<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>