annotate variant_select.xml @ 36:14d47237bb0a draft

Fix commandline template
author Jim Johnson <jj@umn.edu>
date Fri, 01 Mar 2013 08:07:56 -0600
parents a29c7d7d962d
children
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b99c25b0ad4d Update tool version to 0.0.7
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1 <tool id="gatk2_variant_select" name="Select Variants" version="0.0.7">
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2 <description>from 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}" "${reference_source.input_variant.ext}" "input_variant"
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11 -p 'java
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12 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
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13 -T "SelectVariants"
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14 \$GATK2_SITE_OPTIONS
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15 \$GATK2_NUM_THREADS
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16 ##--num_threads 4 ##hard coded, for now
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17 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
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18 -o "${output_vcf}"
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19
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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 -p '
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25 #if $input_concordance:
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26 --concordance "${input_concordance}"
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27 #end if
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28 #if $input_discordance:
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29 --discordance "${input_discordance}"
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30 #end if
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31
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32 #for $exclude_sample_name in $exclude_sample_name_repeat:
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33 --exclude_sample_name "${exclude_sample_name.exclude_sample_name}"
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34 #end for
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35
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36 ${exclude_filtered}
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37
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38 #for $sample_name in $sample_name_repeat:
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39 --sample_name "${sample_name.sample_name}"
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40 #end for
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41
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42 '
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43
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44 #for $select_expressions in $select_expressions_repeat:
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45 #set $select_expression = "--select_expressions '%s'" % ( str( $select_expressions.select_expressions ) )
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46 -o '${ hexlify( $select_expression ) }'
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47 #end for
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48
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49 ##start tool specific options
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50 #if str( $analysis_param_type.analysis_param_type_selector ) == 'advanced':
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51 -p '
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52 #for $exclude_sample_file in $analysis_param_type.exclude_sample_file_repeat:
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53 --exclude_sample_file "${exclude_sample_file.exclude_sample_file}"
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54 #end for
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55
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56 #for $sample_file in $analysis_param_type.sample_file_repeat:
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57 --sample_file "${ample_file.sample_file}"
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58 #end for
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59
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60 #if $analysis_param_type.input_keep_ids:
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61 --keepIDs "${analysis_param_type.input_keep_ids}"
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62 #end if
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63
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64 ${analysis_param_type.keep_original_AC}
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65
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66 ${analysis_param_type.mendelian_violation}
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67
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68 --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}"
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69
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70 --remove_fraction_genotypes "${analysis_param_type.remove_fraction_genotypes}"
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71
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72 --restrictAllelesTo "${analysis_param_type.restrict_alleles_to}"
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73
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74 #if str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_fraction':
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75 --select_random_fraction "${analysis_param_type.select_random_type.select_random_fraction}"
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76 #elif str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_number':
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77 --select_random_number "${analysis_param_type.select_random_type.select_random_number}"
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78 #end if
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79
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80 #if $analysis_param_type.select_type_to_include:
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81 #for $type_to_include in str( $analysis_param_type.select_type_to_include ).split( ',' ):
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82 --selectTypeToInclude "${type_to_include}"
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83 #end for
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84 #end if
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85
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86 ${analysis_param_type.exclude_non_variants}
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87 '
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88
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89 #for $sample_expressions in $analysis_param_type.sample_expressions_repeat:
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90 #set $sample_expression = "--sample_expressions '%s'" % ( str( $sample_expressions.sample_expressions ) )
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91 -o '${ hexlify( $sample_expression ) }'
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92 #end for
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93
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94 #end if
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95 ##end tool specific options
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96
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97 ##start standard gatk options
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98 #if $gatk_param_type.gatk_param_type_selector == "advanced":
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99 #for $pedigree in $gatk_param_type.pedigree:
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100 -p '--pedigree "${pedigree.pedigree_file}"'
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101 #end for
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102 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
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103 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
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104 #end for
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105 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
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106 #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead']
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107 #for $read_filter in $gatk_param_type.read_filter:
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108 -p '
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109 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
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110 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
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111 #end if
0
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112 #for $name, $param in $read_filter.read_filter_type.iteritems():
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113 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
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114 #if hasattr( $param.input, 'truevalue' ):
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115 ${param}
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116 #else:
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117 --${name} "${param}"
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118 #end if
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119 #end if
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120 #end for
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121 '
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122 #end for
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123 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
