annotate base_recalibrator.xml @ 39:fab099dde911 draft default tip

VariantFiltration should not have -nt option since it does not implemnt TreeReducible
author Jim Johnson <jj@umn.edu>
date Tue, 05 Mar 2013 11:15:13 -0600 (2013-03-05)
parents 14d47237bb0a
children
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b99c25b0ad4d Update tool version to 0.0.7
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1 <tool id="gatk2_base_recalibrator" name="Base Recalibrator" version="0.0.7">
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2 <description>on BAM files</description>
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3 <requirements>
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4 <requirement type="package" version="2.3">gatk</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 </requirements>
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7 <command interpreter="python">gatk2_wrapper.py
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8 --max_jvm_heap_fraction "1"
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9 --stdout "${output_log}"
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10 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
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11 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
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12 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
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13 #end if
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14 -p 'java
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15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
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16 -T "BaseRecalibrator"
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17 \$GATK2_SITE_OPTIONS
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18 \$GATK2_CPU_THREADS
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19 ##--num_threads 4 ##hard coded, for now
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20 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
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21 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
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22 #if $reference_source.reference_source_selector != "history":
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23 -R "${reference_source.ref_file.fields.path}"
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24 #end if
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25 #if str($input_recal) != 'None':
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26 --BQSR "${input_recal}"
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27 #end if
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28 --out "${output_recal}"
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29 ${standard_covs}
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30 #if str( $covariates ) != "None":
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31 #for $cov in str( $covariates ).split( ',' ):
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32 -cov "${cov}"
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33 #end for
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34 #end if
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35 #if $plot_pdf:
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36 --plot_pdf_file $output_pdf
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37 #end if
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38 '
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39
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40 #set $snp_dataset_provided = False
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41 #set $rod_binding_names = dict()
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42 #for $rod_binding in $rod_bind:
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43 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
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44 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
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45 #else
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46 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
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47 #end if
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48 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'dbsnp':
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49 #set $snp_dataset_provided = True
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50 #end if
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51 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
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52 -d "--knownSites:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
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53 #end for
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54
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55 ##start standard gatk options
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56 #if $gatk_param_type.gatk_param_type_selector == "advanced":
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57 #for $pedigree in $gatk_param_type.pedigree:
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58 -p '--pedigree "${pedigree.pedigree_file}"'
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59 #end for
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60 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
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61 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
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62 #end for
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63 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
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64 #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MappingQualityZero','MalformedRead','MappingQualityUnavailable','UnmappedRead']
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65 #for $read_filter in $gatk_param_type.read_filter:
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66 -p '
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67 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
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68 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
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69 #end if
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70 ###raise Exception( str( dir( $read_filter ) ) )
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71 #for $name, $param in $read_filter.read_filter_type.iteritems():
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72 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
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73 #if hasattr( $param.input, 'truevalue' ):
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74 ${param}
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75 #else:
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76 --${name} "${param}"
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77 #end if
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78 #end if
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79 #end for
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80 '
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81 #end for
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82 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
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83 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
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84 #end for
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85
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86 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
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87 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
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88 #end for
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89
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90 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
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91
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92 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
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93 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
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94 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
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95 #end if
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96 -p '
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97 --baq "${gatk_param_type.baq}"
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98 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
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99 ${gatk_param_type.use_original_qualities}
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100 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
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101 --validation_strictness "${gatk_param_type.validation_strictness}"
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102 --interval_merging "${gatk_param_type.interval_merging}"
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103 ${gatk_param_type.disable_experimental_low_memory_sharding}
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104 ${gatk_param_type.fix_misencoded_quality_scores}
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105 ${gatk_param_type.non_deterministic_random_seed}
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106 '
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107 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
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108 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
