comparison base_recalibrator.xml @ 24:6460f2ba6a60 draft

Add BQSR and plot_pdf_file options to base_recalibrator.xml

23:2f9bf8bf42b7

    ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
    #if $reference_source.reference_source_selector != "history":
        -R "${reference_source.ref_file.fields.path}"
    #end if
    --out "${output_recal}"
    ${standard_covs}
    #if str( $covariates ) != "None":
        #for $cov in str( $covariates ).split( ',' ):
            -cov "${cov}"
        #end for
    #end if
   '
    
    #set $snp_dataset_provided = False
    #set $rod_binding_names = dict()

            <filter type="data_meta" key="dbkey" ref="input_bam" />
          </options>
        </param>
      </when>
    </conditional>
    <param name="standard_covs" type="boolean" truevalue="" falsevalue="--no_standard_covs" checked="false" label="Do not use the standard set of covariates in addition to the ones selected" help="--no_standard_covs/-noStandard" />
    <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" >
      <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->
      <option value="ReadGroupCovariate" />
      <option value="QualityScoreCovariate" />

              <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
          </when>
        </conditional>
    </repeat>
    
    <conditional name="gatk_param_type">
      <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
        <option value="basic" selected="True">Basic</option>
        <option value="advanced">Advanced</option>
      </param>

    </conditional>
  </inputs>
  <outputs>
    <data format="gatk_report" name="output_recal" label="${tool.name} on ${on_string} (Covariate File)" />
    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
  </outputs>
  <tests>
      <test>
          <param name="reference_source_selector" value="history" />
          <param name="ref_file" value="phiX.fasta" ftype="fasta" />

24:6460f2ba6a60

    ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
    #if $reference_source.reference_source_selector != "history":
        -R "${reference_source.ref_file.fields.path}"
    #end if
    #if str($input_recal) != 'None':
        --BQSR "${input_recal}"
    #end if
    --out "${output_recal}"
    ${standard_covs}
    #if str( $covariates ) != "None":
        #for $cov in str( $covariates ).split( ',' ):
            -cov "${cov}"
        #end for
    #end if
    #if $plot_pdf:
       --plot_pdf_file $output_pdf
    #end if
   '
    
    #set $snp_dataset_provided = False
    #set $rod_binding_names = dict()

            <filter type="data_meta" key="dbkey" ref="input_bam" />
          </options>
        </param>
      </when>
    </conditional>
    <param name="input_recal" type="data" format="gatk_report" 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>
    <param name="standard_covs" type="boolean" truevalue="" falsevalue="--no_standard_covs" checked="false" label="Do not use the standard set of covariates in addition to the ones selected" help="--no_standard_covs/-noStandard" />
    <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" >
      <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->
      <option value="ReadGroupCovariate" />
      <option value="QualityScoreCovariate" />

              <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
          </when>
        </conditional>
    </repeat>
    <param name="plot_pdf" type="boolean" truevalue="--plot_pdf_file" falsevalue="" checked="False" label="Output recalibration plots pdf"/>
    <conditional name="gatk_param_type">
      <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
        <option value="basic" selected="True">Basic</option>
        <option value="advanced">Advanced</option>
      </param>

    </conditional>
  </inputs>
  <outputs>
    <data format="gatk_report" name="output_recal" label="${tool.name} on ${on_string} (Covariate File)" />
    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
    <data format="pdf" name="output_pdf" label="${tool.name} on ${on_string} (plot_pdf_file)">
      <filter>plot_pdf == True</filter>
    </data>
  </outputs>
  <tests>
      <test>
          <param name="reference_source_selector" value="history" />
          <param name="ref_file" value="phiX.fasta" ftype="fasta" />