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<tool id="vcftools" name="VCFtools" version="0.0.1">
	<description>
		The vcftools program is intended for analysis of diploid SNP data in VCF format.
	</description>
	<requirements>
		<requirement type="package" version="0.1.11">vcftools</requirement> 
	</requirements>
	<command>
		vcftools

		#if str($basic) == "gzvcf"
			--gzvcf
		#elif str($basic) == "bcf"
			--bcf
		#else 
			--vcf
		#end if

		$input

		#for $chromosome in $chr
			--chr $chromosome.number
		#end for

		#for $chromosome in $notchr
			--notchr $chromosome.number
		#end for

		#if str($frombp) != ""
			--from-bp $frombp
		#end if

		#if str($tobp) != ""
			--to-bp $tobp
		#end if

		#for $snp in $snps
			--snp $snp.id
		#end for

		#if str(${snpfile.file_name}) != ""
			--snps $snpfile
		#end if

		#if str(${excludesnpfile.file_name}) != ""
			--snps $excludesnpfile
		#end if

		#if str($indels) == "keeponlyindels"
			--keep-only-indels
		#elif str($indels) == "removeindels"
			--removeindels
		#end if

		$removefilterall $recodetostream > out.recode.vcf
	</command>
	<inputs>
		<param name="input" type="data" label="Input vcf file" format="vcf" />
		<param name="basic" type="select" label="Basic Options" value="vcf">
			<option value="vcf">Decompressed vcf file (default)</option>
			<option value="gzvcf">Compressed (gzipped) vcf file</option>
			<option value="bcf">Compressed (bgzf) bcf file</option>
		</param>
		<repeat name="chr" title="Include chromosomes to be processed">
			<param name="number" label="Chromosome number" type="integer" optional="true" />
		</repeat>
		<repeat name="notchr" title="Exclude chromosomes from processing">
			<param name="number" label="Chromosome number" type="integer" optional="true" />
		</repeat>
		<param name="frombp" label="Beginning of range to be processed" help="only if chromosomes are included. You must also specify the end of range to be processed." optional="true" type="integer"/>
		<param name="tobp" label="End of range to be processed" optional="true" type="integer" help="only if chromosomes are included. You must also specify the beginning of range to be processed."/>
		<repeat name="snps" title="SNPs to include">
			<param name="id" label="ID of SNP" type="text" optional="true" help="e.g. a dbSNP rsID"/>
		</repeat>
		<param name="snpfile" type="data" format="txt, tabular" label="List of SNPs to include" help="The file should contain a list of SNP IDs (e.g. dbSNP rsIDs), with one ID per line." optional="true"/>
		<param name="excludesnpfile" type="data" label = "List of SNPs to disclude" format="txt, tabular" help="The file should contain a list of SNP IDs (e.g. dbSNP rsIDs), with one ID per line." optional="true"/>
		<param name="indels" type="select" label="Indel options" value="none">
			<option value="keeponlyindels">Keep only indels</option>
			<option value="none">None</option>
			<option value="removeindels"> Remove indels</option>
		</param>
		<param name="removefilterall" type="boolean" truevalue="--remove-filtered-all" falsevalue="" label="Remove all sites with the FILTER tag" value="false" />
		<param name="recodetostream" type="boolean" truevalue="--recode-to-stream" falsevalue="" label="Recode to stream" value="false" />
	</inputs>
	<outputs>
		<data format="vcf" name="output" from_work_dir="out.recode.vcf" />
	</outputs>
	<help>
		Welcome to VCFtools - a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics. More information at http://vcftools.sourceforge.net/index.html.
	</help>
</tool>