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<tool id="cnvnator" name="cnvnator" version="0.3">
	<description></description>

	<requirements>
		<requirement type="package" version="0.3">cnvnator</requirement>
	</requirements>

	<command interpreter="python">
		cnvnator.py
		-r $inputFastaFile
		-b $inputBamFile
		-s $binSize
		-o1 $outputRawFile
		-o2 $outputVcfFile
		$outputRaw
	</command>

	<inputs>
		<param format="fasta" name="inputFastaFile" type="data" label="reference file" help="" />
		<param format="bam" name="inputBamFile" type="data" label="bam file" help="" />
		<param name="binSize" type="integer" label="bin size" help="" value="100" />
<!-- 		<conditional name="outputChoice">
			<param name="outputChoiceSelect" type="select" label="Conditional output">
				<option value="yes">Yes</option>
				<option value="no">No</option>
			</param>
		</condition> -->
		<param name="outputRaw" type="boolean" label="output raw?" checked="false" />
		<param name="outputVcf" type="boolean" label="output vcf?" checked="true" />
	</inputs>

	<outputs>
		<data format="tabular" name="outputRawFile" >
			<filter>outputRaw == false</filter>
		</data>
		<data format="vcf" name="outputVcfFile" />
	</outputs>

	<help>


	</help>

</tool>