annotate variant_filtration.xml @ 21:6e641ee02851 draft

Fix base_recalibrator.xml option: no_standard_covs
author Jim Johnson <jj@umn.edu>
date Fri, 28 Dec 2012 11:50:20 -0600
parents 7533db8dfb5b
children 6ef8eb568700
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7533db8dfb5b Update tool_dependencies to GATK v 2.3
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1 <tool id="gatk2_variant_filtration" name="Variant Filtration" version="0.0.5">
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2 <description>on VCF 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 </requirements>
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6 <command interpreter="python">gatk2_wrapper.py
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7 #from binascii import hexlify
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8 --max_jvm_heap_fraction "1"
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9 --stdout "${output_log}"
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10 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
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11 -p 'java
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12 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
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13 -T "VariantFiltration"
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14 \$GATK2_SITE_OPTIONS
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15 \$GATK2_THREAD_OPTIONS
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16 ##--num_threads 4 ##hard coded, for now
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17 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
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18 -o "${output_vcf}"
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19 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
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20 #if $reference_source.reference_source_selector != "history":
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21 -R "${reference_source.ref_file.fields.path}"
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22 #end if
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23 '
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24 #for $variant_filter in $variant_filters:
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25 #set $variant_filter = "--%sExpression '%s' --%sName '%s'" % ( str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_expression ), str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_name ) )
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26 -o '${ hexlify( $variant_filter ) }'
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27 #end for
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28
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29 #if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask':
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30 -d "--mask:${mask_rod_bind_type.mask_rod_name},%(file_type)s" "${mask_rod_bind_type.input_mask_rod}" "${mask_rod_bind_type.input_mask_rod.ext}" "input_mask_${mask_rod_bind_type.mask_rod_name}"
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31 -p '
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32 --maskExtension "${mask_rod_bind_type.mask_extension}"
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33 --maskName "${mask_rod_bind_type.mask_rod_name}"
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34 '
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35 #end if
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36
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37 ##start standard gatk options
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38 #if $gatk_param_type.gatk_param_type_selector == "advanced":
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39 #for $pedigree in $gatk_param_type.pedigree:
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40 -p '--pedigree "${pedigree.pedigree_file}"'
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41 #end for
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42 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
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43 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
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44 #end for
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45 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
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46 #for $read_filter in $gatk_param_type.read_filter:
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47 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
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48 ###raise Exception( str( dir( $read_filter ) ) )
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49 #for $name, $param in $read_filter.read_filter_type.iteritems():
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50 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
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51 #if hasattr( $param.input, 'truevalue' ):
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52 ${param}
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53 #else:
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54 --${name} "${param}"
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55 #end if
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56 #end if
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57 #end for
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58 '
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59 #end for
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60 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
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61 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
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62 #end for
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63
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64 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
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65 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
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66 #end for
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67
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68 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
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69
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70 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
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71 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
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72 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
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73 #end if
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74 -p '
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75 --baq "${gatk_param_type.baq}"
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76 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
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77 ${gatk_param_type.use_original_qualities}
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78 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
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79 --validation_strictness "${gatk_param_type.validation_strictness}"
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80 --interval_merging "${gatk_param_type.interval_merging}"
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81 ${gatk_param_type.disable_experimental_low_memory_sharding}
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82 ${gatk_param_type.fix_misencoded_quality_scores}
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83 ${gatk_param_type.non_deterministic_random_seed}
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84 '
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85 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
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86 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
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87 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
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88 #else
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89 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
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90 #end if
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91 #end for
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92 #end if
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93
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94 #if str( $reference_source.reference_source_selector ) == "history":
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95 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
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96 #end if
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97 ##end standard gatk options
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98
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99 ##start analysis specific options
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100 #if $cluster_snp_type.cluster_snp_type_selector == "cluster_snp":
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101 -p '
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102 --clusterSize "${cluster_snp_type.cluster_size}"
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103 --clusterWindowSize "${cluster_snp_type.cluster_window_size}"
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104 '
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105 #end if
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106 -p '${missing_values_in_expressions_should_evaluate_as_failing}'
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107 </command>
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108 <inputs>
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109 <conditional name="reference_source">
