<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0">
    <description>annotate coverage of features from multiple files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[

        bedtools annotate
        -i "${inputA}"
        #if $names.names_select == 'yes':
            -files
            #for $bed in $names.beds:
                "${bed.input}"
            #end for

            -names
            #for $bed in $names.beds:
                "${bed.inputName}"
            #end for
        #else:
            #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] )
            -files "${files}"
            #set names = '" "'.join( [ str( $name.display_name ) for $name in $names.beds ] )
            -names "${names}"
        #end if
        $strand
        $counts
        $both
        > "${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">
                <param name="beds" format="bed" multiple="True" type="data" label="BED file" />
            </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"
            help="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"
            help="Default is to report solely the fraction of the input file covered by each file." />
    </inputs>
    <outputs>
        <data format="bed" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="annotateBed1.bed" ftype="bed" />
            <param name="names_select" value="no" />
            <param name="beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed" />
            <output name="output" file="annotateBed_result.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**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>