annotate variant_combine.xml @ 34:b99c25b0ad4d draft

Update tool version to 0.0.7
author Jim Johnson <jj@umn.edu>
date Thu, 28 Feb 2013 15:41:24 -0600
parents 76f8ca47b810
children a29c7d7d962d
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b99c25b0ad4d Update tool version to 0.0.7
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1 <tool id="gatk2_variant_combine" name="Combine Variants" version="0.0.7">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="2.3">gatk</requirement>
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5 </requirements>
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6 <command interpreter="python">gatk2_wrapper.py
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7 --max_jvm_heap_fraction "1"
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8 --stdout "${output_log}"
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9
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10 #set $priority_order = []
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11 #for $input_variant in $reference_source.input_variants:
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12 -d "--variant:${input_variant.input_variant_name},%(file_type)s" "${input_variant.input_variant}" "${input_variant.input_variant.ext}" "input_variant_${input_variant.input_variant_name}"
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13 #set $input_variant_name = str( $input_variant.input_variant_name )
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14 #assert $input_variant_name not in $priority_order, "Variant Names must be unique" ##this should be handled by a validator
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15 #silent $priority_order.append( $input_variant_name )
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16 #end for
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17 -p 'java
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18 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
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19 -T "CombineVariants"
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20 --out "${output_variants}"
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21 \$GATK2_SITE_OPTIONS
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22 \$GATK2_NUM_THREADS
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23 ##--num_threads 4 ##hard coded, for now
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24 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
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25 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
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26 #if $reference_source.reference_source_selector != "history":
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27 -R "${reference_source.ref_file.fields.path}"
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28 #end if
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29 --genotypemergeoption "${genotype_merge_option}"
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30 --rod_priority_list "${ ','.join( $priority_order ) }"
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31 '
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32
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33 ##start standard gatk options
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34 #if $gatk_param_type.gatk_param_type_selector == "advanced":
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35 #for $pedigree in $gatk_param_type.pedigree:
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36 -p '--pedigree "${pedigree.pedigree_file}"'
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37 #end for
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38 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
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39 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
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40 #end for
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41 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
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42 #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
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43 #for $read_filter in $gatk_param_type.read_filter:
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44 -p '
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45 #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters:
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46 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
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47 #end_if
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48 #for $name, $param in $read_filter.read_filter_type.iteritems():
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49 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
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50 #if hasattr( $param.input, 'truevalue' ):
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51 ${param}
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52 #else:
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53 --${name} "${param}"
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54 #end if
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55 #end if
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56 #end for
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57 '
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58 #end for
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59 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
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60 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
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61 #end for
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62
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63 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
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64 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
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65 #end for
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66
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67 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
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68
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69 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
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70 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
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71 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
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72 #end if
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73 -p '
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74 --baq "${gatk_param_type.baq}"
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75 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
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76 ${gatk_param_type.use_original_qualities}
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77 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
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78 --validation_strictness "${gatk_param_type.validation_strictness}"
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79 --interval_merging "${gatk_param_type.interval_merging}"
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80 ${gatk_param_type.disable_experimental_low_memory_sharding}
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81 ${gatk_param_type.fix_misencoded_quality_scores}
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82 ${gatk_param_type.non_deterministic_random_seed}
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83 '
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84 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
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85 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
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86 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
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87 #else
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88 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
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89 #end if
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90 #end for
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91 #end if
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92
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93 #if $reference_source.reference_source_selector == "history":
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94 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
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95 #end if
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96 ##end standard gatk options
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97
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98
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99 ##start analysis specific options
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100 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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101 -p '
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102 --filteredrecordsmergetype "${analysis_param_type.filtered_records_merge_type}"
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103 ${analysis_param_type.print_complex_merges}
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104 ${analysis_param_type.filtered_are_uncalled}
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105 ${analysis_param_type.minimal_vcf}
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106 ${analysis_param_type.assume_identical_samples}
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107
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108 #if str( $analysis_param_type.set_key ):
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109 --setKey "${analysis_param_type.set_key}"
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110 #end if
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111
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112 --minimumN "${analysis_param_type.minimum_n}"
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113 '
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114 #end if
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115 </command>
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116 <inputs>
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117
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118 <conditional name="reference_source">
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119 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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120 <option value="cached">Locally cached</option>
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121 <option value="history">History</option>
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122 </param>
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123 <when value="cached">
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124 <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &amp;lt;variant&amp;gt;)">
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125 <param name="input_variant" type="data" format="vcf" label="Input variant file" />
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126 <param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique">
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127 <validator type="length" min="1" message="You must provide a unique name for this set of variants" />
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128 </param>
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129 </repeat>
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130 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
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131 <options from_data_table="gatk2_picard_indexes">
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132 <!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" column="dbkey"/> -->
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133 </options>
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134 <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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135 </param>
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136 </when>
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137 <when value="history"> <!-- FIX ME!!!! -->
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138 <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &amp;lt;variant&amp;gt;)">
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139 <param name="input_variant" type="data" format="vcf" label="Input variant file" />
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140 <param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique">
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141 <validator type="length" min="1" message="You must provide a unique name for this set of variants" />
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142 </param>
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143 </repeat>
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144 <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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145 </when>
