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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" version="0.0.3">
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3 <description>Split alleleic primitives (gaps or mismatches) into multiple VCF lines</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"></expand>
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8 <expand macro="stdio" />
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9 <command>
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10 cat "${input}" | vcfallelicprimitives
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11 ${m_option}
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12 -t "${t_option}"
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13 -L "${max_length}"
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14 $keep_info
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15 $keep_geno > "${out_file1}"
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16 </command>
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17 <inputs>
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18 <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
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19 <param name="m_option" type="boolean" checked="false" truevalue="--use-mnps" falsevalue="" label="Retain MNPs as separate events" help="--use-mnps option"/>
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20 <param name="t_option" size="20" type="text" value="Split primitives" label="Tag records which are split apart of a complex allele with this flag. " help="--tag-parsed option"/>
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21 <param name="max_length" type="integer" size="4" value="200" label="Do not manipulate records in which either the ALT or REF is longer than (bp)" help="--max-length option"/>
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22 <param name="keep_info" type="boolean" truevalue="--keep-info" falsevalue="" checked="False"
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23 label="Maintain site and allele-level annotations when decomposing"
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24 help="Note that in many cases, such as multisample VCFs, these won't be valid post-decomposition. For biallelic loci in single-sample VCFs, they should be usable with caution. (--keep-info)"/>
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25 <param name="keep_geno" type="boolean" truevalue="--keep-geno" falsevalue="" checked="False"
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26 label="Maintain genotype-level annotations when decomposing"
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27 help="Similar caution should be used for this as for --keep-info. (--keep-geno)"/>
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28 </inputs>
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29 <outputs>
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30 <data format="vcf" name="out_file1" label="${tool.name} on ${on_string}" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input" value="vcflib.vcf"/>
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35 <output name="out_file1" file="vcfallelicprimitives-test1.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 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.
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41 "Pure" MNPs are split into multiple SNPs unless the -m flag is provided.
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42 Genotypes are phased where complex alleles have been decomposed, provided genotypes in the input.
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43
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44 The options are::
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45
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46 -m, --use-mnps Retain MNPs as separate events (default: false).
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47 -t, --tag-parsed FLAG Tag records which are split apart of a complex allele with this flag.
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48 -L, --max-length LEN Do not manipulate records in which either the ALT or
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49 REF is longer than LEN (default: 200).
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50 -k, --keep-info Maintain site and allele-level annotations when decomposing.
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51 Note that in many cases, such as multisample VCFs, these won't
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52 be valid post-decomposition. For biallelic loci in single-sample
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53 VCFs, they should be usable with caution.
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54 -g, --keep-geno Maintain genotype-level annotations when decomposing. Similar
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55 caution should be used for this as for --keep-info.
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56
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57 ----
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58
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59 Vcfallelicprimitives @IS_PART_OF_VCFLIB@
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60 </help>
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61 <expand macro="citations" />
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62 </tool>
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