<tool id="cnvkit_target" name="CNVkit Target" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Prepare a BED file of baited regions for use with CNVkit</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[    
    ln -s '$input_file' ./capture.bed &&
    #if $annotate
        ln -s '$annotate' ./annotate.bed &&
    #end if
    cnvkit.py target
        '$input_file'
        --output capture.split.bed
        #if $annotate
            --annotate ./annotate.bed
        #end if
        $short_names
        $split
        #if str($avg_size)
             --avg-size $avg_size
        #end if
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="bed" label="capture/target BED file" help="" />
        <param argument="--annotate" optional="true" type="data" format="bed,gff,tabular" label="Use gene models from this file to assign names to the target regions" help="Format: UCSC refFlat.txt or ensFlat.txt file, BED, interval list, GFF, or similar" />
        <param argument="--short-names" type="boolean" checked="false" truevalue="--short-names" falsevalue="" label="Reduce multi-accession bait labels to be short and consistent" help="" />
        <param argument="--split" type="boolean" checked="false" truevalue="--split" falsevalue="" label="Split large tiled intervals into smaller, consecutive targets" help="" />
        <param argument="--avg-size" type="integer" optional="true" label="Average size of split target bins" min ="1" value="266" help="" />
    </inputs>
    <outputs>
        <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: capture split" from_work_dir="capture.split.bed" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_file" ftype="bed" value="capture.bed" />
            <param name="split" value="1" />
            <param name="short_names" value="1" />
            <output name="out_capture_target">
                <assert_contents><has_text_matching expression="chrM"/></assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
             Transform bait intervals into targets more suitable for CNVkit.
    ]]></help>
    <expand macro="citations" />
</tool>