annotate vcfbreakcreatemulti.xml @ 3:9fd5d91eb91b draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit 36e9065027cc7bf721e9d203208477ee88906c57"

<tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="@WRAPPER_VERSION@+galaxy0">
    <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio" />
    <command>
        #if str($break_or_create) == "break":
            vcfbreakmulti '${input1}' > '${out_file1}'
        #elif str($break_or_create) == "create":
            vcfcreatemulti '${input1}' > '${out_file1}'
        #end if
    </command>
    <inputs>
        <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
        <param name="break_or_create" type="select" display="radio" label="Break or Create?">
            <option value="break">Break</option>
            <option value="create">Create</option>
        </param>
    </inputs>
    <outputs>
        <data format="vcf" name="out_file1" />
    </outputs>
    <tests>
        <test>
            <param name="break_or_create" value="break"/>
            <param name="input1" value="vcflib.vcf"/>
            <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/>
        </test>
        <test>
            <param name="break_or_create" value="create"/>
            <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/>
            <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/>
        </test>
    </tests>
    <help>
This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively):

 - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields.
 - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record.

----

This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
    </help>
    <expand macro="citations" />
</tool>