<tool id="Beagle_impute" name="Beagle_impute" >
	<description> beagle as a imputation tools, required phased reference file in VCF format</description>
	<command interpreter="bash">beagle_impute.sh $vcf_input $reference </command>
	<inputs>
		<param format="vcf" name="vcf_input" type="data" label="VCF file to impute"/>
		<param format="vcf" name="reference" type="data" label="reference file"/>
	</inputs>
	<outputs>
		<data format="vcf" name="vcf_ouput" label="Phased and imputed VCF" from_work_dir="out_imputed.vcf.gz"/>
		<data format="txt" name="log" label="Beagle log file" from_work_dir="out.log"/>
	</outputs>
	
	</tool>