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146 </conditional>
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147
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148 <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" help="-genotypeMergeOptions,--genotypemergeoption &amp;lt;genotypemergeoption&amp;gt;" >
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149 <option value="UNIQUIFY" />
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150 <option value="PRIORITIZE" selected="true"/>
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151 <option value="UNSORTED" />
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152 <option value="REQUIRE_UNIQUE" />
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153 </param>
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154
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155 <conditional name="gatk_param_type">
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156 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
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157 <option value="basic" selected="True">Basic</option>
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158 <option value="advanced">Advanced</option>
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159 </param>
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160 <when value="basic">
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161 <!-- Do nothing here -->
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162 </when>
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163 <when value="advanced">
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164 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
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165 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
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166 </repeat>
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167 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
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168 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
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169 </repeat>
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170 <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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171 <option value="STRICT" selected="True">STRICT</option>
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172 <option value="SILENT">SILENT</option>
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173 </param>
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174 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
175 <conditional name="read_filter_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
176 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
177 <option value="BadCigar">BadCigar</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
178 <option value="BadMate">BadMate</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
179 <option value="DuplicateRead">DuplicateRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
180 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
181 <option value="MalformedRead">MalformedRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
182 <option value="MappingQuality">MappingQuality</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
183 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
184 <option value="MappingQualityZero">MappingQualityZero</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
185 <option value="MateSameStrand">MateSameStrand</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
186 <option value="MaxInsertSize">MaxInsertSize</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
187 <option value="MaxReadLength" selected="True">MaxReadLength</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
188 <option value="MissingReadGroup">MissingReadGroup</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
189 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
190 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
191 <option value="Platform454">Platform454</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
192 <option value="Platform">Platform</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
193 <option value="PlatformUnit">PlatformUnit</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
194 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
195 <option value="ReadName">ReadName</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
196 <option value="ReadStrand">ReadStrand</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
197 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
198 <option value="Sample">Sample</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
199 <option value="SingleReadGroup">SingleReadGroup</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
200 <option value="UnmappedRead">UnmappedRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
201 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
202 <when value="BadCigar">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
203 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
204 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
205 <when value="BadMate">
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jjohnson
parents:
diff changeset
206 <!-- no extra options -->
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jjohnson
parents:
diff changeset
207 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
208 <when value="DuplicateRead">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
209 <!-- no extra options -->
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jjohnson
parents:
diff changeset
210 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
211 <when value="FailsVendorQualityCheck">
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jjohnson
parents:
diff changeset
212 <!-- no extra options -->
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jjohnson
parents:
diff changeset
213 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
214 <when value="MalformedRead">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
215 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
216 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
217 <when value="MappingQuality">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
218 <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
219 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
220 <when value="MappingQualityUnavailable">
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jjohnson
parents:
diff changeset
221 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
222 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
223 <when value="MappingQualityZero">
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jjohnson
parents:
diff changeset
224 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
225 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
226 <when value="MateSameStrand">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
227 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
228 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
229 <when value="MaxInsertSize">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
230 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
231 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
232 <when value="MaxReadLength">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
233 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
234 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
235 <when value="MissingReadGroup">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
236 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
237 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
238 <when value="NoOriginalQualityScores">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
239 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
240 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
241 <when value="NotPrimaryAlignment">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
242 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
243 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
244 <when value="Platform454">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
245 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
246 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
247 <when value="Platform">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
248 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
249 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
250 <when value="PlatformUnit">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
251 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
252 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
253 <when value="ReadGroupBlackList">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
254 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
255 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
256 <when value="ReadName">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
257 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
258 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
259 <when value="ReadStrand">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
260 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
261 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
262 <when value="ReassignMappingQuality">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
263 <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
264 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
265 <when value="Sample">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
266 <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
267 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
268 <when value="SingleReadGroup">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
269 <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
270 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
271 <when value="UnmappedRead">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
272 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
273 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
274 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
275 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
276 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
277 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
278 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
279 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
280 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
281 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
282
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
283 <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
284 <option value="UNION" selected="True">UNION</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
285 <option value="INTERSECTION">INTERSECTION</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
286 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
287
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
288 <conditional name="downsampling_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
289 <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
290 <option value="NONE" selected="True">NONE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
291 <option value="ALL_READS">ALL_READS</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
292 <option value="BY_SAMPLE">BY_SAMPLE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
293 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
294 <when value="NONE">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
295 <!-- no more options here -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
296 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
297 <when value="ALL_READS">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
298 <conditional name="downsample_to_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
299 <param name="downsample_to_type_selector" type="select" label="Downsample method">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
300 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
301 <option value="downsample_to_coverage">Downsample by Coverage</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
302 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
303 <when value="downsample_to_fraction">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
304 <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
305 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
306 <when value="downsample_to_coverage">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
307 <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
308 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
309 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
310 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
311 <when value="BY_SAMPLE">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
312 <conditional name="downsample_to_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
313 <param name="downsample_to_type_selector" type="select" label="Downsample method">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
314 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
315 <option value="downsample_to_coverage">Downsample by Coverage</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
316 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