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124 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
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125 #end for
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126
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127 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
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128 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
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129 #end for
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130
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131 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
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132
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133 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
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134 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
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135 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
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136 #end if
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137 -p '
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138 --baq "${gatk_param_type.baq}"
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139 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
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140 ${gatk_param_type.use_original_qualities}
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141 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
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142 --validation_strictness "${gatk_param_type.validation_strictness}"
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143 --interval_merging "${gatk_param_type.interval_merging}"
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144 ${gatk_param_type.disable_experimental_low_memory_sharding}
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145 ${gatk_param_type.fix_misencoded_quality_scores}
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146 ${gatk_param_type.non_deterministic_random_seed}
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147 '
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148 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
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149 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
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150 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
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151 #else
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152 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
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153 #end if
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154 #end for
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155 #end if
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156
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157 #if str( $reference_source.reference_source_selector ) == "history":
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158 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
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159 #end if
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160 ##end standard gatk options
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161
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162
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163 </command>
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164 <inputs>
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165 <conditional name="reference_source">
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166 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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167 <option value="cached">Locally cached</option>
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168 <option value="history">History</option>
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169 </param>
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170 <when value="cached">
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171 <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &amp;lt;variant&amp;gt;" />
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172 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
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173 <options from_data_table="gatk2_picard_indexes">
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174 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
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175 </options>
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176 <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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177 </param>
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178 </when>
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179 <when value="history"> <!-- FIX ME!!!! -->
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180 <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &amp;lt;variant&amp;gt;" />
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181 <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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182 </when>
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183 </conditional>
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jjohnson
parents:
diff changeset
184
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jjohnson
parents:
diff changeset
185 <repeat name="select_expressions_repeat" title="Criteria to use when selecting the data" help="-select,--select_expressions &amp;lt;select_expressions&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
186 <param name="select_expressions" type="text" label="JEXL expression">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
187 <sanitizer>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
188 <valid initial="string.printable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
189 <remove value="&apos;"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
190 </valid>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
191 <mapping initial="none"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
192 </sanitizer>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
193 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
194 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
195
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jjohnson
parents:
diff changeset
196 <param name="input_concordance" type="data" format="vcf" label="Output variants that were also called in this comparison track" optional="True" help="-conc,--concordance &amp;lt;concordance&amp;gt;"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
197 <param name="input_discordance" type="data" format="vcf" label="Output variants that were not called in this comparison track" optional="True" help="-disc,--discordance &amp;lt;discordance&amp;gt;"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
198
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
199 <repeat name="sample_name_repeat" title="Include Samples by name" help="-sn,--sample_name &amp;lt;sample_name&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
200 <param name="sample_name" type="text" label="Include genotypes from this sample"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
201 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
202
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
203 <repeat name="exclude_sample_name_repeat" title="Exclude Samples by name" help="-xl_sn,--exclude_sample_name &amp;lt;exclude_sample_name&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
204 <param name="exclude_sample_name" type="text" label="Exclude genotypes from this sample"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
205 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
206
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
207 <param name="exclude_filtered" type="boolean" truevalue="--excludeFiltered" falsevalue="" label="Don't include filtered loci in the analysis" help="-ef,--excludeFiltered" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
208
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
209 <conditional name="gatk_param_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
210 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
211 <option value="basic" selected="True">Basic</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
212 <option value="advanced">Advanced</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
213 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
214 <when value="basic">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
215 <!-- Do nothing here -->
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jjohnson
parents:
diff changeset
216 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
217 <when value="advanced">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
218 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
219 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
220 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
221 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
222 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
223 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
224 <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
225 <option value="STRICT" selected="True">STRICT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
226 <option value="SILENT">SILENT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
227 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
228 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
229 <conditional name="read_filter_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
230 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
231 <option value="BadCigar">BadCigar</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
