comparison reduce_reads.xml @ 2:8bcc13094767 draft

Uploaded

1:f760c0de8e3a

    \$GATK2_SITE_OPTIONS

    ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975
    --num_cpu_threads_per_data_thread 1

    @THREADS@

    #if $reference_source.reference_source_selector != "history":
        -R "${reference_source.ref_file.fields.path}"
    #end if
    #if str($input_recal) != 'None':
        --BQSR "${input_recal}"

        $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">
      <expand macro="reference_source_selector_param" />
      <when value="cached">
        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
          <validator type="unspecified_build" />

 Minimum proportion of mismatches in a site to trigger a variant region. Anything below this will be considered consensus.

 -noclip_ad / --dont_hardclip_adaptor_sequences ( boolean with default value false )
 Do not hard clip adaptor sequences. Note: You don't have to turn this on for reads that are not mate paired. The program will behave correctly in those cases.

------

@CITATION_SECTION@
  </help>
</tool>

2:8bcc13094767

    \$GATK2_SITE_OPTIONS

    ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975
    --num_cpu_threads_per_data_thread 1

    #if $reference_source.reference_source_selector != "history":
        -R "${reference_source.ref_file.fields.path}"
    #end if
    #if str($input_recal) != 'None':
        --BQSR "${input_recal}"

        $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="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) (-BQSR,--BQSR &amp;lt;recal_file&amp;gt;)" />
    <conditional name="reference_source">
      <expand macro="reference_source_selector_param" />
      <when value="cached">
        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
          <validator type="unspecified_build" />

 Minimum proportion of mismatches in a site to trigger a variant region. Anything below this will be considered consensus.

 -noclip_ad / --dont_hardclip_adaptor_sequences ( boolean with default value false )
 Do not hard clip adaptor sequences. Note: You don't have to turn this on for reads that are not mate paired. The program will behave correctly in those cases.

@CITATION_SECTION@
  </help>
</tool>