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110 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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111 <option value="cached">Locally cached</option>
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112 <option value="history">History</option>
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113 </param>
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114 <when value="cached">
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115 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;" />
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116 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
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117 <options from_data_table="gatk2_picard_indexes">
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118 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
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119 </options>
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120 <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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121 </param>
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122 </when>
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123 <when value="history"> <!-- FIX ME!!!! -->
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124 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&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
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130 <repeat name="variant_filters" title="Variant Filters">
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131 <param name="filter_expression" value="AB &lt; 0.2 || MQ0 &gt; 50" type="text" label="Filter expression" help="JEXL formatted expressions (-filter,--filterExpression &amp;lt;filterExpression&amp;gt;)">
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132 <sanitizer>
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133 <valid initial="string.printable">
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134 <remove value="&apos;"/>
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135 </valid>
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136 <mapping initial="none"/>
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137 </sanitizer>
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138 </param>
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139 <param name="filter_name" value="custom_filter" type="text" label="Filter name" help="-filterName,--filterName &amp;lt;filterName&amp;gt;"/>
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140 <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" help="Use -G_filter,--genotypeFilterExpression &amp;lt;genotypeFilterExpression&amp;gt; and -G_filterName,--genotypeFilterName &amp;lt;genotypeFilterName&amp;gt; for filter type" />
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141 </repeat>
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142
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143
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144
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145 <conditional name="mask_rod_bind_type">
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146 <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file">
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147 <option value="set_mask" selected="True">Set maskP</option>
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148 <option value="exclude_mask">Don't set mask</option>
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149 </param>
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150 <when value="exclude_mask">
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151 <!-- Do nothing here -->
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152 </when>
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153 <when value="set_mask">
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154 <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" help="--mask &amp;lt;mask&amp;gt;" />
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155 <param name="mask_rod_name" type="text" value="Mask" label="Mask Name" help="-maskName,--maskName &amp;lt;maskName&amp;gt;"/>
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156 <param name="mask_extension" type="integer" value="0" label="Mask Extension" help="-maskExtend,--maskExtension &amp;lt;maskExtension&amp;gt;"/>
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157 </when>
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158 </conditional>
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159
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160
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161 <conditional name="gatk_param_type">
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162 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
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163 <option value="basic" selected="True">Basic</option>
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164 <option value="advanced">Advanced</option>
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165 </param>
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166 <when value="basic">
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167 <!-- Do nothing here -->
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168 </when>
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169 <when value="advanced">
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170 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
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171 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
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172 </repeat>
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173 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
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174 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
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175 </repeat>
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jjohnson
parents:
diff changeset
176 <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;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
177 <option value="STRICT" selected="True">STRICT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
178 <option value="SILENT">SILENT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
179 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
180 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
181 <conditional name="read_filter_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
182 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
183 <option value="BadCigar">BadCigar</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
184 <option value="BadMate">BadMate</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
185 <option value="DuplicateRead">DuplicateRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
186 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
187 <option value="MalformedRead">MalformedRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
188 <option value="MappingQuality">MappingQuality</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
189 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
190 <option value="MappingQualityZero">MappingQualityZero</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
191 <option value="MateSameStrand">MateSameStrand</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
192 <option value="MaxInsertSize">MaxInsertSize</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
193 <option value="MaxReadLength" selected="True">MaxReadLength</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
194 <option value="MissingReadGroup">MissingReadGroup</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
195 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
196 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
197 <option value="Platform454">Platform454</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
198 <option value="Platform">Platform</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
199 <option value="PlatformUnit">PlatformUnit</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
200 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
201 <option value="ReadName">ReadName</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
202 <option value="ReadStrand">ReadStrand</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
203 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
204 <option value="Sample">Sample</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
205 <option value="SingleReadGroup">SingleReadGroup</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
206 <option value="UnmappedRead">UnmappedRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
207 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
208 <when value="BadCigar">
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jjohnson
parents:
diff changeset
209 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
210 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
211 <when value="BadMate">
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jjohnson
parents:
diff changeset
212 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
213 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
214 <when value="DuplicateRead">
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jjohnson
parents:
diff changeset
215 <!-- no extra options -->
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jjohnson
parents:
diff changeset
216 </when>
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jjohnson
parents:
diff changeset
217 <when value="FailsVendorQualityCheck">
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jjohnson
parents:
diff changeset
218 <!-- no extra options -->
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jjohnson
parents:
diff changeset
219 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
220 <when value="MalformedRead">
