<tool id="bedtools_windowbed" name="WindowBed" version="@WRAPPER_VERSION@.0">
    <description>find overlapping intervals within a window around an interval</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools window
        #if $inputA.is_of_type('bam'):
            -abam '$inputA'
        #else:
            -a '$inputA'
        #end if
        -b '$inputB'
        $bed
        $strandB
        #if $addition.addition_select == 'window':
            -w $addition.w
        #elif $addition.addition_select == 'lr':
            -l $addition.l
            -r $addition.r
        #end if
        $original
        $number
        $nooverlaps
        $header
        > '$output'
]]>
    </command>
    <inputs>
        <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/>
        <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
        <param name="bed" type="boolean" checked="false" truevalue="-bed" falsevalue=""
            label="When using BAM input, write output as BED. The default is to write output in BAM when using a bam file"
            help="(-bed)" />
        <conditional name="addition">
            <param name="addition_select" type="select" label="Choose what you want to do">
                <option value="window">Add Base pairs for **both** upstream and downstream of each entry in A when searching for overlaps in B</option>
                <option value="lr">Add Base pairs **separately** for upstream and downstream of each entry in A when searching for overlaps in B</option>
            </param>
            <when value="window">
                <param name="w" type="integer" value="1000" label="Base pairs to add upstream and downstream" />
            </when>
            <when value="lr">
                <param name="l" type="integer" value="1000"
                    label="Base pairs added upstream (left) of each entry in A when searching for overlaps in B"
                    help="Allows one to create assymetrical “windows”. Default is 1000bp. (-l)" />
                <param name="r" type="integer" value="1000"
                    label="Base pairs added downstream (right) of each entry in A when searching for overlaps in B"
                    help="Allows one to create assymetrical “windows”. Default is 1000bp. (-r)" />
            </when>
        </conditional>
        <param name="strandB" type="select" label="Calculation based on strandedness?">
            <option value="" selected="True">Report any hit in B</option>
            <option value="-sm">Only report hits in B that overlap A on the **same** strand</option>
            <option value="-Sm">Only report hits in B that overlap A on the **opposite** strand</option>
        </param>
        <param name="original" type="boolean" checked="false" truevalue="-u" falsevalue=""
            label="Write original A entry once if any overlaps found in B"
            help="In other words, just report the fact at least one overlap was found in B. (-u)" />
        <param name="number" type="boolean" checked="false" truevalue="-c" falsevalue=""
            label="For each entry in A, report the number of hits in B"
            help="Reports 0 for A entries that have no overlap with B (-c)" />
        <param name="nooverlaps" type="boolean" checked="false" truevalue="-v" falsevalue=""
            label="Only report those entries in A that have no overlaps with B" help="(-v)" />
        <expand macro="print_header" />
    </inputs>
    <outputs>
        <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="windowBedA.bed" ftype="bed" />
            <param name="inputB" value="windowBedB.bed" ftype="bed" />
            <output name="output" file="windowBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="windowBedA.bed" ftype="bed" />
            <param name="inputB" value="windowBedB.bed" ftype="bed" />
            <param name="addition_select" value="window" />
            <param name="w" value="5000" />
            <output name="output" file="windowBed_result2.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="windowBedA.bed" ftype="bed" />
            <param name="inputB" value="windowBedB.bed" ftype="bed" />
            <param name="addition_select" value="lr" />
            <param name="l" value="200" />
            <param name="r" value="20000" />
            <output name="output" file="windowBed_result2.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Similar to bedtools intersect, window searches for overlapping features in A and B. However, window adds a specified number (1000, by default) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are “near” features in A to be detected.

.. image:: $PATH_TO_IMAGES/window-glyph.png

@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>