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<tool id="vcftools_subset" name="Subset" version="0.1">
    <description>columns from a VCF dataset</description>

    <requirements>
        <requirement type="package">tabix</requirement>
        <requirement type="package" version="0.1.11">vcftools</requirement>
    </requirements>
    
    <command>
        ln -s ${input} input.vcf ;

        ## Sort file.
        sort -k1,1 -k2,2n input.vcf > input.vcf.sorted ;

        ## Compress.
        bgzip input.vcf.sorted ;

        ## Index.
        tabix -p vcf input.vcf.sorted.gz ;

        ## Subset.
        vcf-subset ${trim_alt_alleles} ${exclude_rows_with_no_variants} -c "${columns}" input.vcf.sorted.gz > $output
    </command>
    
    <inputs>
        <param name="input" label="Input dataset" type="data" format="vcf"/>
        <param name="columns" label="Columns" type="text" value=""/>
        <param name="trim_alt_alleles" type="select" label="Remove alternate alleles if not found in the subset" help="">
            <option value="" selected="True">No</option>
            <option value="-a">Yes</option>
        </param>
        <param name="exclude_rows_with_no_variants" type="select" label="Exclude rows not containing variants" help="">
            <option value="" selected="True">No</option>
            <option value="-e">Yes</option>
        </param>
    </inputs>

    <outputs>
        <data name="output" format="vcf"/>
    </outputs>

    <stdio>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

    <tests>
        <test>
            <param name="input" value="subset_in.vcf"/>
            <param name="columns" value="sample1"/>
            <param name="trim_alt_alleles" value="Yes"/>
            <param name="exclude_rows_with_no_variants" value="Yes"/>
            <!-- 2 lines diff because command line with full file path is included in output VCF, and
                 it not possible to match full file path.  -->
            <output name="output" file="subset_out.vcf" lines_diff="2"/>
        </test>
    </tests>

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

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