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109 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
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110 #else
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111 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
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112 #end if
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113 #end for
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114 #end if
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115
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116 #if str( $reference_source.reference_source_selector ) == "history":
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117 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
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118 #end if
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119 ##end standard gatk options
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120
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121 ##start analysis specific options
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122 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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123 -p '
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124 #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set":
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125 --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}"
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126 #end if
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127 #if str( $analysis_param_type.default_platform ) != "default":
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128 --default_platform "${analysis_param_type.default_platform}"
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129 #end if
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130 #if str( $analysis_param_type.force_read_group_type.force_read_group_type_selector ) == "set":
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131 --force_read_group "${analysis_param_type.force_read_group_type.force_read_group}"
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132 #end if
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133 #if str( $analysis_param_type.force_platform ) != "default":
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134 --force_platform "${analysis_param_type.force_platform}"
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135 #end if
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136 ${analysis_param_type.exception_if_no_tile}
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137 #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set":
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138 #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default":
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139 --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}"
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140 #end if
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141 #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default":
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142 --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}"
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143 #end if
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144 #end if
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145 --window_size_nqs "${analysis_param_type.window_size_nqs}"
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146 --homopolymer_nback "${analysis_param_type.homopolymer_nback}"
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147 '
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148 #end if
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149 #if not $snp_dataset_provided:
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150 -p '--run_without_dbsnp_potentially_ruining_quality'
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151 #end if
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152 </command>
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153 <inputs>
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154 <conditional name="reference_source">
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155 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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156 <option value="cached">Locally cached</option>
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157 <option value="history">History</option>
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158 </param>
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159 <when value="cached">
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160 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
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161 <validator type="unspecified_build" />
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162 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
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163 </param>
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164 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" >
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165 <options from_data_table="gatk2_picard_indexes">
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166 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
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167 </options>
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168 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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169 </param>
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170 </when>
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171 <when value="history">
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172 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;" />
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173 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
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174 <options>
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175 <filter type="data_meta" key="dbkey" ref="input_bam" />
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176 </options>
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177 </param>
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178 </when>
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179 </conditional>
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180 <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;" >
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diff changeset
181 <help>The input covariates table file which enables on-the-fly base quality score recalibration.
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diff changeset
182 Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool.
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diff changeset
183 Please be aware that one should only run recalibration with the covariates file created on the same input bam(s).
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184 </help>
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185 </param>
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186 <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" />
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187 <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;" >
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188 <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->
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189 <option value="ReadGroupCovariate" />
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190 <option value="QualityScoreCovariate" />
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191 <option value="CycleCovariate" />
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192 <option value="ContextCovariate" />
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193 <!-- covariates below were pulled from list option -->
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194 <option value="HomopolymerCovariate" />
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195 <option value="GCContentCovariate" />
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196 <option value="MappingQualityCovariate" />
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197 <option value="MinimumNQSCovariate" />
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198 <option value="PositionCovariate" />
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199 <option value="PrimerRoundCovariate" />
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200 <option value="TileCovariate" />
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201 </param>
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202
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203 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-knownSites,--knownSites &amp;lt;knownSites&amp;gt;">
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204 <conditional name="rod_bind_type">
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205 <param name="rod_bind_type_selector" type="select" label="Binding Type">
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206 <option value="dbsnp" selected="True">dbSNP</option>
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207 <option value="snps">SNPs</option>
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208 <option value="indels">INDELs</option>
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209 <option value="mask">Mask</option>
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210 <option value="custom">Custom</option>
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211 </param>
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212 <when value="dbsnp">
