comparison closestBed.xml @ 9:893617de95e5 draft

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8:d0df760f1d32

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        closestBed
        $split
        $strand
        $addition
        -t $ties
        -a $inputA
        -b $inputB

    <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>

9:893617de95e5

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        closestBed
        $strand
        $addition
        -t $ties
        -a $inputA
        -b $inputB

    <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>