view vcftools_merge.xml @ 0:2df3463828ff draft

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<tool id="vcftools_merge" name="Merge" version="0.1">
    <description>multiple VCF datasets</description>

    <requirements>
        <requirement type="package">vcftools</requirement>
    </requirements>
    
    <command>
        ## Preprocessing for each dataset.
        #set dataset_names = []
        #for i, $input in enumerate( $inputs ):
            ## Sort file.         
            vcf-sort ${input.file} > ${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

        ## Merge.
        vcf-merge
        #echo ' '.join( dataset_names ) # > ${output}
        
    </command>
    <inputs>
        <repeat name="inputs" title="Datasets to Merge" min="2">
            <param name="file" label="Dataset" type="data" format="vcf"/>
        </repeat>
    </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, so no tests possible. -->
    </tests>

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

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