annotate gatk2_macros.xml @ 11:83312f73e0e7 draft

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author lz_hust
date Sat, 01 Jun 2019 07:11:19 -0400
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11
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package">gatk2</requirement>
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5 <requirement type="package" version="0.1.19">samtools</requirement>
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6 <requirement type="package" version="1.56.0">picard</requirement>
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7 <requirement type="set_environment">GATK2_PATH</requirement>
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8 <requirement type="set_environment">GATK2_SITE_OPTIONS</requirement>
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9 <yield />
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10 </requirements>
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11 </xml>
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12 <xml name="version_command">
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13 <version_command>java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" --help|grep '^The Genome'</version_command>
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14 </xml>
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15 <token name="@THREADS@">
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16 --num_threads \${GALAXY_SLOTS:-4}
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17 </token>
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18 <token name="@VERSION@">2.8</token>
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19 <token name="@JAR_PATH@">
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20 java -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
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21 </token>
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22 <token name="@DBSNP_OPTIONS@">
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23 #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp'
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24 -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
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25 #end if
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26 </token>
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27 <token name="@BAM_INPUTS@">
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28 #for $i, $input_bam in enumerate( $reference_source.input_bams ):
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29 -d "-I" "${input_bam}" "${input_bam.ext}" "gatk_input_${i}"
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30 #if str( $input_bam.metadata.bam_index ) != "None":
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31 -d "" "${input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
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32 #end if
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33 #end for
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34 </token>
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35 <xml name="input_variants" token_help="-input,--input &amp;lt;input&amp;gt;">
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36 <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" multiple="True" min="1" help="@HELP@"/>
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37 </xml>
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38 <xml name="input_bams_history">
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39 <param name="input_bams" type="data" format="bam" label="BAM file" multiple="True" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;"/>
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40 </xml>
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41 <xml name="input_bams_cached">
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42 <param name="input_bams" type="data" format="bam" label="BAM file" multiple="True" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
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43 <validator type="unspecified_build" />
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44 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
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45 </param>
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46 </xml>
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47 <template name="standard_gatk_options">
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48 ##start standard gatk options
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49 #if $gatk_param_type.gatk_param_type_selector == "advanced":
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50 #for $pedigree in $gatk_param_type.pedigree_files:
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51 -p '--pedigree "${pedigree}"'
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52 #end for
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53 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
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54 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
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55 #end for
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56 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
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57 #set default_read_filters = ['MalformedRead']
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58 #for $read_filter in $gatk_param_type.read_filter:
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59 -p '
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60 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
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61 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
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62 #end if
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63 #for $name, $param in $read_filter.read_filter_type.iteritems():
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64 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
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65 #if hasattr( $param.input, 'truevalue' ):
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66 ${param}
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67 #else:
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68 --${name} "${param}"
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69 #end if
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70 #end if
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71 #end for
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72 '
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73 #end for
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74 #for $interval_count, $input_interval in enumerate( $gatk_param_type.input_intervals ):
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75 -d "--intervals" "${input_interval}" "${input_interval.ext}" "input_intervals_${interval_count}"
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76 #end for
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77
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78 #for $interval_count, $input_interval in enumerate( $gatk_param_type.input_exclude_intervals ):
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79 -d "--excludeIntervals" "${input_interval}" "${input_interval.ext}" "input_exlude_intervals_${interval_count}"
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80 #end for
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81
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82 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
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83 -p '--interval_padding "${gatk_param_type.interval_padding}"'
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84 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
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85 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
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86 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
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87 #end if
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88 -p '
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89 --baq "${gatk_param_type.baq}"
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90 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
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91 ${gatk_param_type.use_original_qualities}
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92 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
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93 --validation_strictness "${gatk_param_type.validation_strictness}"
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94 --interval_merging "${gatk_param_type.interval_merging}"
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95 ${gatk_param_type.disable_experimental_low_memory_sharding}
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96 ${gatk_param_type.fix_misencoded_quality_scores}
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97 ${gatk_param_type.non_deterministic_random_seed}
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98 '
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99 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
