comparison unified_genotyper.xml @ 35:a29c7d7d962d draft

Fix default read filter screening

34:b99c25b0ad4d

  <requirements>
      <requirement type="package" version="2.3">gatk</requirement>
      <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <command interpreter="python">gatk2_wrapper.py
   #set default_read_filters = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'BadMateFilter', 'MappingQualityUnavailableFilter', 'UnmappedReadFilter'] 
   --max_jvm_heap_fraction "1"
   --stdout "${output_log}"
   #for $i, $input_bam in enumerate( $reference_source.input_bams ):
       -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
       #if str( $input_bam.input_bam.metadata.bam_index ) != "None":

        #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 = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'BadMateFilter', 'MappingQualityUnavailableFilter', 'UnmappedReadFilter']
        #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
            #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' ):

              </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

  <requirements>
      <requirement type="package" version="2.3">gatk</requirement>
      <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <command interpreter="python">gatk2_wrapper.py
   --max_jvm_heap_fraction "1"
   --stdout "${output_log}"
   #for $i, $input_bam in enumerate( $reference_source.input_bams ):
       -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
       #if str( $input_bam.input_bam.metadata.bam_index ) != "None":

        #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', 'MalformedRead', 'BadMate', '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
            #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' ):

              </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">