<tool id="bedtools_clusterbed" name="ClusterBed" version="@WRAPPER_VERSION@.0">
    <description>cluster overlapping/nearby intervals</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools cluster
        $strand
        -d $distance
        -i $inputA
        > $output
]]>
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness." 
            help="That is, only cluster features that are the same strand. By default, this is disabled." />
        <param name="distance" type="integer" value="0" 
            label="Maximum distance between features allowed for features to be clustered" 
            help="Default is 0. That is, overlapping and/or book-ended features are clustered." />
    </inputs>
    <outputs>
        <data format_source="inputA" name="output" metadata_source="inputA"/>
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="mergedBed1.bed" ftype="bed" />
            <output name="output" file="clusterBed_result.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Similar to merge, cluster report each set of overlapping or “book-ended” features in an interval file. In contrast to merge, cluster does not flatten the cluster of intervals into a new meta-interval; instead, it assigns an unique cluster ID to each record in each cluster. This is useful for having fine control over how sets of overlapping intervals in a single interval file are combined.

.. image:: $PATH_TO_IMAGES/cluster-glyph.png

.. class:: warningmark

bedtools cluster requires that you presort your data by chromosome and then by start position (e.g., sort -k1,1 -k2,2n in.bed > in.sorted.bed for BED files).

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