annotate vcfallelicprimitives.xml @ 0:239da20770dc

Imported from capsule None

<tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" version="0.0.1">
<requirements>
    <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
</requirements>
  <description>Split alleleic primitives (gaps or mismatches) into multiple VCF lines</description>
  <command>cat "${input}" | vcfallelicprimitives ${m_option} -t "${t_option}" > "${out_file1}"</command>
  <inputs>
    <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
    <param name="m_option" type="boolean" checked="true" truevalue="-m" falsevalue="" label="Retain MNPs as separate events" help="--use-mnps option"/>
    <param name="t_option" size="20" type="text" value="Split primitives" label="Mark records which are split with this tag" help="--tag-parsed option"/>
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="m_option" value="true"/>
      <param name="t_option" value="Split primitives"/>
      <param name="input" value="vcflib.vcf"/>
      <output name="out_file1" file="vcfallelicprimitives-test1.vcf"/>
    </test>
    </tests>
  <help>

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.

The options are::
                                                                                                                           
    --use-mnps (-m)
    Retain MNPs as separate events                                                                          
    
    --tag-parsed (-t) FLAG
    Tag records which are split apart of a complex allele                                                                                                                                                             
    with this flag                                                 

----

Vcfallelicprimitives is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 

</help>
</tool>