view vcftools_merge.xml @ 1:71e19ddf52f5 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge commit a1517c9d22029095120643bbe2c8fa53754dd2b7

<tool id="vcftools_merge" name="Merge" 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

        ## Merge.
        vcf-merge
        #echo ' '.join( dataset_names ) # > ${output}

    </command>
    <inputs>
        <param name="input_files" label="Datasets to Merge" type="data" format="vcf" min="2" multiple="True"/>
    </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>