comparison vcftools_merge.xml @ 2:60743b92cc26 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b

1:eb02907453b4

<tool id="vcftools_merge" name="Merge" version="0.1">
    <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( $inputs ):
            ## Sort file.         
            vcf-sort ${input.file} > ${i}.vcf.sorted ;

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

            ## Index.

        #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>

2:60743b92cc26

<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.

        #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>