<tool id="CIMS" name="CIMS analysis">
	<description></description>

	<command interpreter="perl">
			/home/galaxy/tools/CTK/CIMS.pl  $bigFileFlag -n $iterationNum -p -v --outp $mutPosFile
			$tagBedFile $mutationBedFile $outFile
	</command>

	<inputs>

	<param type="data" format="bed" name="tagBedFile" label="Input file in BED format of unique tags"/>
	<param type="data" format="bed" name="mutationBedFile" label="Input file in BED format of filtered mutation file corresponding to the tags above"/>
	<param name="bigFileFlag" type="boolean" truevalue="-big" falsevalue="" checked="yes" label="The tag BED is a big file (over 6M lines)" />
	<param name="iterationNum" type="integer" value="10" label="Number of iterations of permutation" />	

	</inputs>

	<outputs>
	<data name="outFile" format="tabular" label="CIMS analysis on ${on_string}"/>
	<data name="mutPosFile" format="tabular" label="Mutation position summary on ${on_string}"/>
	</outputs>

	<help>

.. class:: infomark

**What this tool does**

Cross-linking induced mutation site (CIMS) analysis

This tool identifies clustered mutation sites and assigns statistical significance of the clustering based on a permutation based procedure.  This procedure shuffles the position of mutations, but preserves the distribution of CLIP tags and the position of each mutation relative to the 5' end of each tag (specified in the the 5th column of the mutation BED file). 

-----

.. class:: warningmark

**Requirement on input data**

* Make sure the NAME(4th) column of the two BED files gives the same tag names.
* Make sure the position of each mutation relative to the read is in the score(5th) column, provided by the iterative alignment tools (currently only for novoalign).

	</help>
</tool>