<tool id="bedtools_tagbed" name="TagBed" version="@WRAPPER_VERSION@.0">
    <description>tag BAM alignments based on overlaps with interval files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        #set files = '" "'.join( [ str( $file ) for $file in $inputB ] )
        bedtools tag
        -i "${inputA}"
        -files "${files}"
        -f $overlap
        $strand
        -tag "${tag}"
        $field
        > "${output}"
]]>
    </command>
    <inputs>
        <param name="inputA" format="bam" type="data" label="BAM file"/>
        <param name="inputB" format="bed,gff,vcf" multiple="True" type="data" label="BED/VCF/GFF file" />
        <expand macro="strand2" />
        <expand macro="overlap" />
        <param name="tag" type="text" value="YB" label="Specify the tag to use" />
        <param name="field" type="select" label="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="bam" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="srma_in3.bam" ftype="bam" />
            <param name="inputB" value="tagBed1.bed" ftype="bed" />
            <param name="field" value="-names" />
            <output name="output" file="tagBed_result1.bam" ftype="bam" />
        </test>
    </tests>
    <help>
<![CDATA[
**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>
    <expand macro="citations" />
</tool>