annotate windowBed.xml @ 0:b8348686a0b9 draft

Imported from capsule None

<tool id="bedtools_windowbed" name="WindowBed" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        bedtools window
        #if $inputA.ext == "bam":
            -abam $inputA
        #else:
            -a $inputA
        #end if
        -b $inputB
        $ubam
        $bed
        $strandB
        #if $addition.addition_select == 'b':
        -w $addition.b
        #elif $addition.addition_select == 'lr':
        -l $addition.l
        -r $addition.r
        #end if
        $original
        $number
        $nooverlaps
        $header
        &gt; $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="ubam" type="boolean" checked="false" truevalue="-ubam" falsevalue="" label="Write uncompressed BAM output" />
        <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" />
        <conditional name="addition">
            <param name="addition_select" type="select" label="Choose what you want to do">
                <option value="huhn" selected="True">Do not change added base pairs</option>
                <option value="b">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="b">
                <param name="b" label="Give Value" type="integer" value="1000"  />
            </when>
            <when value="lr">
                <param name="l" label="Base pairs added upstream (left of) of each entry in A when searching for overlaps in B. Allows one to create assymetrical “windows”. Default is 1000bp" type="integer" value="1000"  />
                <param name="r" label="Base pairs added downstream (right of) of each entry in A when searching for overlaps in B. Allows one to create assymetrical “windows”. Default is 1000bp" type="integer" value="1000"  />
            </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. In other words, just report the fact at least one overlap was found in B" />
        <param name="number" type="boolean" checked="false" truevalue="-c" falsevalue="" label="For each entry in A, report the number of hits in B while restricting to -f. Reports 0 for A entries that have no overlap with B" />
        <param name="nooverlaps" type="boolean" checked="false" truevalue="-v" falsevalue="" label="Only report those entries in A that have no overlaps with B" />
        <param name="header" type="boolean" checked="false" truevalue="-header" falsevalue="" label="Print the header from the A file prior to results" />

    </inputs>
    <outputs>
        <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
    </outputs>
    <help>

**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>