comparison base_recalibrator.xml @ 35:a29c7d7d962d draft

Fix default read filter screening

34:b99c25b0ad4d

        #end for
        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
        #end for
        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
        #for $read_filter in $gatk_param_type.read_filter:
            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
            ###raise Exception( str( dir( $read_filter ) ) )
            #for $name, $param in $read_filter.read_filter_type.iteritems():
                #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                    #if hasattr( $param.input, 'truevalue' ):
                        ${param}

              </when>
              <when value="FailsVendorQualityCheck">
                  <!-- no extra options -->
              </when>
              <when value="MalformedRead">
                  <!-- no extra options -->
              </when>
              <when value="MappingQuality">
                  <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
              </when>
              <when value="MappingQualityUnavailable">

35:a29c7d7d962d

        #end for
        #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
            -p '--pedigreeString "${pedigree_string.pedigree_string}"'
        #end for
        -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
        #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MappingQualityZero','MalformedRead','MappingQualityUnavailable','UnmappedRead']
        #for $read_filter in $gatk_param_type.read_filter:
            -p '
            #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
            #end_if
            ###raise Exception( str( dir( $read_filter ) ) )
            #for $name, $param in $read_filter.read_filter_type.iteritems():
                #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                    #if hasattr( $param.input, 'truevalue' ):
                        ${param}

              </when>
              <when value="FailsVendorQualityCheck">
                  <!-- no extra options -->
              </when>
              <when value="MalformedRead">
                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
              </when>
              <when value="MappingQuality">
                  <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
              </when>
              <when value="MappingQualityUnavailable">