annotate print_reads.xml @ 35:a29c7d7d962d draft

Fix default read filter screening
author Jim Johnson <jj@umn.edu>
date Fri, 01 Mar 2013 07:52:02 -0600
parents b99c25b0ad4d
children 14d47237bb0a
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b99c25b0ad4d Update tool version to 0.0.7
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1 <tool id="gatk2_print_reads" name="Print Reads" version="0.0.7">
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2 <description>on BAM files</description>
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3 <requirements>
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4 <requirement type="package" version="2.3">gatk</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 </requirements>
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7 <command interpreter="python">gatk2_wrapper.py
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8 --max_jvm_heap_fraction "1"
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9 --stdout "${output_log}"
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10 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
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11 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
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12 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
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13 #end if
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14 -p 'java
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15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
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16 -T "PrintReads"
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17 -o "${output_bam}"
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18 \$GATK2_SITE_OPTIONS
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19 \$GATK2_NUM_CPU_THREADS
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20 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
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21 ##--num_threads 4 ##not supported yet
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22 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
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23 #if $reference_source.reference_source_selector != "history":
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24 -R "${reference_source.ref_file.fields.path}"
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25 #end if
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26 #if str($input_recal) != 'None':
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27 --BQSR "${input_recal}"
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28 #end if
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29 --disable_bam_indexing
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30 '
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31 ##start standard gatk options
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32 #if $gatk_param_type.gatk_param_type_selector == "advanced":
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33 #for $pedigree in $gatk_param_type.pedigree:
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34 -p '--pedigree "${pedigree.pedigree_file}"'
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35 #end for
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36 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
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37 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
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38 #end for
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39 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
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40 #set default_read_filters = ['MalformedRead']
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41 #for $read_filter in $gatk_param_type.read_filter:
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42 -p '
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43 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
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44 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
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45 #end_if
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46 #for $name, $param in $read_filter.read_filter_type.iteritems():
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47 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
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48 #if hasattr( $param.input, 'truevalue' ):
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49 ${param}
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50 #else:
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51 --${name} "${param}"
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52 #end if
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53 #end if
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54 #end for
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55 '
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56 #end for
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57 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
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58 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
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59 #end for
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60
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61 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
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62 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
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63 #end for
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64
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65 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
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66
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67 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
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68 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
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69 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
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70 #end if
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71 -p '
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72 --baq "${gatk_param_type.baq}"
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73 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
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74 ${gatk_param_type.use_original_qualities}
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75 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
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76 --validation_strictness "${gatk_param_type.validation_strictness}"
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77 --interval_merging "${gatk_param_type.interval_merging}"
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78 ${gatk_param_type.disable_experimental_low_memory_sharding}
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79 ${gatk_param_type.fix_misencoded_quality_scores}
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80 ${gatk_param_type.non_deterministic_random_seed}
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81 '
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82 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
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83 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
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84 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
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85 #else
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86 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
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87 #end if
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88 #end for
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89 #end if
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90
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91 #if str( $reference_source.reference_source_selector ) == "history":
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92 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
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93 #end if
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94 ##end standard gatk options
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95
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96 ##start analysis specific options
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97 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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98 -p '
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99 #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set":
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100 --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}"
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101 #end if
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102 #if str( $analysis_param_type.default_platform ) != "default":
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103 --default_platform "${analysis_param_type.default_platform}"
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104 #end if
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105 #if str( $analysis_param_type.force_read_group_type.force_read_group_type_selector ) == "set":
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106 --force_read_group "${analysis_param_type.force_read_group_type.force_read_group}"
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107 #end if
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108 #if str( $analysis_param_type.force_platform ) != "default":
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109 --force_platform "${analysis_param_type.force_platform}"
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110 #end if
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111 ${analysis_param_type.exception_if_no_tile}
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112 #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set":
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113 #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default":
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114 --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}"
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115 #end if
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116 #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default":
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117 --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}"
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118 #end if
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119 #end if
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120 ${analysis_param_type.simplify_bam}
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121 --preserve_qscores_less_than "${analysis_param_type.preserve_qscores_less_than}"
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122 --smoothing "${analysis_param_type.smoothing}"
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123 --max_quality_score "${analysis_param_type.max_quality_score}"
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124 --window_size_nqs "${analysis_param_type.window_size_nqs}"
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125 --homopolymer_nback "${analysis_param_type.homopolymer_nback}"
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126 ${analysis_param_type.do_not_write_original_quals}
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127 '
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128 #end if
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129 </command>
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130 <inputs>
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131 <param name="input_recal" type="data" format="csv" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" />
