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<tool id="tag2cluster" name="Cluster genomic regions">
	<command interpreter="perl">
		/home/galaxy/tools/CTK/tag2cluster.pl -v $bigFile $strand -maxGap $MaxGap $input $output
	</command>
	<inputs>
		<param type="data" format="bed" name="input" label="Input BED file of unique CLIP tags (.gz file accepted)"/>
		
		<param name="bigFile" type="boolean" truevalue="-big" falsevalue="" checked="no" label="This is a big file (over 6M lines)" />
		<param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="yes" label="Same strand required" />
		<param name="MaxGap" type="integer" value="-1" label="The max gap to be considered as an overlap" />

	</inputs>
	<outputs>
		<data name="output" format="bed" />
	</outputs>
	<help>
.. class:: infomark

**What it does**

This tool will cluster overlapping tags or nearby regions into clusters and report tag count in each cluster.
It will take as input files in BED format of unique CLIP tags and output files in BED format of clustered overlapping CLIP tags.

	</help>

</tool>