232 <option value="BadMate">BadMate</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
233 <option value="DuplicateRead">DuplicateRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
234 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
235 <option value="MalformedRead">MalformedRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
236 <option value="MappingQuality">MappingQuality</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
237 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
238 <option value="MappingQualityZero">MappingQualityZero</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
239 <option value="MateSameStrand">MateSameStrand</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
240 <option value="MaxInsertSize">MaxInsertSize</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
241 <option value="MaxReadLength" selected="True">MaxReadLength</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
242 <option value="MissingReadGroup">MissingReadGroup</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
243 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
244 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
245 <option value="Platform454">Platform454</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
246 <option value="Platform">Platform</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
247 <option value="PlatformUnit">PlatformUnit</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
248 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
249 <option value="ReadName">ReadName</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
250 <option value="ReadStrand">ReadStrand</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
251 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
252 <option value="Sample">Sample</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
253 <option value="SingleReadGroup">SingleReadGroup</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
254 <option value="UnmappedRead">UnmappedRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
255 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
256 <when value="BadCigar">
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="BadMate">
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="DuplicateRead">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
263 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
264 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
265 <when value="FailsVendorQualityCheck">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
266 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
267 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
268 <when value="MalformedRead">
35
a29c7d7d962d Fix default read filter screening
Jim Johnson <jj@umn.edu>
parents: 34
diff changeset
269 <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
0
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
270 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
271 <when value="MappingQuality">
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jjohnson
parents:
diff changeset
272 <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
273 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
274 <when value="MappingQualityUnavailable">
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jjohnson
parents:
diff changeset
275 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
276 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
277 <when value="MappingQualityZero">
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 <when value="MateSameStrand">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
281 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
282 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
283 <when value="MaxInsertSize">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
284 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
285 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
286 <when value="MaxReadLength">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
287 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
288 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
289 <when value="MissingReadGroup">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
290 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
291 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
292 <when value="NoOriginalQualityScores">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
293 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
294 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
295 <when value="NotPrimaryAlignment">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
296 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
297 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
298 <when value="Platform454">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
299 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
300 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
301 <when value="Platform">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
302 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
303 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
304 <when value="PlatformUnit">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
305 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
306 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
307 <when value="ReadGroupBlackList">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
308 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
309 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
310 <when value="ReadName">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
311 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
312 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
313 <when value="ReadStrand">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
314 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
315 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
316 <when value="ReassignMappingQuality">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
317 <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
318 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
319 <when value="Sample">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
320 <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
321 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
322 <when value="SingleReadGroup">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
323 <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
324 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
325 <when value="UnmappedRead">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
326 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
327 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
328 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
329 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
330 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
331 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
332 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
333 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
334 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
335 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
336
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
337 <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
338 <option value="UNION" selected="True">UNION</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
339 <option value="INTERSECTION">INTERSECTION</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
340 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
341
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
342 <conditional name="downsampling_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
343 <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
344 <option value="NONE" selected="True">NONE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
345 <option value="ALL_READS">ALL_READS</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
346 <option value="BY_SAMPLE">BY_SAMPLE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
347 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
348 <when value="NONE">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
349 <!-- no more options here -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
350 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
351 <when value="ALL_READS">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
352 <conditional name="downsample_to_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
353 <param name="downsample_to_type_selector" type="select" label="Downsample method">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
354 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
355 <option value="downsample_to_coverage">Downsample by Coverage</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
356 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
357 <when value="downsample_to_fraction">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
358 <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
359 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
360 <when value="downsample_to_coverage">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
361 <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
362 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
363 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
364 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
365 <when value="BY_SAMPLE">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
366 <conditional name="downsample_to_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
367 <param name="downsample_to_type_selector" type="select" label="Downsample method">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
368 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
369 <option value="downsample_to_coverage">Downsample by Coverage</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
370 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
