--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/cgatools17/tv2vcf.xml	Wed Oct 21 10:09:15 2015 -0400
@@ -0,0 +1,34 @@
+<tool id="tv2vcf" name="TestVariants-2-VCF" version="v2">
+
+	<description> Convert CG MasterVar format to VCF format </description>
+
+	<requirements>
+		<requirement type="package" version="1">cgatools17</requirement>
+	</requirements>
+
+	<command interpreter="perl">
+		testvariants2VCF-v2.pl $testvarIn ${crr.fields.crr_path} > $output
+	</command>
+
+	<inputs>
+		<param name="testvarIn" type="data" format="tabular" label="TestVariants file to be converted to VCF"/>
+		<param name="crr" type="select" label="Reference Build">
+			<options from_data_table="cg_anno_files" />
+		</param>
+	</inputs>
+
+	<outputs>
+		<data format="vcf" name="output" label="${tool.name} on ${on_string}"/>
+	</outputs>
+
+	<help>
+This program converts the output of the cgatools *testvariants* command into a multi-sample VCF file.
+
+Variants that share the same location (chr,begin,end) will be merged into one locus and their flags (0,1,N) will be converted into genotype calls.
+Samples that are positive for more than two alleles within the same locus will be flagged and their genotype calls set to unknown (./.).
+For a non-SNP locus, the VCF format requires that an extra reference base immediately upstream of the variant locus be included in the REF and ALT columns.
+
+Author: Zuoming Deng, zdeng@completegenomics.com
+
+	</help>
+</tool>