<tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@TOOL_VERSION@">
    <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 name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness."
            help="That is, only cluster features that are the same strand. By default, this is disabled." />
        <param name="distance" argument="-d" 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 name="output" format_source="inputA" 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>