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213 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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214 </when>
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215 <when value="snps">
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216 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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217 </when>
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218 <when value="indels">
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219 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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220 </when>
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221 <when value="mask">
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222 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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223 </when>
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224 <when value="custom">
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225 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
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226 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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227 </when>
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228 </conditional>
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229 </repeat>
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230 <param name="plot_pdf" type="boolean" truevalue="--plot_pdf_file" falsevalue="" checked="False" label="Output recalibration plots pdf"/>
0
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231 <conditional name="gatk_param_type">
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232 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
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233 <option value="basic" selected="True">Basic</option>
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234 <option value="advanced">Advanced</option>
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235 </param>
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236 <when value="basic">
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237 <!-- Do nothing here -->
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238 </when>
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239 <when value="advanced">
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240 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
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241 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
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242 </repeat>
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243 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
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244 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
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245 </repeat>
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246 <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
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247 <option value="STRICT" selected="True">STRICT</option>
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248 <option value="SILENT">SILENT</option>
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249 </param>
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250 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
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251 <conditional name="read_filter_type">
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252 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
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253 <option value="BadCigar">BadCigar</option>
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254 <option value="BadMate">BadMate</option>
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255 <option value="DuplicateRead">DuplicateRead</option>
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256 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
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257 <option value="MalformedRead">MalformedRead</option>
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258 <option value="MappingQuality">MappingQuality</option>
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259 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
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260 <option value="MappingQualityZero">MappingQualityZero</option>
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261 <option value="MateSameStrand">MateSameStrand</option>
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262 <option value="MaxInsertSize">MaxInsertSize</option>
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263 <option value="MaxReadLength" selected="True">MaxReadLength</option>
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264 <option value="MissingReadGroup">MissingReadGroup</option>
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265 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
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266 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
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267 <option value="Platform454">Platform454</option>
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268 <option value="Platform">Platform</option>
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269 <option value="PlatformUnit">PlatformUnit</option>
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270 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
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271 <option value="ReadName">ReadName</option>
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272 <option value="ReadStrand">ReadStrand</option>
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273 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
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274 <option value="Sample">Sample</option>
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275 <option value="SingleReadGroup">SingleReadGroup</option>
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276 <option value="UnmappedRead">UnmappedRead</option>
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277 </param>
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278 <when value="BadCigar">
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279 <!-- no extra options -->
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280 </when>
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jjohnson
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281 <when value="BadMate">
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282 <!-- no extra options -->
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283 </when>
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284 <when value="DuplicateRead">
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285 <!-- no extra options -->
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286 </when>
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287 <when value="FailsVendorQualityCheck">
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288 <!-- no extra options -->
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289 </when>
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290 <when value="MalformedRead">
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291 <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"/>
0
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292 </when>
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293 <when value="MappingQuality">
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294 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
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295 </when>
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296 <when value="MappingQualityUnavailable">
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297 <!-- no extra options -->
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298 </when>
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299 <when value="MappingQualityZero">
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300 <!-- no extra options -->
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301 </when>
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302 <when value="MateSameStrand">
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303 <!-- no extra options -->
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304 </when>
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305 <when value="MaxInsertSize">
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306 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
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307 </when>
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308 <when value="MaxReadLength">
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309 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
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310 </when>
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311 <when value="MissingReadGroup">
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312 <!-- no extra options -->
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313 </when>
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314 <when value="NoOriginalQualityScores">
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315 <!-- no extra options -->
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316 </when>
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317 <when value="NotPrimaryAlignment">
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318 <!-- no extra options -->
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319 </when>
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320 <when value="Platform454">
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321 <!-- no extra options -->
