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<tool id="ensemble_vcf" name="ensemble_vcf" version="0.1.1">

	<description>
		integrates VCF files from different SNV detection methods for ensemble calling.
	</description>

	<requirements>
		<requirement type="package" version="0.1.2">morinkit</requirement>
	</requirements>

	<command detect_errors="aggressive">
		<![CDATA[

			morinkit ensemble_vcf

			--output $output_vcf

			--min_support $min_support

			#if $sorted:
				--sorted
			#end if

			${" ".join(map(str, $input_vcfs))}

		]]>
	</command>

	<inputs>
		<param name="input_vcfs" type="data" format="vcf" multiple="true" label="Input VCF Files"/>
		<param name="min_support" size="4" type="float" value="0.5" label="Minimum number of supporting methods. 
			If less than 1, considered as minimum fraction of methods." />
		<param name="sorted" type="boolean" label="Are the input VCF files sorted?" />
	</inputs>

	<outputs>
		<data name="output_vcf" format="vcf" label="Ensemble VCF File" />
	</outputs>

	<help>
		This tool integrates the VCF files generated by different SNV detection methods 
		in order to perform ensemble SNV calling.
	</help>	

</tool>