genome" type="data" format="fasta" label="Select genome"/>
    </xml>
    <xml name="genoqual">
        <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
    </xml>
    <xml name="minclip">
        <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
    </xml>
    <xml name="maxreadsep" token_default="40">
        <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
    </xml>
    <xml name="maxsize" token_default="1000000">
        <param argument="--maxsize" type="integer" value="@DEFAULT@" label="Set maximum SV size"/>
    </xml>
    <xml name="mincliquesize">
        <param name="mincliquesize" type="integer" value="2" label="Set minimum min. PE/SR clique size" help="(--min-clique-size)"/>
    </xml>
    <xml name="minrefsep" token_default="25">
        <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
    </xml>
    <xml name="minsize">
        <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/>
    </xml>
    <xml name="samples" token_format="bam" token_multiple="true" token_label="Select sample file(s)">
        <param name="samples" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
    </xml>
    <xml name="svtype">
        <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
            <option value="ALL" selected="true">All types (ALL)</option>
            <option value="DEL">Deletion (DEL)</option>
            <option value="INS">Insertion (INS)</option>
            <option value="DUP">Duplication (DUP)</option>
            <option value="INV">Inversion (INV)</option>
            <option value="BND">Translocation (BND)</option>
        </param>
    </xml>
    <xml name="vcffile">
        <param argument="--vcffile" type="data" format="vcf,bcf" optional="true" label="Select genotyping file"/>
    </xml>

    <!--
        output 
    -->

    <xml name="vcf">
        <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
            <filter>'vcf' in oo['out']</filter>
        </data>
    </xml>
     <xml name="bcf">
        <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
            <filter>'bcf' in oo['out']</filter>
        </data>
    </xml>
    <xml name="dump">
        <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
            <filter>'dump' in oo['out']</filter>
        </data>
    </xml>
    <xml name="log">
        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
            <filter>'log' in oo['out']</filter>
        </data>
    </xml>

    <!--
        Help
    -->

    <token name="@WID@"><![CDATA[
Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.
    ]]></token>
    <token name="@REFERENCES@"><![CDATA[
More information are available on `GitHub <https://github.com/dellytools/delly>`_.
    ]]></token>
</macros>