view vcf2tsv.xml @ 0:77e1141bbd29 draft

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<tool id="vcf2tsv" name="VCFtoTab-delimited:" version="0.0.2">
  <description>Convert VCF data into TAB-delimited format</description>
  <macros>
      <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio" />
  <command>vcf2tsv ${g_option} -n "${null_filler}" "${input}" > "${out_file1}"</command>
  <inputs>
    <param format="vcf" name="input" type="data" label="Select VCF dataset to convert"/>
    <param name="g_option" type="boolean" checked="true" truevalue="-g" falsevalue="" label="Report data per sample" help="-g option"/>
    <param name="null_filler" type="select" label="Fill empty fields with" help="-n option" >
      <option value="">Nothing</option>
      <option value=".">.</option>
      <option value="*">*</option>
      <option value="NULL">NULL</option>
    </param>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="g_option" value="true"/>
      <param name="null_filler" value="."/>
      <param name="input" value="vcflib.vcf"/>
      <output name="out_file1" file="vcf2tsv-test1.tab"/>
    </test>
   <test>
      <param name="g_option" value="false"/>
      <param name="null_filler" value="."/>
      <param name="input" value="vcflib.vcf"/>
      <output name="out_file1" file="vcf2tsv-test2.tab"/>
    </test>
    </tests>
  <help>

Converts VCF dataset to tab-delimited format, using null string to replace empty values in the table.
Specifying "**Report data per sample**" (-g) will output one line per sample with genotype information.

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Vcf2Tsv @IS_PART_OF_VCFLIB@
</help>
  <expand macro="citations" />
</tool>