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100 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
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101 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
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102 #else
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103 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
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104 #end if
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105 #end for
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106 #end if
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107
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108 #if str( $reference_source.reference_source_selector ) == "history":
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109 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
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110 #end if
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111 ##end standard gatk options
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112 </template>
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113 <xml name="gatk_param_type_conditional">
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114 <conditional name="gatk_param_type">
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115 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
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116 <option value="basic" selected="True">Basic</option>
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117 <option value="advanced">Advanced</option>
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118 </param>
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119 <when value="basic">
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120 <!-- Do nothing here -->
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121 </when>
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122 <when value="advanced">
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123 <param name="pedigree_files" type="data" format="txt" label="Pedigree files for samples" multiple="True" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;"/>
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124 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
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125 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
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126 </repeat>
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127 <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
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128 <option value="STRICT" selected="True">STRICT</option>
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129 <option value="SILENT">SILENT</option>
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130 </param>
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131 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
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132 <conditional name="read_filter_type">
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133 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
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134 <option value="BadCigar">BadCigar</option>
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135 <option value="BadMate">BadMate</option>
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136 <option value="DuplicateRead">DuplicateRead</option>
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137 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
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138 <option value="MalformedRead">MalformedRead</option>
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139 <option value="MappingQuality">MappingQuality</option>
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140 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
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141 <option value="MappingQualityZero">MappingQualityZero</option>
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142 <option value="MateSameStrand">MateSameStrand</option>
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143 <option value="MaxInsertSize">MaxInsertSize</option>
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144 <option value="MaxReadLength" selected="True">MaxReadLength</option>
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145 <option value="MissingReadGroup">MissingReadGroup</option>
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146 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
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147 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
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148 <option value="Platform454">Platform454</option>
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149 <option value="Platform">Platform</option>
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150 <option value="PlatformUnit">PlatformUnit</option>
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151 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
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152 <option value="ReadName">ReadName</option>
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153 <option value="ReadStrand">ReadStrand</option>
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154 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
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155 <option value="Sample">Sample</option>
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156 <option value="SingleReadGroup">SingleReadGroup</option>
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157 <option value="UnmappedRead">UnmappedRead</option>
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158 </param>
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159 <when value="BadCigar">
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160 <!-- no extra options -->
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161 </when>
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162 <when value="BadMate">
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163 <!-- no extra options -->
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164 </when>
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165 <when value="DuplicateRead">
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166 <!-- no extra options -->
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167 </when>
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168 <when value="FailsVendorQualityCheck">
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169 <!-- no extra options -->
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170 </when>
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lz_hust
parents:
diff changeset
171 <when value="MalformedRead">
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lz_hust
parents:
diff changeset
172 <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"/>
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lz_hust
parents:
diff changeset
173 </when>
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lz_hust
parents:
diff changeset
174 <when value="MappingQuality">
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lz_hust
parents:
diff changeset
175 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
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lz_hust
parents:
diff changeset
176 </when>
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lz_hust
parents:
diff changeset
177 <when value="MappingQualityUnavailable">
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lz_hust
parents:
diff changeset
178 <!-- no extra options -->
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lz_hust
parents:
diff changeset
179 </when>
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lz_hust
parents:
diff changeset
180 <when value="MappingQualityZero">
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lz_hust
parents:
diff changeset
181 <!-- no extra options -->
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lz_hust
parents:
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182 </when>
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lz_hust
parents:
diff changeset
183 <when value="MateSameStrand">
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lz_hust
parents:
diff changeset
184 <!-- no extra options -->
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lz_hust
parents:
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185 </when>
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lz_hust
parents:
diff changeset
186 <when value="MaxInsertSize">
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lz_hust
parents:
diff changeset
187 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
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lz_hust
parents:
diff changeset
188 </when>
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lz_hust
parents:
diff changeset
189 <when value="MaxReadLength">
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lz_hust
parents:
diff changeset
190 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
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lz_hust
parents:
diff changeset
191 </when>
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lz_hust
