Mercurial > repos > saskia-hiltemann > virtual_normal_analysis

diff vcf2lv.xml @ 0:1209f18a5a83 draft

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author saskia-hiltemann
date Mon, 03 Aug 2015 05:01:15 -0400
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children 1c6710924e80
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcf2lv.xml	Mon Aug 03 05:01:15 2015 -0400
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+<tool id="vcf2lv" name="VCF-2-VariantList" version="1">
+ 	<description> convert VCF file to CG-compatible variant list </description>
+  
+  	<command interpreter="bash"> 
+  		vcf2lv.sh $vcffile $outputfile	
+  	</command>
+
+  	<inputs>
+  		<param name="vcffile" type="data" label="Select vcf file" />
+  		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>	
+  	</inputs>
+
+	<outputs>
+  		<data format="tabular" name="outputfile" label="${fname} VCF-2-VariantList conversion"/>
+  	</outputs>
+  	
+  	<help>  
+**what it does**
+
+Converts a VCF file containing small variants (SNVs, indels and substitutions) to a Complete Genomics type variantlist.
+		
+After conversion, the file can be used as input to the Virtual Normal filtering pipeline. 
+
+
+
+	</help>
+</tool>