<tool id="vcftools_isec" name="Intersect" version="0.1.1">
    <description>multiple VCF datasets</description>

    <requirements>
        <requirement type="package">tabix</requirement>
        <requirement type="package" version="0.1.11">vcftools</requirement>
    </requirements>

    <command>
        ## Preprocessing for each dataset.
        #set dataset_names = []
        #for i, $input in enumerate( $input_files ):
            ## Sort file.
            vcf-sort ${input} > ${i}.vcf.sorted ;

            ## Compress.
            bgzip ${i}.vcf.sorted ;

            ## Index.
            tabix -p vcf ${i}.vcf.sorted.gz ;

            #silent dataset_names.append( str($i) + '.vcf.sorted.gz' )
        #end for

        ## Intersect.
        vcf-isec -f
        #if $complement:
        -c
        #end if
        #echo ' '.join( dataset_names ) # > ${output}
    </command>
    <inputs>
        <param name="input_files" label="Datasets" type="data" format="vcf" min="2" multiple="True"/>
        <param name="complement" type="boolean" label="Complement intersection" help="If checked, output positions present in the first file but missing from the other files"/>
    </inputs>

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

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

    <tests>
        <!-- Cannot specify multiple repeats in test framework right now.
        <test>
            <param name='input_files|1' value='1.vcf' />
            <param name='input_files|2' value='2.vcf' />
            <param name='complement' value='False' />
            <output name='output' file='out.vcf' />
        </test>
        -->
    </tests>

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

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