annotate variant_apply_recalibration.xml @ 29:77c0583db74f draft

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author david-hoover
date Thu, 20 Sep 2012 10:08:03 -0400
parents e6e2bb189314
children 1326b011a3b9
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1 <tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.1">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="2.1">gatk</requirement>
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5 </requirements>
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6 <command interpreter="python">gatk2_wrapper.py
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7 --max_jvm_heap_fraction "1"
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8 --stdout "${output_log}"
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9 #for $var_count, $variant in enumerate( $reference_source.variants ):
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10 -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
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11 #end for
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12 -p 'java
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13 -jar "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/GenomeAnalysisTK.jar"
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14 -T "ApplyRecalibration"
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15 ##--num_threads 4 ##hard coded, for now
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16 -et "NO_ET" -K "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/gatk2_key_file" ##ET no phone home
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17 #if $reference_source.reference_source_selector != "history":
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18 -R "${reference_source.ref_file.fields.path}"
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19 #end if
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20 --recal_file "${reference_source.input_recal}"
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21 --tranches_file "${reference_source.input_tranches}"
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22 --out "${output_variants}"
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23 '
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24
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25 ##start standard gatk options
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26 #if $gatk_param_type.gatk_param_type_selector == "advanced":
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27 #for $pedigree in $gatk_param_type.pedigree:
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28 -p '--pedigree "${pedigree.pedigree_file}"'
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29 #end for
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30 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
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31 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
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32 #end for
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33 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
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34 #for $read_filter in $gatk_param_type.read_filter:
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35 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
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36 ###raise Exception( str( dir( $read_filter ) ) )
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37 #for $name, $param in $read_filter.read_filter_type.iteritems():
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38 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
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39 #if hasattr( $param.input, 'truevalue' ):
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40 ${param}
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41 #else:
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42 --${name} "${param}"
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43 #end if
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44 #end if
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45 #end for
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46 '
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47 #end for
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48 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
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49 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
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50 #end for
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51
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52 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
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53 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
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54 #end for
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55
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56 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
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57
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58 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
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59 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
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60 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
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61 #end if
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62 -p '
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63 --baq "${gatk_param_type.baq}"
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64 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
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65 ${gatk_param_type.use_original_qualities}
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66 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
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67 --validation_strictness "${gatk_param_type.validation_strictness}"
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68 --interval_merging "${gatk_param_type.interval_merging}"
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69 ${gatk_param_type.disable_experimental_low_memory_sharding}
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70 ${gatk_param_type.non_deterministic_random_seed}
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71 '
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72 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
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73 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
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74 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
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75 #else
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76 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
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77 #end if
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78 #end for
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79 #end if
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80
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81 #if str( $reference_source.reference_source_selector ) == "history":
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82 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
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83 #end if
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84 ##end standard gatk options
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85
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86 ##start analysis specific options
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87 -p '
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88 --mode "${mode}"
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89
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90 #for $ignore_filter in $ignore_filters:
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91 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
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92 #if $ignore_filter_name == "custom":
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93 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name )
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94 #end if
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95 --ignore_filter "${ignore_filter_name}"
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96 #end for
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97 --ts_filter_level "${ts_filter_level}"
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98 '
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99 </command>
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100 <inputs>
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101 <conditional name="reference_source">
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102 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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103 <option value="cached">Locally cached</option>
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104 <option value="history">History</option>
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105 </param>
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106 <when value="cached">
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107 <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
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108 <param name="input_variants" type="data" format="vcf" label="Variant file to annotate"/>
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109 </repeat>
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110 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
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111 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" />
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112 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
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113 <options from_data_table="gatk2_picard_indexes">
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114 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
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115 </options>
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116 <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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117 </param>
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118 </when>
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119 <when value="history"> <!-- FIX ME!!!! -->
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120 <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;">
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121 <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" />
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122 </repeat>
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123 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
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124 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" />
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125 <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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126 </when>
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127 </conditional>
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128
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129 <conditional name="gatk_param_type">
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130 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
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131 <option value="basic" selected="True">Basic</option>
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132 <option value="advanced">Advanced</option>
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133 </param>
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134 <when value="basic">