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132 <conditional name="reference_source">
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133 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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134 <option value="cached">Locally cached</option>
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135 <option value="history">History</option>
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136 </param>
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137 <when value="cached">
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138 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
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139 <validator type="unspecified_build" />
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140 <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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141 </param>
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142 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" >
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143 <options from_data_table="gatk2_picard_indexes">
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144 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
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145 </options>
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146 <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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147 </param>
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148 </when>
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149 <when value="history">
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150 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;" />
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151 <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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152 <options>
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153 <filter type="data_meta" key="dbkey" ref="input_bam" />
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154 </options>
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155 </param>
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156 </when>
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157 </conditional>
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158
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159 <conditional name="gatk_param_type">
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160 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
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161 <option value="basic" selected="True">Basic</option>
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162 <option value="advanced">Advanced</option>
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163 </param>
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164 <when value="basic">
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165 <!-- Do nothing here -->
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166 </when>
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167 <when value="advanced">
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168 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
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169 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
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170 </repeat>
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171 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
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jjohnson
parents:
diff changeset
172 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
173 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
174 <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
175 <option value="STRICT" selected="True">STRICT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
176 <option value="SILENT">SILENT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
177 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
178 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
179 <conditional name="read_filter_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
180 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
181 <option value="BadCigar">BadCigar</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
182 <option value="BadMate">BadMate</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
183 <option value="DuplicateRead">DuplicateRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
184 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
185 <option value="MalformedRead">MalformedRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
186 <option value="MappingQuality">MappingQuality</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
187 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
188 <option value="MappingQualityZero">MappingQualityZero</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
189 <option value="MateSameStrand">MateSameStrand</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
190 <option value="MaxInsertSize">MaxInsertSize</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
191 <option value="MaxReadLength" selected="True">MaxReadLength</option>
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jjohnson
parents:
diff changeset
192 <option value="MissingReadGroup">MissingReadGroup</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
193 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
194 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
195 <option value="Platform454">Platform454</option>
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jjohnson
parents:
diff changeset
196 <option value="Platform">Platform</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
197 <option value="PlatformUnit">PlatformUnit</option>
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jjohnson
parents:
diff changeset
198 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
199 <option value="ReadName">ReadName</option>
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jjohnson
parents:
diff changeset
200 <option value="ReadStrand">ReadStrand</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
201 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
202 <option value="Sample">Sample</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
203 <option value="SingleReadGroup">SingleReadGroup</option>
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jjohnson
parents:
diff changeset
204 <option value="UnmappedRead">UnmappedRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
205 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
206 <when value="BadCigar">
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jjohnson
parents:
diff changeset
207 <!-- no extra options -->
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jjohnson
parents:
diff changeset
208 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
209 <when value="BadMate">
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jjohnson
parents:
diff changeset
210 <!-- no extra options -->
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jjohnson
parents:
diff changeset
211 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
212 <when value="DuplicateRead">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
213 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
214 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
215 <when value="FailsVendorQualityCheck">
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jjohnson
parents:
diff changeset
216 <!-- no extra options -->
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jjohnson
parents:
diff changeset
217 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
218 <when value="MalformedRead">
35
a29c7d7d962d Fix default read filter screening
Jim Johnson <jj@umn.edu>
parents: 34
diff changeset
219 <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
220 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
221 <when value="MappingQuality">
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jjohnson
parents:
diff changeset
222 <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
223 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
224 <when value="MappingQualityUnavailable">
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jjohnson
parents:
diff changeset
225 <!-- no extra options -->
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jjohnson
parents:
diff changeset
226 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
227 <when value="MappingQualityZero">
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jjohnson
parents:
diff changeset
228 <!-- no extra options -->
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jjohnson
parents:
diff changeset
229 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
230 <when value="MateSameStrand">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
231 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
232 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
233 <when value="MaxInsertSize">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
234 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
235 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
236 <when value="MaxReadLength">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
237 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
238 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
239 <when value="MissingReadGroup">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
240 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
241 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
242 <when value="NoOriginalQualityScores">
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jjohnson
parents:
diff changeset
243 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
244 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
245 <when value="NotPrimaryAlignment">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
246 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
247 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
248 <when value="Platform454">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
249 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
250 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
251 <when value="Platform">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
252 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
253 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
254 <when value="PlatformUnit">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
255 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
256 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
257 <when value="ReadGroupBlackList">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
258 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
259 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
260 <when value="ReadName">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
261 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
262 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
263 <when value="ReadStrand">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
264 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
265 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
266 <when value="ReassignMappingQuality">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
267 <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
268 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
269 <when value="Sample">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
270 <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
271 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
272 <when value="SingleReadGroup">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
273 <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
274 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
275 <when value="UnmappedRead">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
276 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
277 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
278 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
