comparison reduce_reads.xml @ 11:5faf7ace8aee draft

Add HaplotypeCaller

10:a14e79e7ac75

        $analysis_param_type.dont_hardclip_adaptor_sequences
        '
    #end if
  </command>
  <inputs>
    <param name="input_recal" type="data" format="csv" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" />
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
        <option value="cached">Locally cached</option>
        <option value="history">History</option>
      </param>

11:5faf7ace8aee

        $analysis_param_type.dont_hardclip_adaptor_sequences
        '
    #end if
  </command>
  <inputs>
    <param name="input_recal" type="data" format="csv" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" >
      <help>The input covariates table file which enables on-the-fly base quality score recalibration. 
            Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool. 
            Please be aware that one should only run recalibration with the covariates file created on the same input bam(s).
      </help>
    </param>
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
        <option value="cached">Locally cached</option>
        <option value="history">History</option>
      </param>