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changeset 0:d2e300747919 draft

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Uploaded
author morinlab
date Wed, 30 Nov 2016 19:11:43 -0500
parents
children d4bb51697f95
files ensemble_vcf.xml
diffstat 1 files changed, 45 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ensemble_vcf.xml	Wed Nov 30 19:11:43 2016 -0500
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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="0.1.1">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>