comparison pileup_to_vcf.xml @ 9:c0a6e8f595ec default tip

Add option to set VCF ID field value, this can be used to ID germline variants for SnpSift

8:07cd87e94fbe

<tool id="pileup_to_vcf" name="Pileup to VCF" version="2.1">
  <description>Converts a pileup to VCF with filtering</description>
  <command interpreter="python">pileup_to_vcf.py -i $input_file -o $output_file 
    #if $min_cvrg.__str__  != '':
      --min_coverage $min_cvrg 
    #end if

    #if $depth_as.__str__ != 'None':
      --report_depth $depth_as
    #end if
    $allow_multiples
    $snps_only
    #if $cols.select_order == 'yes' :
      #if $chrom_col.__str__  != '':
        --chrom_col $chrom_col 
      #end if
      #if $pos_col.__str__  != '':

      <option value="source">Read coverage reported in pileup</option>
      <option value="ref" selected="true">Reads at this position that have a base call</option>
      <option value="qual">Reads at this position taht pass the base call quality threshold</option>
      <option value="all">All reads and indels</option>
    </param>
  </inputs>
  <outputs>
    <data format="vcf" metadata_source="input_file" name="output_file" />
  </outputs>
  <stdio>

9:c0a6e8f595ec

<tool id="pileup_to_vcf" name="Pileup to VCF" version="2.2">
  <description>Converts a pileup to VCF with filtering</description>
  <command interpreter="python">pileup_to_vcf.py -i $input_file -o $output_file 
    #if $min_cvrg.__str__  != '':
      --min_coverage $min_cvrg 
    #end if

    #if $depth_as.__str__ != 'None':
      --report_depth $depth_as
    #end if
    $allow_multiples
    $snps_only
    #if $vcf_id.__str__ != '':
      --id $vcf_id
    #end if
    #if $cols.select_order == 'yes' :
      #if $chrom_col.__str__  != '':
        --chrom_col $chrom_col 
      #end if
      #if $pos_col.__str__  != '':

      <option value="source">Read coverage reported in pileup</option>
      <option value="ref" selected="true">Reads at this position that have a base call</option>
      <option value="qual">Reads at this position taht pass the base call quality threshold</option>
      <option value="all">All reads and indels</option>
    </param>
    <param name="vcf_id" type="text" optional="true" value="" label="The VCF ID" help="The VCF output will use this as the ID field value">
      <validator type="regex" message="whitespace characters not allowed">^\S*$</validator>
    </param>
  </inputs>
  <outputs>
    <data format="vcf" metadata_source="input_file" name="output_file" />
  </outputs>
  <stdio>