317 <when value="downsample_to_fraction">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
318 <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
319 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
320 <when value="downsample_to_coverage">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
321 <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
322 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
323 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
324 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
325 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
326 <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
327 <option value="OFF" selected="True">OFF</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
328 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
329 <option value="RECALCULATE">RECALCULATE</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
330 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
331 <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
332 <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
333 <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
334 <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
335 <option value="STRICT" selected="True">STRICT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
336 <option value="LENIENT">LENIENT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
337 <option value="SILENT">SILENT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
338 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
339 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
340 <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
341 <option value="ALL" selected="True">ALL</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
342 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
343 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
344
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
345 <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
346 <conditional name="read_group_black_list_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
347 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
348 <option value="file" selected="True">Filters in file</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
349 <option value="text">Specify filters as a string</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
350 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
351 <when value="file">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
352 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
353 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
354 <when value="text">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
355 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
356 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
357 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
358 </repeat>
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jjohnson
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359
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360 <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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361 <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
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362 <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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363
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364 </when>
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365 </conditional>
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366
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367
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368 <conditional name="analysis_param_type">
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369 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
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370 <option value="basic" selected="True">Basic</option>
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371 <option value="advanced">Advanced</option>
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372 </param>
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373 <when value="basic">
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374 <!-- Do nothing here -->
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375 </when>
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376 <when value="advanced">
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377 <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields?" help="-filteredRecordsMergeType,--filteredrecordsmergetype &amp;lt;filteredrecordsmergetype&amp;gt;" >
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378 <option value="KEEP_IF_ANY_UNFILTERED" selected="true"/>
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379 <option value="KEEP_IF_ALL_UNFILTERED" />
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380 </param>
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381
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382 <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,--printComplexMerges" />
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383 <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" help="-filteredAreUncalled,--filteredAreUncalled" />
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384 <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" help="-minimalVCF,--minimalVCF" />
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385
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386 <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from." help="-setKey,--setKey &amp;lt;setKey&amp;gt;"/>
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387 <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." help="-assumeIdenticalSamples,--assumeIdenticalSamples" />
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388 <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files." help="-minN,--minimumN &amp;lt;minimumN&amp;gt;"/>
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389
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390 </when>
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391 </conditional>
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392
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393
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394 </inputs>
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395 <outputs>
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396 <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (variants)" />
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397 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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398 </outputs>
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399 <tests>
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400 <test>
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401 <param name="reference_source_selector" value="history" />
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402 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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403 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
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404 <param name="input_variant_name" value="from_variant_annotator" />
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405 <param name="genotype_merge_option" value="PRIORITIZE" />
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406 <param name="gatk_param_type_selector" value="basic" />
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407 <param name="analysis_param_type_selector" value="basic" />
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408 <output name="output_variants" file="gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf" lines_diff="4" />
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409 <output name="output_log" file="gatk/gatk_variant_combine/gatk_variant_combine_out_1.log.contains" compare="contains" />
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410 </test>
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411 </tests>
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412 <help>
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413 **What it does**
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414
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415 Combines VCF records from different sources; supports both full merges and set unions. Merge: combines multiple records into a single one; if sample names overlap then they are uniquified. Union: assumes each rod represents the same set of samples (although this is not enforced); using the priority list (if provided), emits a single record instance at every position represented in the rods.
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416
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417 For more information on using the CombineVariants module, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_CombineVariants.html&gt;`_.
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418
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419 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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420
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421 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
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422
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423 ------
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424
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425 **Inputs**
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426
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427 GenomeAnalysisTK: CombineVariants accepts variant files as input.
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428
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429 ------
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430
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431 **Outputs**
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432
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433 The output is a combined vcf file.
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434
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435
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436 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
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437
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438 -------
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439
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440 **Settings**::
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441
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442 out File to which variants should be written
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443 genotypemergeoption How should we merge genotype records for samples shared across the ROD files? (UNIQUIFY|PRIORITIZE|UNSORTED|REQUIRE_UNIQUE)
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444 filteredrecordsmergetype How should we deal with records seen at the same site in the VCF, but with different FILTER fields? KEEP_IF_ANY_UNFILTERED PASSes the record if any record is unfiltered, KEEP_IF_ALL_UNFILTERED requires all records to be unfiltered (KEEP_IF_ANY_UNFILTERED|KEEP_IF_ALL_UNFILTERED)
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445 rod_priority_list When taking the union of variants containing genotypes: a comma-separated string describing the priority ordering for the genotypes as far as which record gets emitted; a complete priority list MUST be provided
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446 printComplexMerges Print out interesting sites requiring complex compatibility merging
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447 filteredAreUncalled If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF
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448 minimalVCF If true, then the output VCF will contain no INFO or genotype INFO field
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449 setKey Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from. Set to null if you don't want the set field emitted.
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450 assumeIdenticalSamples If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime.
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451 minimumN Combine variants and output site only if variant is present in at least N input files.
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452
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453 ------
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454
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455 **Citation**
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456
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457 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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458
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459 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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460
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461 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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462
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463 </help>
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464 </tool>