view closestBed.xml @ 9:893617de95e5 draft

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<tool id="bedtools_closestbed" name="ClosestBed" version="0.2.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        closestBed
        $strand
        $addition
        -t $ties
        -a $inputA
        -b $inputB
        &gt; $output
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
        <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="overlap intervals in this BED/VCF/GFF file?"/>

        <param name="ties" type="select" label="How ties for closest feature should be handled" help="This occurs when two features in B have exactly the same overlap with a feature in A.">
            <option value="all" selected="True">all - Report all ties (default)</option>
            <option value="first">first - Report the first tie that occurred in the B file</option>
            <option value="last">last - Report the last tie that occurred in the B file</option>
        </param>

        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness" help="That is, find the closest feature in B overlaps A on the same strand. By default, this is disabled" />
        <param name="addition" type="boolean" checked="false" truevalue="-d" falsevalue="" label="In addition to the closest feature in B, report its distance to A as an extra column. The reported distance for overlapping features will be 0" />
    </inputs>
    <outputs>
        <data format_source="inputA" name="output" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}"/>
    </outputs>
    <help>

**What it does**

Similar to intersectBed, closestBed searches for overlapping features in A and B. In the event that no feature in B overlaps the current feature in A, closestBed will report the closest (that is, least genomic distance from the start or end of A) feature in B. For example, one might want to find which is the closest gene to a significant GWAS polymorphism. Note that closestBed will report an overlapping feature as the closest—that is, it does not restrict to closest non-overlapping feature.
@REFERENCES@
    </help>
</tool>