<tool id="bedtools_tagbed" name="bedtools TagBed" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>tag BAM alignments based on overlaps with interval files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
bedtools tag
-i '${inputA}'
-files
#for $file in $inputB
    '$file'
#end for
@OVERLAP@
$strand
-tag '${tag}'
$field
> '${output}'
    ]]></command>
    <inputs>
        <param name="inputA" argument="-i" type="data" format="bam" label="BAM file"/>
        <param name="inputB" argument="-files" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
        <expand macro="strand2" />
        <expand macro="overlap" fracof="the alignment"/>
        <param argument="-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 name="output" format="bam" />
    </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 @STD_BEDTOOLS_INPUT_LABEL@ files on the intervals in an input bam file

@REFERENCES@
    ]]></help>
    <expand macro="citations" />
</tool>