371 <when value="downsample_to_fraction">
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jjohnson
parents:
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372 <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;"/>
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jjohnson
parents:
diff changeset
373 </when>
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jjohnson
parents:
diff changeset
374 <when value="downsample_to_coverage">
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jjohnson
parents:
diff changeset
375 <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
376 </when>
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jjohnson
parents:
diff changeset
377 </conditional>
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jjohnson
parents:
diff changeset
378 </when>
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jjohnson
parents:
diff changeset
379 </conditional>
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jjohnson
parents:
diff changeset
380 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
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jjohnson
parents:
diff changeset
381 <option value="OFF" selected="True">OFF</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
382 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
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jjohnson
parents:
diff changeset
383 <option value="RECALCULATE">RECALCULATE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
384 </param>
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jjohnson
parents:
diff changeset
385 <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:
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386 <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
387 <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
388 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
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jjohnson
parents:
diff changeset
389 <option value="STRICT" selected="True">STRICT</option>
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jjohnson
parents:
diff changeset
390 <option value="LENIENT">LENIENT</option>
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jjohnson
parents:
diff changeset
391 <option value="SILENT">SILENT</option>
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jjohnson
parents:
diff changeset
392 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
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jjohnson
parents:
diff changeset
393 </param>
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jjohnson
parents:
diff changeset
394 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
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jjohnson
parents:
diff changeset
395 <option value="ALL" selected="True">ALL</option>
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jjohnson
parents:
diff changeset
396 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
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jjohnson
parents:
diff changeset
397 </param>
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jjohnson
parents:
diff changeset
398
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jjohnson
parents:
diff changeset
399 <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;">
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jjohnson
parents:
diff changeset
400 <conditional name="read_group_black_list_type">
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jjohnson
parents:
diff changeset
401 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
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jjohnson
parents:
diff changeset
402 <option value="file" selected="True">Filters in file</option>
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jjohnson
parents:
diff changeset
403 <option value="text">Specify filters as a string</option>
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jjohnson
parents:
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404 </param>
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jjohnson
parents:
diff changeset
405 <when value="file">
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jjohnson
parents:
diff changeset
406 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
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jjohnson
parents:
diff changeset
407 </when>
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jjohnson
parents:
diff changeset
408 <when value="text">
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jjohnson
parents:
diff changeset
409 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
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jjohnson
parents:
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410 </when>
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jjohnson
parents:
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411 </conditional>
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jjohnson
parents:
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412 </repeat>
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jjohnson
parents:
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413
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jjohnson
parents:
diff changeset
414 <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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jjohnson
parents:
diff changeset
415 <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
18
7533db8dfb5b Update tool_dependencies to GATK v 2.3
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
416 <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False" help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
0
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jjohnson
parents:
diff changeset
417
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jjohnson
parents:
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418 </when>
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jjohnson
parents:
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419 </conditional>
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jjohnson
parents:
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420
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jjohnson
parents:
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421
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jjohnson
parents:
diff changeset
422 <conditional name="analysis_param_type">
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jjohnson
parents:
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423 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
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jjohnson
parents:
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424 <option value="basic" selected="True">Basic</option>
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jjohnson
parents:
diff changeset
425 <option value="advanced">Advanced</option>
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jjohnson
parents:
diff changeset
426 </param>
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jjohnson
parents:
diff changeset
427 <when value="basic">
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jjohnson
parents:
diff changeset
428 <!-- Do nothing here -->
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jjohnson
parents:
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429 </when>
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jjohnson
parents:
diff changeset
430 <when value="advanced">
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jjohnson
parents:
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431
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jjohnson
parents:
diff changeset
432 <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file" help="-xl_sf,--exclude_sample_file &amp;lt;exclude_sample_file&amp;gt;">
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jjohnson
parents:
diff changeset
433 <param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/>
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jjohnson
parents:
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434 </repeat>
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jjohnson
parents:
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435
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jjohnson
parents:
diff changeset
436 <repeat name="sample_file_repeat" title="Samples by file" help="-sf,--sample_file &amp;lt;sample_file&amp;gt;">
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jjohnson
parents:
diff changeset
437 <param name="sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to include" />
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jjohnson
parents:
diff changeset
438 </repeat>
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jjohnson
parents:
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439
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jjohnson
parents:
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440 <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &amp;lt;keepIDs&amp;gt;"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
441
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jjohnson
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442 <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" help="-keepOriginalAC,--keepOriginalAC" />
74c05070a3f8 Uploaded
jjohnson
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diff changeset
443
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jjohnson
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444 <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" help="-mv,--mendelianViolation" />
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jjohnson
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diff changeset
445
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jjohnson
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446 <param name="mendelian_violation_qual_threshold" type="float" label="Minimum genotype QUAL score for each trio member required to accept a site as a mendelian violation" value="0" help="-mvq,--mendelianViolationQualThreshold &amp;lt;mendelianViolationQualThreshold&amp;gt;" />