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135 <!-- Do nothing here -->
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136 </when>
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137 <when value="advanced">
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138 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
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139 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
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140 </repeat>
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141 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
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142 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
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143 </repeat>
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144 <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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145 <option value="STRICT" selected="True">STRICT</option>
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146 <option value="SILENT">SILENT</option>
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147 </param>
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148 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
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149 <conditional name="read_filter_type">
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150 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
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151 <option value="BadCigar">BadCigar</option>
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152 <option value="BadMate">BadMate</option>
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153 <option value="DuplicateRead">DuplicateRead</option>
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154 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
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155 <option value="MalformedRead">MalformedRead</option>
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156 <option value="MappingQuality">MappingQuality</option>
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157 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
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158 <option value="MappingQualityZero">MappingQualityZero</option>
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159 <option value="MateSameStrand">MateSameStrand</option>
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160 <option value="MaxInsertSize">MaxInsertSize</option>
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161 <option value="MaxReadLength" selected="True">MaxReadLength</option>
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162 <option value="MissingReadGroup">MissingReadGroup</option>
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163 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
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164 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
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165 <option value="Platform454">Platform454</option>
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166 <option value="Platform">Platform</option>
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167 <option value="PlatformUnit">PlatformUnit</option>
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168 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
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169 <option value="ReadName">ReadName</option>
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170 <option value="ReadStrand">ReadStrand</option>
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171 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
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172 <option value="Sample">Sample</option>
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173 <option value="SingleReadGroup">SingleReadGroup</option>
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174 <option value="UnmappedRead">UnmappedRead</option>
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175 </param>
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parents:
diff changeset
176 <when value="BadCigar">
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david-hoover
parents:
diff changeset
177 <!-- no extra options -->
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david-hoover
parents:
diff changeset
178 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
179 <when value="BadMate">
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david-hoover
parents:
diff changeset
180 <!-- no extra options -->
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david-hoover
parents:
diff changeset
181 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
182 <when value="DuplicateRead">
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david-hoover
parents:
diff changeset
183 <!-- no extra options -->
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david-hoover
parents:
diff changeset
184 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
185 <when value="FailsVendorQualityCheck">
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david-hoover
parents:
diff changeset
186 <!-- no extra options -->
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david-hoover
parents:
diff changeset
187 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
188 <when value="MalformedRead">
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david-hoover
parents:
diff changeset
189 <!-- no extra options -->
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
190 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
191 <when value="MappingQuality">
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david-hoover
parents:
diff changeset
192 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
193 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
194 <when value="MappingQualityUnavailable">
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david-hoover
parents:
diff changeset
195 <!-- no extra options -->
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
196 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
197 <when value="MappingQualityZero">
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david-hoover
parents:
diff changeset
198 <!-- no extra options -->
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david-hoover
parents:
diff changeset
199 </when>
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david-hoover
parents:
diff changeset
200 <when value="MateSameStrand">
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david-hoover
parents:
diff changeset
201 <!-- no extra options -->
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david-hoover
parents:
diff changeset
202 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
203 <when value="MaxInsertSize">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
204 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
205 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
206 <when value="MaxReadLength">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
207 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
208 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
209 <when value="MissingReadGroup">
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david-hoover
parents:
diff changeset
210 <!-- no extra options -->
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david-hoover
parents:
diff changeset
211 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
212 <when value="NoOriginalQualityScores">
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david-hoover
parents:
diff changeset
213 <!-- no extra options -->
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david-hoover
parents:
diff changeset
214 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
215 <when value="NotPrimaryAlignment">
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david-hoover
parents:
diff changeset
216 <!-- no extra options -->
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david-hoover
parents:
diff changeset
217 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
218 <when value="Platform454">
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david-hoover
parents:
diff changeset
219 <!-- no extra options -->
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david-hoover
parents:
diff changeset
220 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
221 <when value="Platform">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
222 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
223 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
224 <when value="PlatformUnit">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
225 <!-- no extra options -->
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
226 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
227 <when value="ReadGroupBlackList">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
228 <!-- no extra options -->
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david-hoover
parents:
diff changeset
229 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
230 <when value="ReadName">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
231 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
232 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
233 <when value="ReadStrand">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
234 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
235 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
236 <when value="ReassignMappingQuality">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
237 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
238 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
239 <when value="Sample">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
240 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
241 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
242 <when value="SingleReadGroup">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
243 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
244 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
245 <when value="UnmappedRead">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
246 <!-- no extra options -->
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
247 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
248 </conditional>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
249 </repeat>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
250 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
251 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
252 </repeat>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
253 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
254 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
255 </repeat>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
256
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
257 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
258 <option value="UNION" selected="True">UNION</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
259 <option value="INTERSECTION">INTERSECTION</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
260 </param>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
261
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
262 <conditional name="downsampling_type">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
263 <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;">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
264 <option value="NONE" selected="True">NONE</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
265 <option value="ALL_READS">ALL_READS</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
266 <option value="BY_SAMPLE">BY_SAMPLE</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
267 </param>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
268 <when value="NONE">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
269 <!-- no more options here -->
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