parents:
diff changeset
192 <when value="MissingReadGroup">
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lz_hust
parents:
diff changeset
193 <!-- no extra options -->
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lz_hust
parents:
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194 </when>
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lz_hust
parents:
diff changeset
195 <when value="NoOriginalQualityScores">
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lz_hust
parents:
diff changeset
196 <!-- no extra options -->
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lz_hust
parents:
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197 </when>
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lz_hust
parents:
diff changeset
198 <when value="NotPrimaryAlignment">
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lz_hust
parents:
diff changeset
199 <!-- no extra options -->
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lz_hust
parents:
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200 </when>
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lz_hust
parents:
diff changeset
201 <when value="Platform454">
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lz_hust
parents:
diff changeset
202 <!-- no extra options -->
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lz_hust
parents:
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203 </when>
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lz_hust
parents:
diff changeset
204 <when value="Platform">
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lz_hust
parents:
diff changeset
205 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
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lz_hust
parents:
diff changeset
206 </when>
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lz_hust
parents:
diff changeset
207 <when value="PlatformUnit">
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lz_hust
parents:
diff changeset
208 <!-- no extra options -->
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lz_hust
parents:
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209 </when>
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lz_hust
parents:
diff changeset
210 <when value="ReadGroupBlackList">
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lz_hust
parents:
diff changeset
211 <!-- no extra options -->
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lz_hust
parents:
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212 </when>
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lz_hust
parents:
diff changeset
213 <when value="ReadName">
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lz_hust
parents:
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214 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
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lz_hust
parents:
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215 </when>
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lz_hust
parents:
diff changeset
216 <when value="ReadStrand">
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lz_hust
parents:
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217 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
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lz_hust
parents:
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218 </when>
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lz_hust
parents:
diff changeset
219 <when value="ReassignMappingQuality">
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lz_hust
parents:
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220 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
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lz_hust
parents:
diff changeset
221 </when>
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lz_hust
parents:
diff changeset
222 <when value="Sample">
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lz_hust
parents:
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223 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
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lz_hust
parents:
diff changeset
224 </when>
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lz_hust
parents:
diff changeset
225 <when value="SingleReadGroup">
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lz_hust
parents:
diff changeset
226 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
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lz_hust
parents:
diff changeset
227 </when>
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lz_hust
parents:
diff changeset
228 <when value="UnmappedRead">
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lz_hust
parents:
diff changeset
229 <!-- no extra options -->
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lz_hust
parents:
diff changeset
230 </when>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
231 </conditional>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
232 </repeat>
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lz_hust
parents:
diff changeset
233 <param name="input_intervals" multiple="True" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;" />
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lz_hust
parents:
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234 <param name="input_exclude_intervals" multiple="True" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;" />
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lz_hust
parents:
diff changeset
235
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
236 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
237 <option value="UNION" selected="True">UNION</option>
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lz_hust
parents:
diff changeset
238 <option value="INTERSECTION">INTERSECTION</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
239 </param>
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lz_hust
parents:
diff changeset
240 <param name="interval_padding" type="integer" value="0" min="0" label="Amount of padding (in bp) to add to each interval"
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
241 help="This is typically used to add padding around exons when analyzing exomes. (--interval_padding / -ip)"/>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
242
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
243 <conditional name="downsampling_type">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
244 <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
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lz_hust
parents:
diff changeset
245 <option value="NONE" selected="True">NONE</option>
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lz_hust
parents:
diff changeset
246 <option value="ALL_READS">ALL_READS</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
247 <option value="BY_SAMPLE">BY_SAMPLE</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
248 </param>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
249 <when value="NONE">
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lz_hust
parents:
diff changeset
250 <!-- no more options here -->
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lz_hust
parents:
diff changeset
251 </when>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
252 <when value="ALL_READS">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
253 <conditional name="downsample_to_type">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
254 <param name="downsample_to_type_selector" type="select" label="Downsample method">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
255 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
256 <option value="downsample_to_coverage">Downsample by Coverage</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
257 </param>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
258 <when value="downsample_to_fraction">
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lz_hust
parents:
diff changeset
259 <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;"/>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
260 </when>
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lz_hust
parents:
diff changeset
261 <when value="downsample_to_coverage">
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lz_hust
parents:
diff changeset
262 <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;"/>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
263 </when>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
264 </conditional>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
265 </when>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
266 <when value="BY_SAMPLE">
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lz_hust
parents:
diff changeset
267 <conditional name="downsample_to_type">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
268 <param name="downsample_to_type_selector" type="select" label="Downsample method">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
269 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
270 <option value="downsample_to_coverage">Downsample by Coverage</option>
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lz_hust
parents:
diff changeset
271 </param>
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lz_hust
parents:
diff changeset
272 <when value="downsample_to_fraction">