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jjohnson
parents:
diff changeset
221 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
222 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
223 <when value="MappingQuality">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
224 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
225 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
226 <when value="MappingQualityUnavailable">
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jjohnson
parents:
diff changeset
227 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
228 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
229 <when value="MappingQualityZero">
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jjohnson
parents:
diff changeset
230 <!-- no extra options -->
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jjohnson
parents:
diff changeset
231 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
232 <when value="MateSameStrand">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
233 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
234 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
235 <when value="MaxInsertSize">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
236 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
237 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
238 <when value="MaxReadLength">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
239 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
240 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
241 <when value="MissingReadGroup">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
242 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
243 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
244 <when value="NoOriginalQualityScores">
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jjohnson
parents:
diff changeset
245 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
246 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
247 <when value="NotPrimaryAlignment">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
248 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
249 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
250 <when value="Platform454">
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jjohnson
parents:
diff changeset
251 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
252 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
253 <when value="Platform">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
254 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
255 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
256 <when value="PlatformUnit">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
257 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
258 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
259 <when value="ReadGroupBlackList">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
260 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
261 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
262 <when value="ReadName">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
263 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
264 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
265 <when value="ReadStrand">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
266 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
267 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
268 <when value="ReassignMappingQuality">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
269 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
270 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
271 <when value="Sample">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
272 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
273 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
274 <when value="SingleReadGroup">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
275 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
276 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
277 <when value="UnmappedRead">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
278 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
279 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
280 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
281 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
282 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
283 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
284 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
285 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
286 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
287 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
288
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
289 <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
290 <option value="UNION" selected="True">UNION</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
291 <option value="INTERSECTION">INTERSECTION</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
292 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
293
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
294 <conditional name="downsampling_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
295 <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;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
296 <option value="NONE" selected="True">NONE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
297 <option value="ALL_READS">ALL_READS</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
298 <option value="BY_SAMPLE">BY_SAMPLE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
299 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
300 <when value="NONE">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
301 <!-- no more options here -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
302 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
303 <when value="ALL_READS">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
304 <conditional name="downsample_to_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
305 <param name="downsample_to_type_selector" type="select" label="Downsample method">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
306 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
307 <option value="downsample_to_coverage">Downsample by Coverage</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
308 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
309 <when value="downsample_to_fraction">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
310 <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
311 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
312 <when value="downsample_to_coverage">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
313 <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
314 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
315 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
316 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
317 <when value="BY_SAMPLE">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
318 <conditional name="downsample_to_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
319 <param name="downsample_to_type_selector" type="select" label="Downsample method">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
320 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
321 <option value="downsample_to_coverage">Downsample by Coverage</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
322 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
323 <when value="downsample_to_fraction">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
324 <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
325 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
326 <when value="downsample_to_coverage">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
327 <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
328 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
329 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
330 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
331 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
332 <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
333 <option value="OFF" selected="True">OFF</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
334 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
335 <option value="RECALCULATE">RECALCULATE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
336 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
337 <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
338 <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
339 <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
340 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
341 <option value="STRICT" selected="True">STRICT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
342 <option value="LENIENT">LENIENT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
343 <option value="SILENT">SILENT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
344 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
345 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
346 <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
347 <option value="ALL" selected="True">ALL</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
348 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
349 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
350
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
351 <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
352 <conditional name="read_group_black_list_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
353 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
354 <option value="file" selected="True">Filters in file</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
355 <option value="text">Specify filters as a string</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
356 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
357 <when value="file">
74c05070a3f8 Uploaded
jjohnson
parents:
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358 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
