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1 <tool id="gatk2_variant_annotator" name="Variant Annotator" version="0.0.7">
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2 <description></description>
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3 <expand macro="requirements" />
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4 <macros>
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5 <import>gatk2_macros.xml</import>
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6 </macros>
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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 #if str( $reference_source.input_bam ) != "None":
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11 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
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12 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
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13 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
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14 #end if
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15 #end if
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16 -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
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17 -p '
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18 @JAR_PATH@
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19 ##--list
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20 -T "VariantAnnotator"
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21 \$GATK2_SITE_OPTIONS
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22
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23 @THREADS@
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24
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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 -o "${output_vcf}"
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30 #if str( $annotations_type.annotations_type_selector ) == "use_all_annotations":
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31 --useAllAnnotations
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32 #else:
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33 #if $annotations_type.annotations:
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34 #for $annotation in str( $annotations_type.annotations.fields.gatk_value ).split( ',' ):
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35 --annotation "${annotation}"
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36 #end for
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37 #end if
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38 #end if
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39 #if $exclude_annotations:
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40 #for $annotation in str( $exclude_annotations.fields.gatk_value ).split( ',' ):
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41 --excludeAnnotation "${annotation}"
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42 #end for
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43 #end if
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44 #for $additional_annotation in $additional_annotations:
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45 --annotation "${additional_annotation.additional_annotation_name}"
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46 #end for
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47 '
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48 #if $reference_source.input_variant_bti:
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49 -d "--intervals" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant_bti"
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50 #end if
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51
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52 #for $rod_binding in $comp_rod_bind:
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53 -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
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54 #end for
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55
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56 #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
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57 -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
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58 #end if
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59
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60
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61 #for $rod_binding in $resource_rod_bind:
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62 -d "--resource:${rod_binding.resource_rod_name},%(file_type)s" "${rod_binding.resource_input_rod}" "${rod_binding.resource_input_rod.ext}" "input_resource_${rod_binding.resource_rod_name}"
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63 #end for
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64
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65 #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
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66 -p '--annotation "SnpEff"'
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67 -d "--snpEffFile:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}"
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68 #else:
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69 -p '--excludeAnnotation "SnpEff"'
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70 #end if
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71
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72 #for $expression in $expressions:
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73 -p '--expression "${expression.expression}"'
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74 #end for
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75
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76 #include source=$standard_gatk_options#
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77
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78 -p '
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79 #if str( $annotation_group ) != "None":
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80 #for $group in str( $annotation_group ).split( ',' ):
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81 --group "${group}"
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82 #end for
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83 #end if
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84 #if str( $family_string ) != "":
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85 --family_string "${family_string}"
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86 #end if
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87 --MendelViolationGenotypeQualityThreshold "${mendel_violation_genotype_quality_threshold}"
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88 '
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89 </command>
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90 <inputs>
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91 <conditional name="reference_source">
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92 <expand macro="reference_source_selector_param" />
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93 <when value="cached">
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94 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;"/>
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95 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/>
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96 <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &lt;input_file&gt;)" >
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97 <validator type="unspecified_build" />
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98 <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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99 </param>
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100 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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101 <options from_data_table="gatk2_picard_indexes">
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102 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
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103 </options>
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104 <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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105 </param>
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106 </when>
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107 <when value="history"> <!-- FIX ME!!!! -->
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108 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;"/>
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109 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/>
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110 <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &lt;input_file&gt;)" >
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111 </param>
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112 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
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113 </when>
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114 </conditional>
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115 <conditional name="annotations_type">
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116 <param name="annotations_type_selector" type="select" label="Use all possible annotations">
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117 <option value="use_all_annotations">Use all</option>
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118 <option value="choose" selected="True">Use selected</option>
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119 </param>
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120 <when value="use_all_annotations">
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121 <!-- no extra options here -->
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122 </when>
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123 <when value="choose">
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124 <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" help="-A,--annotation &lt;annotation&gt;" >
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125 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
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126 <options from_data_table="gatk2_annotations">
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127 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
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128 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
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129 </options>
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130 </param>
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131 </when>
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132 </conditional>
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133
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134 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &lt;annotation&gt;">
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135 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
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136 </repeat>
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137
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138 <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &lt;comp&gt;">
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139 <param name="comp_input_rod" type="data" format="vcf" label="ROD file" />
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140 <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