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lz_hust
parents:
diff changeset
273 <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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lz_hust
parents:
diff changeset
274 </when>
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lz_hust
parents:
diff changeset
275 <when value="downsample_to_coverage">
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lz_hust
parents:
diff changeset
276 <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;"/>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
277 </when>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
278 </conditional>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
279 </when>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
280 </conditional>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
281 <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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lz_hust
parents:
diff changeset
282 <option value="OFF" selected="True">OFF</option>
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lz_hust
parents:
diff changeset
283 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
284 <option value="RECALCULATE">RECALCULATE</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
285 </param>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
286 <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;" />
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
287 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
288 <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;"/>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
289 <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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lz_hust
parents:
diff changeset
290 <option value="STRICT" selected="True">STRICT</option>
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lz_hust
parents:
diff changeset
291 <option value="LENIENT">LENIENT</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
292 <option value="SILENT">SILENT</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
293 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
294 </param>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
295 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
296 <option value="ALL" selected="True">ALL</option>
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lz_hust
parents:
diff changeset
297 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
298 </param>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
299
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
300 <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;">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
301 <conditional name="read_group_black_list_type">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
302 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
303 <option value="file" selected="True">Filters in file</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
304 <option value="text">Specify filters as a string</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
305 </param>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
306 <when value="file">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
307 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
308 </when>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
309 <when value="text">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
310 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
311 </when>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
312 </conditional>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
313 </repeat>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
314
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
315 <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"/>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
316 <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"/>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
317 <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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lz_hust
parents:
diff changeset
318
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
319 </when>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
320 </conditional>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
321 </xml>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
322 <xml name="analysis_type_conditional">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
323 <conditional name="analysis_param_type">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
324 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
325 <option value="basic" selected="True">Basic</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
326 <option value="advanced">Advanced</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
327 </param>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
328 <when value="basic">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
329 <!-- Do nothing here -->
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
330 </when>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
331 <when value="advanced">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
332 <yield />
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
333 </when>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
334 </conditional>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
335 </xml>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
336 <xml name="reference_source_selector_param">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
337 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
338 <option value="cached">Locally cached</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
339 <option value="history">History</option>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
340 </param>
83312f73e0e7 Uploaded
lz_hust
parents:
diff changeset
341 </xml>
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lz_hust
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342
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343 <xml name="allow_n_cigar_reads">
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344 <param name="allow_n_cigar_reads" type="boolean" truevalue="-U ALLOW_N_CIGAR_READS" falsevalue=""
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345 label="Allow N in CIGAR strings" help="This is required for RNA-seq data. (-U ALLOW_N_CIGAR_READS)" />
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346 </xml>
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347
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348 <xml name="dbsnp_param">
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349 <conditional name="dbsnp_rod_bind_type">
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350 <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP Reference-Ordered Data (ROD) file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
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351 <option value="set_dbsnp" selected="True">Set dbSNP</option>
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352 <option value="exclude_dbsnp">Don't set dbSNP</option>
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353 </param>
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354 <when value="exclude_dbsnp" />
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355 <when value="set_dbsnp">
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356 <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" />
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357 <param name="dbsnp_rod_name" type="text" value="dbsnp" label="dbsnp ROD name">
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358 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
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359 </param>
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360 </when>
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361 </conditional>
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362 </xml>
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363 <token name="@CITATION_SECTION@">------
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364
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365 **Citation**
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366
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367 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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368
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369 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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370
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371 </token>
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372 <xml name="citations">
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373 <citations>
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374 <citation type="doi">10.1038/ng.806</citation>
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375 <citation type="doi">10.1101/gr.107524.110</citation>
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376 <citation type="doi">10.1002/0471250953.bi1110s43</citation>
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377 </citations>
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378 </xml>
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379 </macros>