<tool id="MergingDataClusterize" name="Clusterize">
	<description>Clusterize features when their genomic intervals overlap.</description>
	<command interpreter="python">
		../Java/Python/clusterize.py -i $formatType.inputFileName
		#if $formatType.FormatInputFileName == 'bed':
			-f bed
		#elif $formatType.FormatInputFileName == 'gff':
			-f gff
		#elif $formatType.FormatInputFileName == 'gff2':
			-f gff2
		#elif $formatType.FormatInputFileName == 'gff3':
			-f gff3
		#elif $formatType.FormatInputFileName == 'sam':
			-f sam
		#end if
		-o $outputFileGff 
		$colinear
		$normalize
		-d $distance
		$log $outputFileLog
	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName" type="select" label="Input File Format">
				<option value="bed">bed</option>
				<option value="gff">gff</option>
				<option value="gff2">gff2</option>
				<option value="gff3">gff3</option>
				<option value="sam">sam</option>
			</param>
			<when value="bed">
				<param name="inputFileName" format="bed" type="data" label="Input File"/>
			</when>
			<when value="gff">
				<param name="inputFileName" format="gff" type="data" label="Input File"/>
			</when>
			<when value="gff2">
				<param name="inputFileName" format="gff2" type="data" label="Input File"/>
			</when>
			<when value="gff3">
				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
			</when>
			<when value="sam">
				<param name="inputFileName" format="sam" type="data" label="Input File"/>
			</when>
		</conditional>

		<param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Only merge collinear data"/>
		<param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Normalize data." help="This only works if the tag nbOccurrences is set."/>
		<param name="distance" type="integer" value="0" label="Merge features if their relative distance is withing N nt"/>
	</inputs>

	<outputs>
		<data name="outputFileGff" format="gff3" label="[clusterize]output file"/>
	</outputs> 
</tool>