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annotate vcfallelicprimitives.xml @ 0:239da20770dc

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author anton
date Wed, 11 Jun 2014 17:10:38 -0400 (2014-06-11)
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children e66cbd28cdfa
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1 <tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" 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>Split alleleic primitives (gaps or mismatches) into multiple VCF lines</description>
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6 <command>cat "${input}" | vcfallelicprimitives ${m_option} -t "${t_option}" > "${out_file1}"</command>
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7 <inputs>
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8 <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
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9 <param name="m_option" type="boolean" checked="true" truevalue="-m" falsevalue="" label="Retain MNPs as separate events" help="--use-mnps option"/>
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10 <param name="t_option" size="20" type="text" value="Split primitives" label="Mark records which are split with this tag" help="--tag-parsed option"/>
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11 </inputs>
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12 <outputs>
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13 <data format="vcf" name="out_file1" />
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="m_option" value="true"/>
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18 <param name="t_option" value="Split primitives"/>
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19 <param name="input" value="vcflib.vcf"/>
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20 <output name="out_file1" file="vcfallelicprimitives-test1.vcf"/>
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21 </test>
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22 </tests>
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23 <help>
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24
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25 If multiple alleleic primitives (gaps or mismatches) are specified in a single VCF record, this tools splits the record into multiple lines, but drops all INFO fields. "Pure" MNPs are split into multiple SNPs unless the -m flag is provided. Genotypes are phased where complex alleles have been decomposed, provided genotypes in the input.
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26
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27 The options are::
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28
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29 --use-mnps (-m)
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30 Retain MNPs as separate events
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31
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32 --tag-parsed (-t) FLAG
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33 Tag records which are split apart of a complex allele
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34 with this flag
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35
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36 ----
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37
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38 Vcfallelicprimitives is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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39
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40 </help>
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41 </tool>