<tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>annotate coverage of features from multiple files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />
    <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:
    -files
    #for $bed in $names.beds:
        '$bed'
    #end for
    -names
    #for $bed in $names.beds:
        '${bed.display_name}'
    #end for
#end if
$strand
$counts
$both
> '${output}'
    ]]></command>
    <inputs>
        <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
        <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" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
                    <param name="inputName" type="text" label="Name of the file" />
                </repeat>
            </when>
            <when value="no">
                <param name="beds" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
            </when>
        </conditional>
        <expand macro="strand2" />
        <param argument="-counts" type="boolean" truevalue="-counts" falsevalue="" checked="false"
            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 argument="-both" type="boolean" truevalue="-both" falsevalue="" checked="false"
            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 name="output" format="bed" />
    </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 @STD_BEDTOOLS_INPUT_LABEL@ file with the coverage and number of overlaps observed from multiple other @STD_BEDTOOLS_INPUT_LABEL@ 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>