279 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
280 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
281 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
282 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
283 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
284 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
285 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
286
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
287 <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
288 <option value="UNION" selected="True">UNION</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
289 <option value="INTERSECTION">INTERSECTION</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
290 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
291
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
292 <conditional name="downsampling_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
293 <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
294 <option value="NONE" selected="True">NONE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
295 <option value="ALL_READS">ALL_READS</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
296 <option value="BY_SAMPLE">BY_SAMPLE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
297 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
298 <when value="NONE">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
299 <!-- no more options here -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
300 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
301 <when value="ALL_READS">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
302 <conditional name="downsample_to_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
303 <param name="downsample_to_type_selector" type="select" label="Downsample method">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
304 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
305 <option value="downsample_to_coverage">Downsample by Coverage</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
306 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
307 <when value="downsample_to_fraction">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
308 <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
309 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
310 <when value="downsample_to_coverage">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
311 <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
312 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
313 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
314 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
315 <when value="BY_SAMPLE">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
316 <conditional name="downsample_to_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
317 <param name="downsample_to_type_selector" type="select" label="Downsample method">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
318 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
319 <option value="downsample_to_coverage">Downsample by Coverage</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
320 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
321 <when value="downsample_to_fraction">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
322 <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
323 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
324 <when value="downsample_to_coverage">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
325 <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
326 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
327 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
328 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
329 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
330 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
331 <option value="OFF" selected="True">OFF</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
332 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
333 <option value="RECALCULATE">RECALCULATE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
334 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
335 <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
336 <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
337 <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
338 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
339 <option value="STRICT" selected="True">STRICT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
340 <option value="LENIENT">LENIENT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
341 <option value="SILENT">SILENT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
342 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
343 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
344 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
345 <option value="ALL" selected="True">ALL</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
346 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
347 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
348
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
349 <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
350 <conditional name="read_group_black_list_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
351 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
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jjohnson
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352 <option value="file" selected="True">Filters in file</option>
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jjohnson
parents:
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353 <option value="text">Specify filters as a string</option>
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jjohnson
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354 </param>
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jjohnson
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355 <when value="file">
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jjohnson
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356 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
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jjohnson
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357 </when>
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jjohnson
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358 <when value="text">
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jjohnson
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359 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
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jjohnson
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360 </when>
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jjohnson
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361 </conditional>
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jjohnson
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362 </repeat>
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jjohnson
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363
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jjohnson
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364 <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
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365 <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: 6
diff changeset
366 <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
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367
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jjohnson
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368 </when>
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jjohnson
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369 </conditional>
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jjohnson
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370
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jjohnson
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371
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jjohnson
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372 <conditional name="analysis_param_type">
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jjohnson
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373 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
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jjohnson
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374 <option value="basic" selected="True">Basic</option>
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jjohnson
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375 <option value="advanced">Advanced</option>
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jjohnson
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376 </param>
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jjohnson
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377 <when value="basic">
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jjohnson
parents:
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378 <!-- Do nothing here -->
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jjohnson
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379 </when>
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jjohnson
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380 <when value="advanced">
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jjohnson
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381 <conditional name="default_read_group_type">
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jjohnson
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382 <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
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jjohnson
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383 <option value="default" selected="True">Don't Set</option>
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jjohnson
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384 <option value="set">Set</option>
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jjohnson
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385 </param>
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jjohnson
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386 <when value="default">
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jjohnson
parents:
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387 <!-- do nothing here -->
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jjohnson
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388 </when>
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jjohnson
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389 <when value="set">
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jjohnson
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390 <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/>
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jjohnson
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391 </when>
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jjohnson
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392 </conditional>
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jjohnson
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393 <param name="default_platform" type="select" label="Set default Platform" help="--default_platform">
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jjohnson
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394 <option value="default" selected="True">Don't Set</option>
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jjohnson
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395 <option value="illumina">illumina</option>
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jjohnson
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396 <option value="454">454</option>
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jjohnson
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397 <option value="solid">solid</option>
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jjohnson
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398 </param>
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jjohnson