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322 </when>
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323 <when value="Platform">
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324 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
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325 </when>
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326 <when value="PlatformUnit">
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327 <!-- no extra options -->
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328 </when>
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329 <when value="ReadGroupBlackList">
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330 <!-- no extra options -->
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331 </when>
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332 <when value="ReadName">
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333 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
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334 </when>
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335 <when value="ReadStrand">
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336 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
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337 </when>
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338 <when value="ReassignMappingQuality">
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339 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
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jjohnson
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340 </when>
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jjohnson
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341 <when value="Sample">
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342 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
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343 </when>
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344 <when value="SingleReadGroup">
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345 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
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346 </when>
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347 <when value="UnmappedRead">
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jjohnson
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348 <!-- no extra options -->
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349 </when>
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jjohnson
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350 </conditional>
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jjohnson
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351 </repeat>
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diff changeset
352 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
353 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
354 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
355 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
356 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
357 </repeat>
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jjohnson
parents:
diff changeset
358
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
359 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
360 <option value="UNION" selected="True">UNION</option>
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jjohnson
parents:
diff changeset
361 <option value="INTERSECTION">INTERSECTION</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
362 </param>
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jjohnson
parents:
diff changeset
363
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
364 <conditional name="downsampling_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
365 <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
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jjohnson
parents:
diff changeset
366 <option value="NONE" selected="True">NONE</option>
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jjohnson
parents:
diff changeset
367 <option value="ALL_READS">ALL_READS</option>
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jjohnson
parents:
diff changeset
368 <option value="BY_SAMPLE">BY_SAMPLE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
369 </param>
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jjohnson
parents:
diff changeset
370 <when value="NONE">
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jjohnson
parents:
diff changeset
371 <!-- no more options here -->
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jjohnson
parents:
diff changeset
372 </when>
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jjohnson
parents:
diff changeset
373 <when value="ALL_READS">
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jjohnson
parents:
diff changeset
374 <conditional name="downsample_to_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
375 <param name="downsample_to_type_selector" type="select" label="Downsample method">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
376 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
377 <option value="downsample_to_coverage">Downsample by Coverage</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
378 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
379 <when value="downsample_to_fraction">
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jjohnson
parents:
diff changeset
380 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
381 </when>
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jjohnson
parents:
diff changeset
382 <when value="downsample_to_coverage">
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jjohnson
parents:
diff changeset
383 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
384 </when>
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jjohnson
parents:
diff changeset
385 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
386 </when>
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jjohnson
parents:
diff changeset
387 <when value="BY_SAMPLE">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
388 <conditional name="downsample_to_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
389 <param name="downsample_to_type_selector" type="select" label="Downsample method">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
390 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
391 <option value="downsample_to_coverage">Downsample by Coverage</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
392 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
393 <when value="downsample_to_fraction">
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jjohnson
parents:
diff changeset
394 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
395 </when>
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jjohnson
parents:
diff changeset
396 <when value="downsample_to_coverage">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
397 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
398 </when>
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jjohnson
parents:
diff changeset
399 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
400 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
401 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
402 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
403 <option value="OFF" selected="True">OFF</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
404 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
405 <option value="RECALCULATE">RECALCULATE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
406 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
407 <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
408 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
409 <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
410 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
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jjohnson
parents:
diff changeset
411 <option value="STRICT" selected="True">STRICT</option>
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jjohnson
parents:
diff changeset
412 <option value="LENIENT">LENIENT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
413 <option value="SILENT">SILENT</option>
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jjohnson
parents:
diff changeset
414 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
415 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
416 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
417 <option value="ALL" selected="True">ALL</option>
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jjohnson
parents:
diff changeset
418 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
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jjohnson
parents:
diff changeset
419 </param>
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jjohnson
parents:
diff changeset
420
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jjohnson
parents:
diff changeset
421 <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
422 <conditional name="read_group_black_list_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
423 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
424 <option value="file" selected="True">Filters in file</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
425 <option value="text">Specify filters as a string</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
426 </param>
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jjohnson
parents:
diff changeset
427 <when value="file">
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jjohnson
parents:
diff changeset
428 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
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jjohnson
parents:
diff changeset
429 </when>
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jjohnson
parents:
diff changeset
430 <when value="text">
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jjohnson
parents:
diff changeset
431 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
432 </when>
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jjohnson
parents:
diff changeset
433 </conditional>
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jjohnson
parents:
diff changeset
434 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
435
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jjohnson
parents:
diff changeset
436 <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
437 <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
18
7533db8dfb5b Update tool_dependencies to GATK v 2.3
Jim Johnson <jj@umn.edu>
parents: 16
diff changeset
438 <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False" help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
0
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jjohnson
parents:
diff changeset
439 </when>
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jjohnson
parents:
diff changeset
440 </conditional>
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jjohnson
parents:
diff changeset
441
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jjohnson
parents:
diff changeset
442 <conditional name="analysis_param_type">
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jjohnson
parents:
diff changeset
443 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
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jjohnson
parents:
diff changeset
444 <option value="basic" selected="True">Basic</option>
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jjohnson
parents:
diff changeset
445 <option value="advanced">Advanced</option>
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jjohnson
parents:
diff changeset
446 </param>
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jjohnson
parents:
diff changeset
447 <when value="basic">
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jjohnson
parents:
diff changeset
448 <!-- Do nothing here -->
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jjohnson
parents:
diff changeset
449 </when>
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jjohnson
parents:
diff changeset
450 <when value="advanced">
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jjohnson
parents:
diff changeset
451 <conditional name="default_read_group_type">
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jjohnson
parents:
diff changeset
452 <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
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jjohnson
parents:
diff changeset
453 <option value="default" selected="True">Don't Set</option>
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jjohnson
parents:
diff changeset
454 <option value="set">Set</option>
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jjohnson
parents:
diff changeset
455 </param>
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jjohnson
parents:
diff changeset
456 <when value="default">
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jjohnson
parents:
diff changeset
457 <!-- do nothing here -->
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jjohnson
parents:
diff changeset
458 </when>
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jjohnson
parents:
diff changeset
459 <when value="set">
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jjohnson
parents:
diff changeset
460 <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/>
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jjohnson
parents:
diff changeset
461 </when>
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jjohnson
parents:
diff changeset
462 </conditional>
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jjohnson
parents:
diff changeset
463 <param name="default_platform" type="select" label="Set default Platform" help="--default_platform">
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jjohnson
parents:
diff changeset
464 <option value="default" selected="True">Don't Set</option>
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jjohnson
parents:
diff changeset
465 <option value="illumina">illumina</option>
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jjohnson
parents:
diff changeset
466 <option value="454">454</option>
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jjohnson
parents:
diff changeset
467 <option value="solid">solid</option>
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jjohnson
parents:
diff changeset
468 </param>
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jjohnson
parents:
diff changeset
469 <conditional name="force_read_group_type">
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jjohnson
parents:
diff changeset
470 <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group">
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jjohnson
parents:
diff changeset
471 <option value="default" selected="True">Don't Force</option>
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jjohnson
parents:
diff changeset
472 <option value="set">Force</option>
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jjohnson
parents:
diff changeset
473 </param>
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jjohnson
parents:
diff changeset
474 <when value="default">
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jjohnson
parents:
diff changeset
475 <!-- do nothing here -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
476 </when>
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jjohnson
parents:
diff changeset
477 <when value="set">
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jjohnson
parents:
diff changeset
478 <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/>
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jjohnson
parents:
diff changeset
479 </when>
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jjohnson
parents:
diff changeset
480 </conditional>
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jjohnson
parents:
diff changeset
481 <param name="force_platform" type="select" label="Force Platform" help="--force_platform">
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jjohnson
parents:
diff changeset
482 <option value="default" selected="True">Don't Force</option>
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jjohnson
parents:
diff changeset
483 <option value="illumina">illumina</option>
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jjohnson
parents:
diff changeset
484 <option value="454">454</option>
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jjohnson
parents:
diff changeset
485 <option value="solid">solid</option>
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jjohnson
parents:
diff changeset
486 </param>
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jjohnson
parents:
diff changeset
487 <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
488 <conditional name="solid_options_type">
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jjohnson
parents:
diff changeset
489 <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options">
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jjohnson
parents:
diff changeset
490 <option value="default" selected="True">Don't Set</option>
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jjohnson
parents:
diff changeset
491 <option value="set">Set</option>
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jjohnson
parents:
diff changeset
492 </param>
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jjohnson
parents:
diff changeset
493 <when value="default">
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jjohnson
parents:
diff changeset
494 <!-- do nothing here -->
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jjohnson
parents:
diff changeset
495 </when>
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jjohnson
parents:
diff changeset
496 <when value="set">
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jjohnson
parents:
diff changeset
497 <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode &amp;lt;solid_recal_mode&amp;gt;">
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jjohnson
parents:
diff changeset
498 <option value="default" selected="True">Don't set</option>
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jjohnson
parents:
diff changeset
499 <option value="DO_NOTHING">DO_NOTHING</option>
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jjohnson
parents:
diff changeset
500 <option value="SET_Q_ZERO">SET_Q_ZERO</option>
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jjohnson
parents:
diff changeset
501 <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option>
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jjohnson
parents:
diff changeset
502 <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option>
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jjohnson
parents:
diff changeset
503 </param>
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jjohnson
parents:
diff changeset
504 <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy &amp;lt;solid_nocall_strategy&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
505 <option value="default" selected="True">Don't set</option>
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jjohnson
parents:
diff changeset
506 <option value="THROW_EXCEPTION">THROW_EXCEPTION</option>
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jjohnson
parents:
diff changeset
507 <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option>
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jjohnson
parents:
diff changeset
508 <option value="PURGE_READ">PURGE_READ</option>
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jjohnson
parents:
diff changeset
509 </param>
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jjohnson
parents:
diff changeset
510 </when>
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jjohnson
parents:
diff changeset