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141 </repeat>
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142
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143 <conditional name="dbsnp_rod_bind_type">
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144 <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &lt;dbsnp&gt;">
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145 <option value="set_dbsnp" selected="True">Set dbSNP</option>
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146 <option value="exclude_dbsnp">Don't set dbSNP</option>
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147 </param>
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148 <when value="exclude_dbsnp">
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149 <!-- Do nothing here -->
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150 </when>
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151 <when value="set_dbsnp">
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152 <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
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153 <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/>
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154 </when>
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155 </conditional>
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156
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157 <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data" help="-resource,--resource &lt;resource&gt;">
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158 <param name="resource_input_rod" type="data" format="vcf" label="ROD file" />
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159 <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/>
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160 </repeat>
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161
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162 <conditional name="snpEff_rod_bind_type">
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163 <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file" help="-snpEffFile,--snpEffFile &lt;snpEffFile&gt;">
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164 <option value="set_snpEff">Set snpEff</option>
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165 <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
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166 </param>
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167 <when value="exclude_snpEff">
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168 <!-- Do nothing here -->
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169 </when>
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170 <when value="set_snpEff">
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171 <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
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172 <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
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173 </when>
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174 </conditional>
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175
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176 <repeat name="expressions" title="Expression" help="-E,--expression &lt;expression&gt;">
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177 <param name="expression" type="text" value="" label="Expression"/>
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178 </repeat>
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179
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180 <expand macro="gatk_param_type_conditional" />
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181
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182 <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls" help="-G,--group &lt;group&gt;">
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183 <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
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184 <option value="Standard">Standard</option>
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185 <option value="Experimental">Experimental</option>
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186 <option value="WorkInProgress">WorkInProgress</option>
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187 <option value="RankSumTest">RankSumTest</option>
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188 </param>
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189 <param name="family_string" type="text" value="" label="Family String" help="--family_string"/>
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190 <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio." help="-mvq,--MendelViolationGenotypeQualityThreshold &lt;MendelViolationGenotypeQualityThreshold&gt;"/>
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191 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &lt;excludeAnnotation&gt;" >
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192 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
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193 <options from_data_table="gatk2_annotations">
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194 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
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195 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
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196 </options>
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197 </param>
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198
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199 </inputs>
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200 <outputs>
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201 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
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202 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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203 </outputs>
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204 <tests>
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205 <test>
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206 <param name="reference_source_selector" value="history" />
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207 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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208 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
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209 <param name="input_variant" value="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" ftype="vcf" />
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210 <param name="input_variant_bti" />
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211 <param name="annotations_type_selector" value="choose" />
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212 <param name="annotations" value="AlleleBalance,BaseQualityRankSumTest,DepthOfCoverage,HomopolymerRun,MappingQualityRankSumTest,MappingQualityZero,QualByDepth,RMSMappingQuality,SpanningDeletions,HaplotypeScore" />
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213 <param name="additional_annotations" value="0" />
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214 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
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215 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
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216 <param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" />
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217 <param name="gatk_param_type_selector" value="basic" />
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218 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" />
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219 <output name="output_log" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.log.contains" compare="contains" />
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220 <param name="comp_rod_bind" value="0" />
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221 <param name="resource_rod_bind" value="0" />
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222 <param name="expressions" value="0" />
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223 <!-- <param name="annotation_group" /> -->
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224 </test>
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225 </tests>
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226 <help>
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227 **What it does**
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228
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229 Annotates variant calls with context information. Users can specify which of the available annotations to use.
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230
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231 For more information on using the VariantAnnotator, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_VariantAnnotator.html>`_.
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232
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233 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_.
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234
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235 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_.
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236
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237 ------
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238
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239
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240 **Inputs**
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241
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242 GenomeAnalysisTK: VariantAnnotator accepts a variant input file.
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243
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244
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245 **Outputs**
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246
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247 The output is in VCF format.
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248
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249
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250 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats.
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251
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252 -------
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253
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254 **Settings**::
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255
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256
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257 sampleName The sample (NA-ID) corresponding to the variant input (for non-VCF input only)
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258 annotation One or more specific annotations to apply to variant calls
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259 group One or more classes/groups of annotations to apply to variant calls
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260 expression One or more specific expressions to apply to variant calls; see documentation for more details
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261 useAllAnnotations Use all possible annotations (not for the faint of heart)
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262
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263 @CITATION_SECTION@
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264 </help>
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265 </tool>
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