<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        bedtools annotate
        -i $inputA
        -files 
        #for $bed in $names.beds:
            $bed.input
        #end for

        #if $names.names_select == 'yes':
            -names
            #for $bed in $names.beds:
                $bed.inputName
            #end for
        #end if
        $strand
        $counts
        $both
        &gt; $output
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" />
        <!-- Additional files, if the user needs more -->
         <conditional name="names">
            <param name="names_select" type="select" label="Specify names for each file">
                <option value="no" selected="True">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <repeat name="beds" title="Add BED files and names" >
                    <param name="input" format="bed" type="data" label="BED file" />
                    <param name="inputName" type="text" label="Name of the file" />
                </repeat>
            </when>
            <when value="no">
                <repeat name="beds" title="Add BED files" >
                    <param name="input" format="bed" type="data" label="BED file" />
                </repeat>
            </when>
        </conditional>
        
        <expand macro="strand2" />
        <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue="" label="Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of -i covered by each file." />
        <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue="" label="Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of the input file covered by each file." />
    </inputs>

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

bedtools annotate, well, annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command.

@REFERENCES@

    </help>
    <expand macro="citations" />
</tool>