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1 <tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="0.0.1">
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2 <requirements>
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3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
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4 </requirements>
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5 <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description>
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6 <command>
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7
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8 #if str($break_or_create) == "break":
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9 vcfbreakmulti "${input1}" > "${out_file1}"
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10 #elif str($break_or_create) == "create":
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11 vcfcreatemulti "${input1}" > "${out_file1}"
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12 #end if
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13
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14 </command>
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15
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16 <inputs>
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17 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
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18 <param name="break_or_create" type="select" display="radio" label="Break or Create?">
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19 <option value="break">Break</option>
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20 <option value="create">Create</option>
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21 </param>
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22 </inputs>
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23 <outputs>
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24 <data format="vcf" name="out_file1" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="break_or_create" value="break"/>
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29 <param name="input1" value="vcflib.vcf"/>
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30 <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/>
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31 </test>
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32 <test>
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33 <param name="break_or_create" value="create"/>
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34 <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/>
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35 <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/>
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36 </test>
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37 </tests>
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38 <help>
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39
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40 This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively):
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41
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42 - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields.
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43 - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record.
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44
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45 ----
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46
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47 This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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48
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49 </help>
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50 </tool>
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