<tool id="vcftools_slice" name="Slice VCF" version="0.1">
    <description>to get data from selected regions</description>

    <requirements>
        <requirement type="binary">echo</requirement>
        <requirement type="package" version="0.1.11">vcftools</requirement>
    </requirements>
    
    <command>
        ## Only works if input is sorted.
        vcf-sort ${input} > sorted.vcf

        ## As of v0.1.10, the first line of a BED file is assumed to be a header and ignored,
        ## so add a dummy header line if necessary.
        #set first_line = open( str($regions) ).readline()
        #if first_line.startswith( '#' ):
            ## Header already exists, so just link.
            ; ln -s $regions regions.bed
        #else:
            ## Add dummy header.
            ; echo '#dummy header' | cat - $regions > regions.bed
        #end if

        ## Slice VCF.
        ; vcftools --vcf sorted.vcf --out output --bed regions.bed --recode
    </command>
    
    <inputs>
        <param name="input" label="Input dataset" type="data" format="vcf"/>
        <param name="regions" label="Regions" type="data" format="bed"/>
    </inputs>

    <outputs>
        <data name="output" format="vcf" from_work_dir="output.recode.vcf"/>
    </outputs>

    <tests>
        <test>
            <param name="input" value="slice_in.vcf"/>
            <param name="regions" value="regions.bed"/>
            <output name="output" file="slice_out.vcf"/>
        </test>
    </tests>

    <help>
        Please see the VCFtools `documentation`__ for help and further information.

        .. __: http://vcftools.sourceforge.net/docs.html
    </help>
</tool>