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jjohnson
parents:
diff changeset
447
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jjohnson
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448 <param name="remove_fraction_genotypes" type="float" label="Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall" value="0" min="0" max="1" help="-fractionGenotypes,--remove_fraction_genotypes &amp;lt;remove_fraction_genotypes&amp;gt;" />
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jjohnson
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449
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jjohnson
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450 <param name="restrict_alleles_to" type="select" label="Select only variants of a particular allelicity" help="-restrictAllelesTo,--restrictAllelesTo &amp;lt;restrictAllelesTo&amp;gt;">
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jjohnson
parents:
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451 <option value="ALL" selected="True">ALL</option>
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jjohnson
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452 <option value="MULTIALLELIC">MULTIALLELIC</option>
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jjohnson
parents:
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453 <option value="BIALLELIC">BIALLELIC</option>
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jjohnson
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454 </param>
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jjohnson
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455
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jjohnson
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456 <repeat name="sample_expressions_repeat" title="Regular expression to select many samples from the ROD tracks provided" help="-se,--sample_expressions &amp;lt;sample_expressions&amp;gt;">
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jjohnson
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457 <param name="sample_expressions" type="text" label="Regular expression">
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jjohnson
parents:
diff changeset
458 <sanitizer>
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jjohnson
parents:
diff changeset
459 <valid initial="string.printable">
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jjohnson
parents:
diff changeset
460 <remove value="&apos;"/>
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jjohnson
parents:
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461 </valid>
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jjohnson
parents:
diff changeset
462 <mapping initial="none"/>
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jjohnson
parents:
diff changeset
463 </sanitizer>
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jjohnson
parents:
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464 </param>
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jjohnson
parents:
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465 </repeat>
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jjohnson
parents:
diff changeset
466
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jjohnson
parents:
diff changeset
467 <conditional name="select_random_type">
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jjohnson
parents:
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468 <param name="select_random_type_selector" type="select" label="Select a random subset of variants">
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jjohnson
parents:
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469 <option value="select_all" selected="True">Use all variants</option>
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jjohnson
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470 <option value="select_random_fraction">Select random fraction</option>
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jjohnson
parents:
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471 <option value="select_random_number">Select random number</option>
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jjohnson
parents:
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472 </param>
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jjohnson
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473 <when value="select_all">
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jjohnson
parents:
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474 <!-- Do nothing here -->
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jjohnson
parents:
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475 </when>
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jjohnson
parents:
diff changeset
476 <when value="select_random_fraction">
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jjohnson
parents:
diff changeset
477 <param name="select_random_fraction" type="float" value="0" label="Fraction" min="0" max="1" help="-fraction,--select_random_fraction &amp;lt;select_random_fraction&amp;gt;"/>
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jjohnson
parents:
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478 </when>
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jjohnson
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diff changeset
479 <when value="select_random_number">
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jjohnson
parents:
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480 <param name="select_random_number" type="integer" value="0" label="Count" help="-number,--select_random_number &amp;lt;select_random_number&amp;gt;" />
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jjohnson
parents:
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481 </when>
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jjohnson
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482 </conditional>
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jjohnson
parents:
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483
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jjohnson
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484 <param name="exclude_non_variants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the subsetting procedure" help="-env,--excludeNonVariants" />
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jjohnson
parents:
diff changeset
485
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jjohnson
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486 <param name="select_type_to_include" type="select" label="Select only a certain type of variants from the input file" multiple="True" display="checkboxes" help="-selectType,--selectTypeToInclude &amp;lt;selectTypeToInclude&amp;gt;">
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jjohnson
parents:
diff changeset
487 <option value="INDEL">INDEL</option>
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jjohnson
parents:
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488 <option value="SNP">SNP</option>
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jjohnson
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489 <option value="MIXED">MIXED</option>
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jjohnson
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490 <option value="MNP">MNP</option>
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jjohnson
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491 <option value="SYMBOLIC">SYMBOLIC</option>
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jjohnson
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492 <option value="NO_VARIATION">NO_VARIATION</option>
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jjohnson
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493 </param>
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jjohnson
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diff changeset
494
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jjohnson
parents:
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495 </when>
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jjohnson
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496 </conditional>
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jjohnson
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497
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jjohnson
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498 </inputs>
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jjohnson
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499 <outputs>
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jjohnson
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500 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
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jjohnson
parents:
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501 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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jjohnson
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502 </outputs>
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jjohnson
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503 <tests>
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jjohnson
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504 <test>
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jjohnson
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505 <param name="reference_source_selector" value="history" />
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jjohnson
parents:
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506 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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jjohnson
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507 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
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jjohnson