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399 <conditional name="force_read_group_type">
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jjohnson
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400 <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group">
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jjohnson
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401 <option value="default" selected="True">Don't Force</option>
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jjohnson
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402 <option value="set">Force</option>
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jjohnson
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403 </param>
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jjohnson
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404 <when value="default">
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jjohnson
parents:
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405 <!-- do nothing here -->
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jjohnson
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406 </when>
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jjohnson
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407 <when value="set">
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jjohnson
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408 <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/>
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jjohnson
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409 </when>
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jjohnson
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410 </conditional>
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jjohnson
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411 <param name="force_platform" type="select" label="Force Platform" help="--force_platform">
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jjohnson
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412 <option value="default" selected="True">Don't Force</option>
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jjohnson
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413 <option value="illumina">illumina</option>
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jjohnson
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414 <option value="454">454</option>
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jjohnson
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415 <option value="solid">solid</option>
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jjohnson
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416 </param>
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jjohnson
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417 <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/>
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jjohnson
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418 <conditional name="solid_options_type">
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jjohnson
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419 <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options">
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jjohnson
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420 <option value="default" selected="True">Don't Set</option>
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jjohnson
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421 <option value="set">Set</option>
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jjohnson
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422 </param>
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jjohnson
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423 <when value="default">
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jjohnson
parents:
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424 <!-- do nothing here -->
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jjohnson
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425 </when>
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jjohnson
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426 <when value="set">
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jjohnson
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427 <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode &amp;lt;solid_recal_mode&amp;gt;">
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jjohnson
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428 <option value="default" selected="True">Don't set</option>
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jjohnson
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429 <option value="DO_NOTHING">DO_NOTHING</option>
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jjohnson
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430 <option value="SET_Q_ZERO">SET_Q_ZERO</option>
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jjohnson
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431 <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option>
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jjohnson
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432 <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option>
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jjohnson
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433 </param>
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jjohnson
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434 <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy &amp;lt;solid_nocall_strategy&amp;gt;">
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jjohnson
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435 <option value="default" selected="True">Don't set</option>
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jjohnson
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436 <option value="THROW_EXCEPTION">THROW_EXCEPTION</option>
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jjohnson
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437 <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option>
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jjohnson
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438 <option value="PURGE_READ">PURGE_READ</option>
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jjohnson
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439 </param>
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jjohnson
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440 </when>
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jjohnson
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441 </conditional>
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jjohnson
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442 <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/>
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jjohnson
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443 <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="--window_size_nqs"/>
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jjohnson
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444 <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &amp;lt;homopolymer_nback&amp;gt;" />
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jjohnson
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445 <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated" help="-pQ,--preserve_qscores_less_than &amp;lt;preserve_qscores_less_than&amp;gt;"/>
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jjohnson
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446 <param name="smoothing" type="integer" value="1" label="smoothing" help="-sm,--smoothing &amp;lt;smoothing&amp;gt;"/>
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jjohnson
parents:
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447 <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &amp;lt;max_quality_score&amp;gt;"/>
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jjohnson
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448 <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag" help="-noOQs,--doNotWriteOriginalQuals"/>
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jjohnson
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449 </when>
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jjohnson
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450 </conditional>
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jjohnson
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451 </inputs>
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jjohnson
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452 <outputs>
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jjohnson
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453 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
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jjohnson
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454 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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jjohnson
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455 </outputs>
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jjohnson
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456 <tests>
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jjohnson
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457 <test>
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jjohnson
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458 <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" />
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jjohnson
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459 <param name="reference_source_selector" value="history" />
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jjohnson
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460 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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jjohnson
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461 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
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jjohnson
parents:
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462 <param name="gatk_param_type_selector" value="basic" />
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jjohnson
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463 <param name="analysis_param_type_selector" value="basic" />
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jjohnson
parents:
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464 <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" lines_diff="4" />
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jjohnson
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465 <output name="output_log" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains" compare="contains" />
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jjohnson
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466 </test>
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jjohnson
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467 </tests>
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jjohnson
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468 <help>
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jjohnson
parents:
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469 **What it does**
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jjohnson
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470
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jjohnson
parents:
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471 This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. For each base in each read this walker calculates various user-specified covariates (such as read group, reported quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file with these updated (recalibrated) reads. Note: This walker expects as input the recalibration table file generated previously by CovariateCounterWalker. Note: This walker is designed to be used in conjunction with CovariateCounterWalker.
