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annotate vcfbreakcreatemulti.xml @ 2:596a7f6ef564 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
author iuc
date Mon, 26 Mar 2018 12:12:17 -0400
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596a7f6ef564 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
iuc
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1 <tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="@WRAPPER_VERSION@+galaxy0">
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2 <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio" />
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8 <command>
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9 #if str($break_or_create) == "break":
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10 vcfbreakmulti "${input1}" > "${out_file1}"
a7253d23c34d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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11 #elif str($break_or_create) == "create":
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12 vcfcreatemulti "${input1}" > "${out_file1}"
a7253d23c34d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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13 #end if
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14 </command>
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15 <inputs>
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16 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
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17 <param name="break_or_create" type="select" display="radio" label="Break or Create?">
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18 <option value="break">Break</option>
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19 <option value="create">Create</option>
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20 </param>
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21 </inputs>
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22 <outputs>
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23 <data format="vcf" name="out_file1" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="break_or_create" value="break"/>
a7253d23c34d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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28 <param name="input1" value="vcflib.vcf"/>
a7253d23c34d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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29 <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/>
a7253d23c34d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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30 </test>
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31 <test>
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32 <param name="break_or_create" value="create"/>
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33 <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/>
a7253d23c34d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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34 <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/>
a7253d23c34d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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35 </test>
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36 </tests>
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37 <help>
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38 This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively):
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39
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40 - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields.
a7253d23c34d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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41 - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record.
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42
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43 ----
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44
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45 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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46 </help>
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47 <expand macro="citations" />
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48 </tool>