<tool id="cnvkit_antitarget" name="CNVkit Antitarget" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>lists the chromosomal coordinates for targeted resequencing</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[  
        ln -s '$targets_file' ./capture.bed &&
        #if $access
            ln -s '$access' ./access.bed &&
        #end if
        cnvkit.py antitarget
            ./capture.bed
            #if $access
                --access ./access.bed
            #end if
            #if str($avg_size)
                --avg-size $avg_size
            #end if
            #if str($min_size)
                --min-size $min_size
            #end if
            --output capture.antitarget.bed
    ]]></command>
    <inputs>
        <param name="targets_file" type="data" format="bed" label="input BED or interval file" help="" />
        <param argument="--access" type="data" optional="true" format="bed" label=" Regions of accessible sequence on chromosomes" help="" />
        <param argument="--avg-size" optional="true" type="integer" label="Average size of antitarget bins" min="1" value="150000" help="" />
        <param argument="--min-size" optional="true" type="integer" label="Minimum size of antitarget bins" min="1" value="25000" help="" />
    </inputs>
    <outputs>
        <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: capture antitarget regions" from_work_dir="capture.antitarget.bed" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="targets_file" ftype="bed" value="capture.bed" />
            <param name="access" ftype="bed" value="access-excludes.bed" />
            <output name="out_capture_antitarget" file="capture.antitarget.bed" /> 
        </test>
    </tests>
    <help><![CDATA[
         Given a “target” BED file that lists the chromosomal coordinates of the tiled
         regions used for targeted resequencing, derive a BED file off-target/”antitarget” regions.
    ]]></help>
    <expand macro="citations" />
</tool>