view tagBed.xml @ 11:e526617a6bb9 draft

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<tool id="bedtools_tagbed" name="TagBed" version="0.2.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        bedtools tag
        -i $inputA
        -files 
        #for $bed in beds:
            $bed.input
        #end for
        -f $overlap
        $strand
        -tag $tag
        $field
        &gt; $output
    </command>
    <inputs>
        <param format="bam" name="inputA" type="data" label="BAM file"/>

        <repeat name="beds" title="Add files" >
            <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file" />
        </repeat>
        <expand macro="strand2" />
        <expand macro="overlap" />
        
        <param name="tag" type="text" value="YB" label="Dictate what the tag should be." />
        <param name="field" type="select" label="Use which field from the annotation files to populate tags?">
            <option value="-labels" selected="True">labels</option>
            <option value="-scores">Scores</option>
            <option value="-names">Names</option>
            <option value="-labels -intervals">Intervals</option>
        </param>
    </inputs>

    <outputs>
        <data format="bed" name="output" label="" />
    </outputs>
    <help>
    
**What it does**

Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in an input bam file

@REFERENCES@

    </help>
</tool>