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jjohnson
parents:
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472
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jjohnson
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473 For more information on base quality score recalibration using the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_PrintReads.html&gt;`_.
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jjohnson
parents:
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474
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jjohnson
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475 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:
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476
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jjohnson
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477 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
478
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jjohnson
parents:
diff changeset
479 ------
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jjohnson
parents:
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480
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jjohnson
parents:
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481 **Inputs**
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jjohnson
parents:
diff changeset
482
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jjohnson
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483 GenomeAnalysisTK: PrintReads accepts an aligned BAM and a recalibration CSV input files.
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jjohnson
parents:
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484
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jjohnson
parents:
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485
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jjohnson
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486 **Outputs**
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jjohnson
parents:
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487
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jjohnson
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488 The output is in BAM format.
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jjohnson
parents:
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489
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jjohnson
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490
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jjohnson
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491 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
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jjohnson
parents:
diff changeset
492
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jjohnson
parents:
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493 -------
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jjohnson
parents:
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494
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jjohnson
parents:
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495 **Settings**::
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jjohnson
parents:
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496
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jjohnson
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497 default_read_group If a read has no read group then default to the provided String.
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jjohnson
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498 default_platform If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.
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jjohnson
parents:
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499 force_read_group If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group.
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jjohnson
parents:
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500 force_platform If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.
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jjohnson
parents:
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501 window_size_nqs The window size used by MinimumNQSCovariate for its calculation
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jjohnson
parents:
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502 homopolymer_nback The number of previous bases to look at in HomopolymerCovariate
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jjohnson
parents:
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503 exception_if_no_tile If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1
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jjohnson
parents:
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504 solid_recal_mode How should we recalibrate solid bases in whichthe reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING|SET_Q_ZERO|SET_Q_ZERO_BASE_N|REMOVE_REF_BIAS)
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jjohnson
parents:
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505 solid_nocall_strategy Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ (THROW_EXCEPTION|LEAVE_READ_UNRECALIBRATED|PURGE_READ)
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jjohnson
parents:
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506 recal_file Filename for the input covariates table recalibration .csv file
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jjohnson
parents:
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507 out The output BAM file
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jjohnson
parents:
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508 bam_compression Compression level to use for writing BAM files
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jjohnson
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509 disable_bam_indexing Turn off on-the-fly creation of indices for output BAM files.
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jjohnson
parents:
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510 simplifyBAM If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier
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jjohnson
parents:
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511 preserve_qscores_less_than Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below &lt; 5, since base callers use these values to indicate random or bad bases
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jjohnson
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512 smoothing Number of imaginary counts to add to each bin bin order to smooth out bins with few data points, default=1
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jjohnson
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513 max_quality_score The integer value at which to cap the quality scores, default=50
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jjohnson
parents:
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514 doNotWriteOriginalQuals If true, we will not write the original quality (OQ) tag for each read
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jjohnson
parents:
diff changeset
515
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parents:
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516 ------
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jjohnson
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517
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jjohnson
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518 **Citation**
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jjohnson
parents:
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519
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520 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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521
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522 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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523
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524 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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525
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526 </help>
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527 </tool>