511 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
512 <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="window_size_nqs"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
513 <param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &amp;lt;homopolymer_nback&amp;gt;" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
514 </when>
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jjohnson
parents:
diff changeset
515 </conditional>
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jjohnson
parents:
diff changeset
516 </inputs>
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jjohnson
parents:
diff changeset
517 <outputs>
16
d56503a12975 base_recalibrator out_puts gatk_report
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
518 <data format="gatk_report" name="output_recal" label="${tool.name} on ${on_string} (Covariate File)" />
0
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
519 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
24
6460f2ba6a60 Add BQSR and plot_pdf_file options to base_recalibrator.xml
Jim Johnson <jj@umn.edu>
parents: 23
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520 <data format="pdf" name="output_pdf" label="${tool.name} on ${on_string} (plot_pdf_file)">
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521 <filter>plot_pdf == True</filter>
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522 </data>
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523 </outputs>
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524 <tests>
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525 <test>
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526 <param name="reference_source_selector" value="history" />
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527 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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528 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
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529 <param name="rod_bind_type_selector" value="dbsnp" />
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530 <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
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531 <param name="standard_covs" value="True" />
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532 <param name="covariates" value="ReadGroupCovariate,HomopolymerCovariate,MinimumNQSCovariate,PositionCovariate" />
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533 <param name="gatk_param_type_selector" value="basic" />
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534 <param name="analysis_param_type_selector" value="basic" />
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535 <output name="output_recal" file="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" />
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536 <output name="output_log" file="gatk/gatk_count_covariates/gatk_count_covariates_out_1.log.contains" compare="contains" />
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537 </test>
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538 </tests>
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539 <help>
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540 .. class:: warningmark
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541
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542 "This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation."
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543 However, if you do not provide this file, the '--run_without_dbsnp_potentially_ruining_quality' flag will be automatically used, and the command will be allowed to run.
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544
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545 **What it does**
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546
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547 This walker is designed to work as the first pass in a two-pass processing step. It does a by-locus traversal operating only at sites that are not in dbSNP. We assume that all reference mismatches we see are therefore errors and indicative of poor base quality. This walker generates tables based on various user-specified covariates (such as read group, reported quality score, cycle, and dinucleotide) Since there is a large amount of data one can then calculate an empirical probability of error given the particular covariates seen at this site, where p(error) = num mismatches / num observations The output file is a CSV list of (the several covariate values, num observations, num mismatches, empirical quality score) The first non-comment line of the output file gives the name of the covariates that were used for this calculation. Note: ReadGroupCovariate and QualityScoreCovariate are required covariates and will be added for the user regardless of whether or not they were specified Note: This walker is designed to be used in conjunction with TableRecalibrationWalker.
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548
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549 For more information on base quality score recalibration using the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_bqsr_BaseRecalibrator.html&gt;`_.
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550
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551 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
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552
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553 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
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554
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555 ------
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556
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557 **Inputs**
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558
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559 GenomeAnalysisTK: BaseRecalibrator accepts an aligned BAM input file.
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560
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561
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562 **Outputs**
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563
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564 The output is in CSV format.
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565
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566
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567 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
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568
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569 -------
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570
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571 **Settings**::
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572
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573
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574 default_read_group If a read has no read group then default to the provided String.
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575 default_platform If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.
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576 force_read_group If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group.
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577 force_platform If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.
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578 window_size_nqs The window size used by MinimumNQSCovariate for its calculation
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579 homopolymer_nback The number of previous bases to look at in HomopolymerCovariate
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580 exception_if_no_tile If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1
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581 solid_recal_mode How should we recalibrate solid bases in whichthe reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING|SET_Q_ZERO|SET_Q_ZERO_BASE_N|REMOVE_REF_BIAS)
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582 solid_nocall_strategy Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ (THROW_EXCEPTION|LEAVE_READ_UNRECALIBRATED|PURGE_READ)
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583 recal_file Filename for the input covariates table recalibration .csv file
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584 out The output CSV file
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585 standard_covs Use the standard set of covariates in addition to the ones listed using the -cov argument
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586 run_without_dbsnp_potentially_ruining_quality If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only.
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587
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588 ------
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589
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590 **Citation**
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591
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592 For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21478889&gt;`_
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593
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594 Please also site `McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303. Epub 2010 Jul 19. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20644199&gt;`_
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595
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596 If you use this tool in Galaxy, please cite `Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20069535&gt;`_
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597
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598 </help>
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599 </tool>