<tool id="gops_cluster_1" name="Cluster" version="1.0.0">
    <description>the intervals of a dataset</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <code file="operation_filter.py">
        <hook exec_after_process="exec_after_cluster" />
    </code>
    <command><![CDATA[
python '$__tool_directory__/gops_cluster.py'
'$input1'
'$output'
-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
-d $distance
-m $minregions
-o $returntype
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="interval" label="Cluster intervals of" />
        <param name="distance" type="integer" value="1" label="Max distance between intervals" help="(bp)" />
        <param name="minregions" type="integer" value="2" label="Min number of intervals per cluster" />
        <param name="returntype" type="select" label="Return type">
            <option value="1">Merge clusters into single intervals</option>
            <option value="2">Find cluster intervals; preserve comments and order</option>
            <option value="3">Find cluster intervals; output grouped by clusters</option>
            <option value="4">Find the smallest interval in each cluster</option>
            <option value="5">Find the largest interval in each cluster</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format_source="input1" metadata_source="input1" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="5.bed" />
            <param name="distance" value="1" />
            <param name="minregions" value="2" />
            <param name="returntype" value="1" />
            <output name="output" file="gops-cluster-1.bed" />
        </test>
        <test>
            <param name="input1" value="gops_cluster_bigint.bed" />
            <param name="distance" value="1" />
            <param name="minregions" value="2" />
            <param name="returntype" value="1" />
            <output name="output" file="gops-cluster-1.bed" />
        </test>
        <test>
            <param name="input1" value="5.bed" />
            <param name="distance" value="1" />
            <param name="minregions" value="2" />
            <param name="returntype" value="2" />
            <output name="output" file="gops-cluster-2.bed" />
        </test>
        <test>
            <param name="input1" value="5.bed" />
            <param name="distance" value="1" />
            <param name="minregions" value="2" />
            <param name="returntype" value="3" />
            <output name="output" file="gops-cluster-3.bed" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.

@SCREENCASTS@

**Syntax**

- **Maximum distance** is greatest distance in base pairs allowed between intervals that will be considered &quot;clustered&quot;.  **Negative** values for distance are allowed, and are useful for clustering intervals that overlap.
- **Minimum intervals per cluster** allow a threshold to be set on the minimum number of intervals to be considered a cluster.  Any area with less than this minimum will not be included in the output.
- **Merge clusters into single intervals** outputs intervals that span the entire cluster.
- **Find cluster intervals; preserve comments and order** filters out non-cluster intervals while maintaining the original ordering and comments in the file.
- **Find cluster intervals; output grouped by clusters** filters out non-cluster intervals, but outputs the cluster intervals so that they are grouped together. Comments and original ordering in the file are lost.

-----

**Examples**

Find Clusters:

.. image:: gops_clusterFind.gif

Merge Clusters:

.. image:: gops_clusterMerge.gif
    ]]></help>
</tool>