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508 <param name="select_expressions_repeat" value="0" />
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jjohnson
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509 <param name="input_concordance" />
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jjohnson
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510 <param name="input_discordance" />
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jjohnson
parents:
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511 <param name="exclude_sample_name_repeat" value="0" />
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jjohnson
parents:
diff changeset
512 <param name="exclude_filtered" />
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jjohnson
parents:
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513 <param name="sample_name_repeat" value="0" />
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jjohnson
parents:
diff changeset
514 <param name="gatk_param_type_selector" value="basic" />
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jjohnson
parents:
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515 <param name="analysis_param_type_selector" value="basic" />
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jjohnson
parents:
diff changeset
516 <output name="output_vcf" file="gatk/gatk_variant_select/gatk_variant_select_out_1.vcf" lines_diff="4" />
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jjohnson
parents:
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517 <output name="output_log" file="gatk/gatk_variant_select/gatk_variant_select_out_1.log.contains" compare="contains" />
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jjohnson
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518 </test>
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jjohnson
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519 </tests>
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jjohnson
parents:
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520 <help>
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jjohnson
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521 **What it does**
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jjohnson
parents:
diff changeset
522
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jjohnson
parents:
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523 Often, a VCF containing many samples and/or variants will need to be subset in order to facilitate certain analyses (e.g. comparing and contrasting cases vs. controls; extracting variant or non-variant loci that meet certain requirements, displaying just a few samples in a browser like IGV, etc.). SelectVariants can be used for this purpose. Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion, i.e. "DP &gt; 1000" (depth of coverage greater than 1000x), "AF &lt; 0.25" (sites with allele frequency less than 0.25). These JEXL expressions are documented in the `Using JEXL expressions section &lt;http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk&gt;`_. One can optionally include concordance or discordance tracks for use in selecting overlapping variants.
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jjohnson
parents:
diff changeset
524
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jjohnson
parents:
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525 For more information on using the SelectVariants module, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_SelectVariants.html&gt;`_.
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jjohnson
parents:
diff changeset
526
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jjohnson
parents:
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527 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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jjohnson
parents:
diff changeset
528
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jjohnson
parents:
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529 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
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jjohnson
parents:
diff changeset
530
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jjohnson
parents:
diff changeset
531 ------
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jjohnson
parents:
diff changeset
532
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jjohnson
parents:
diff changeset
533 **Inputs**
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jjohnson
parents:
diff changeset
534
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jjohnson
parents:
diff changeset
535 GenomeAnalysisTK: SelectVariants accepts a VCF input file.
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jjohnson
parents:
diff changeset
536
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jjohnson
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537
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538 **Outputs**
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539
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540 The output is in VCF format.
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541
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542
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543 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
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544
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545 -------
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546
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547 **Settings**::
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548
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549
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550 out VCFWriter stdout File to which variants should be written
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551 variant RodBinding[VariantContext] NA Input VCF file
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552 concordance RodBinding[VariantContext] none Output variants that were also called in this comparison track
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553 discordance RodBinding[VariantContext] none Output variants that were not called in this comparison track
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554 exclude_sample_file Set[File] [] File containing a list of samples (one per line) to exclude. Can be specified multiple times
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555 exclude_sample_name Set[String] [] Exclude genotypes from this sample. Can be specified multiple times
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556 excludeFiltered boolean false Don't include filtered loci in the analysis
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557 excludeNonVariants boolean false Don't include loci found to be non-variant after the subsetting procedure
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558 keepIDs File NA Only emit sites whose ID is found in this file (one ID per line)
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559 keepOriginalAC boolean false Don't update the AC, AF, or AN values in the INFO field after selecting
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560 mendelianViolation Boolean false output mendelian violation sites only
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561 mvq double 0.0 Minimum genotype QUAL score for each trio member required to accept a site as a violation
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562 remove_fraction_genotypes double 0.0 Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall
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563 restrictAllelesTo NumberAlleleRestriction ALL Select only variants of a particular allelicity. Valid options are ALL (default), MULTIALLELIC or BIALLELIC
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564 sample_expressions Set[String] NA Regular expression to select many samples from the ROD tracks provided. Can be specified multiple times
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565 sample_file Set[File] NA File containing a list of samples (one per line) to include. Can be specified multiple times
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566 sample_name Set[String] [] Include genotypes from this sample. Can be specified multiple times
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567 select_expressions ArrayList[String] [] One or more criteria to use when selecting the data
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568 select_random_fraction double 0.0 Selects a fraction (a number between 0 and 1) of the total variants at random from the variant track
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569 select_random_number int 0 Selects a number of variants at random from the variant track
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570 selectTypeToInclude List[Type] [] Select only a certain type of variants from the input file. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Can be specified multiple times
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571
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572 ------
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573
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574 **Citation**
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575
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576 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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577
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578 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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579
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580 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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581
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582 </help>
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583 </tool>