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359 </when>
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360 <when value="text">
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361 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
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362 </when>
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363 </conditional>
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364 </repeat>
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365
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366 <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"/>
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367 <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"/>
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7533db8dfb5b Update tool_dependencies to GATK v 2.3
Jim Johnson <jj@umn.edu>
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368 <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"/>
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369
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370 </when>
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371 </conditional>
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372
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373 <conditional name="cluster_snp_type">
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374 <param name="cluster_snp_type_selector" type="select" label="Cluster SNPs">
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375 <option value="cluster_snp">Cluster SNPs</option>
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376 <option value="do_not_cluster_snp" selected="True">Do not cluster SNPs</option>
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377 </param>
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378 <when value="do_not_cluster_snp">
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379 <!-- Do nothing here -->
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380 </when>
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381 <when value="cluster_snp">
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382 <param name="cluster_size" type="integer" value="3" label="The number of SNPs which make up a cluster" help="-cluster,--clusterSize &amp;lt;clusterSize&amp;gt;"/>
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383 <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs" help="-window,--clusterWindowSize &amp;lt;clusterWindowSize&amp;gt;"/>
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384 </when>
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385 </conditional>
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386
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387 <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" help="--missingValuesInExpressionsShouldEvaluateAsFailing" />
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388
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389 </inputs>
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390 <outputs>
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391 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
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392 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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393 </outputs>
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394 <tests>
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395 <test>
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396 <param name="reference_source_selector" value="history" />
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397 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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398 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
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399 <param name="filter_expression" value="MQ &lt; 37.74 || MQ0 &gt; 50" />
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400 <param name="filter_name" value="Galaxy_filter" />
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401 <param name="is_genotype_filter" />
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402 <param name="mask_rod_bind_type_selector" value="set_mask" />
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403 <param name="input_mask_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
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404 <param name="mask_rod_name" value="." />
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405 <param name="mask_extension" value="0" />
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406 <param name="gatk_param_type_selector" value="basic" />
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407 <param name="cluster_snp_type_selector" value="do_not_cluster_snp" />
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408 <param name="missing_values_in_expressions_should_evaluate_as_failing" />
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409 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" />
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410 <output name="output_log" file="gatk/gatk_variant_filtration/gatk_variant_filtration_out_1.log.contains" compare="contains" />
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411 </test>
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412 </tests>
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413 <help>
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414 **What it does**
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415
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416 Filters variant calls using a number of user-selectable, parameterizable criteria.
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417
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418 For more information on using the VariantFiltration module, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_filters_VariantFiltration.html&gt;`_.
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419
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420 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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421
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422 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
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423
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424 ------
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425
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426 **Inputs**
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427
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428 GenomeAnalysisTK: VariantFiltration accepts a VCF input file.
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429
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430
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431 **Outputs**
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432
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433 The output is in VCF format.
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434
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435 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
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436
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437 -------
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438
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439 **Settings**::
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440
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441
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442 filterExpression One or more expression used with INFO fields to filter (see wiki docs for more info)
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443 filterName Names to use for the list of filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered
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444 genotypeFilterExpression One or more expression used with FORMAT (sample/genotype-level) fields to filter (see wiki docs for more info)
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445 genotypeFilterName Names to use for the list of sample/genotype filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered
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446 clusterSize The number of SNPs which make up a cluster (see also --clusterWindowSize); [default:3]
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447 clusterWindowSize The window size (in bases) in which to evaluate clustered SNPs (to disable the clustered SNP filter, set this value to less than 1); [default:0]
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448 maskName The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask']
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449 missingValuesInExpressionsShouldEvaluateAsFailing When evaluating the JEXL expressions, should missing values be considered failing the expression (by default they are considered passing)?
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450
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451 ------
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452
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453 **Citation**
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454
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455 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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456
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457 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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458
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459 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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460
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461
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462 </help>
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463 </tool>