270 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
271 <when value="ALL_READS">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
272 <conditional name="downsample_to_type">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
273 <param name="downsample_to_type_selector" type="select" label="Downsample method">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
274 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
275 <option value="downsample_to_coverage">Downsample by Coverage</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
276 </param>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
277 <when value="downsample_to_fraction">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
278 <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;"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
279 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
280 <when value="downsample_to_coverage">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
281 <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;"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
282 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
283 </conditional>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
284 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
285 <when value="BY_SAMPLE">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
286 <conditional name="downsample_to_type">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
287 <param name="downsample_to_type_selector" type="select" label="Downsample method">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
288 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
289 <option value="downsample_to_coverage">Downsample by Coverage</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
290 </param>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
291 <when value="downsample_to_fraction">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
292 <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;"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
293 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
294 <when value="downsample_to_coverage">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
295 <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;"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
296 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
297 </conditional>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
298 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
299 </conditional>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
300 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
301 <option value="OFF" selected="True">OFF</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
302 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
303 <option value="RECALCULATE">RECALCULATE</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
304 </param>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
305 <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;" />
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
306 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
307 <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;"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
308 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
309 <option value="STRICT" selected="True">STRICT</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
310 <option value="LENIENT">LENIENT</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
311 <option value="SILENT">SILENT</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
312 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
313 </param>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
314 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
315 <option value="ALL" selected="True">ALL</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
316 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
317 </param>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
318
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
319 <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;">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
320 <conditional name="read_group_black_list_type">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
321 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
322 <option value="file" selected="True">Filters in file</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
323 <option value="text">Specify filters as a string</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
324 </param>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
325 <when value="file">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
326 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
327 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
328 <when value="text">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
329 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
330 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
331 </conditional>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
332 </repeat>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
333
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
334 <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"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
335 <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"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
336
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
337 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
338 </conditional>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
339
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
340 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
341 <option value="SNP" selected="True">SNP</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
342 <option value="INDEL">INDEL</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
343 <option value="BOTH">BOTH</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
344 </param>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
345 <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &amp;lt;ignore_filter&amp;gt;">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
346 <conditional name="ignore_filter_type">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
347 <param name="ignore_filter_type_selector" type="select" label="Filter Type">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
348 <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
349 <option value="LowQual" >LowQual</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
350 <option value="custom" selected="True">Other</option>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
351 </param>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
352 <when value="custom">
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
353 <param name="filter_name" type="text" value="" label="Filter name"/>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
354 </when>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
355 <when value="HARD_TO_VALIDATE" />
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
356 <when value="LowQual" />
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
357 </conditional>
432aafa6830a Uploaded
david-hoover
parents:
diff changeset
358 </repeat>
432aafa6830a Uploaded
david-hoover
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359 <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &amp;lt;ts_filter_level&amp;gt;"/>
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360 </inputs>
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361 <outputs>
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362 <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (Variants File)" />
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363 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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364 </outputs>
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365 <tests>
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366 <!-- ADD TESTS -->
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367 </tests>
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368 <help>
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369 **What it does**
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370
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371 Applies cuts to the input vcf file (by adding filter lines) to achieve the desired novel FDR levels which were specified during VariantRecalibration
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372
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373 For more information on using the ApplyRecalibration module, see this `tool specific page &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration&gt;`_.
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374
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375 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3&gt;`_.
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376
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377 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions&gt;`_.
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378
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379 ------
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380
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381 **Inputs**
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382
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383 GenomeAnalysisTK: ApplyRecalibration accepts a variant input file, a recalibration file and a tranches file.
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384
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385
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386 **Outputs**
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387
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388 The output is in VCF format.
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389
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390
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391 Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK&gt;`_ for details on GATK file formats.
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392
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393 -------
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394
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395 **Settings**::
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396
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397
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398 recal_file The output recal file used by ApplyRecalibration
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399 tranches_file The input tranches file describing where to cut the data
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400 out The output filtered, recalibrated VCF file
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401 ts_filter_level The truth sensitivity level at which to start filtering
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402 ignore_filter If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file
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403 mode Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously. (SNP|INDEL|BOTH)
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404
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405 ------
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406
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407 **Citation**
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408
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409 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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410
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411 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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412
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413 </help>
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414 </tool>