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1 <tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.5">
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2 <description>on VCF files</description>
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3 <requirements>
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4 <requirement type="package" version="1.4">gatk</requirement>
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5 </requirements>
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6 <macros>
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7 <import>gatk_macros.xml</import>
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8 </macros>
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9 <command interpreter="python">gatk_wrapper.py
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10 #from binascii import hexlify
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11 --max_jvm_heap_fraction "1"
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12 --stdout "${output_log}"
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13 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
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14 -p 'java
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15 -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar"
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16 -T "VariantFiltration"
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17 ##--num_threads 4 ##hard coded, for now
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18 -et "NO_ET" ##ET no phone home
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19 -o "${output_vcf}"
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20 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
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21 #if $reference_source.reference_source_selector != "history":
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22 -R "${reference_source.ref_file.fields.path}"
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23 #end if
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24 '
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25 #for $variant_filter in $variant_filters:
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26 #set $variant_filter = "--%sExpression '%s' --%sName '%s'" % ( str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_expression ), str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_name ) )
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27 -o '${ hexlify( $variant_filter ) }'
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28 #end for
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29
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30 #if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask':
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31 -d "--mask:${mask_rod_bind_type.mask_rod_name},%(file_type)s" "${mask_rod_bind_type.input_mask_rod}" "${mask_rod_bind_type.input_mask_rod.ext}" "input_mask_${mask_rod_bind_type.mask_rod_name}"
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32 -p '
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33 --maskExtension "${mask_rod_bind_type.mask_extension}"
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34 --maskName "${mask_rod_bind_type.mask_rod_name}"
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35 '
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36 #end if
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37
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38 #include source=$standard_gatk_options#
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39
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40 ##start analysis specific options
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41 #if $cluster_snp_type.cluster_snp_type_selector == "cluster_snp":
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42 -p '
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43 --clusterSize "${cluster_snp_type.cluster_size}"
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44 --clusterWindowSize "${cluster_snp_type.cluster_window_size}"
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45 '
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46 #end if
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47 -p '${missing_values_in_expressions_should_evaluate_as_failing}'
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48 </command>
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49 <inputs>
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50 <conditional name="reference_source">
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51 <expand macro="reference_source_selector_param" />
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52 <when value="cached">
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53 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;" />
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54 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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55 <options from_data_table="gatk_picard_indexes">
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56 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
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57 </options>
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58 <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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59 </param>
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60 </when>
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61 <when value="history"> <!-- FIX ME!!!! -->
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62 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;" />
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63 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
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64 </when>
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65 </conditional>
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66
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67
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68 <repeat name="variant_filters" title="Variant Filters">
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69 <param name="filter_expression" value="AB < 0.2 || MQ0 > 50" type="text" label="Filter expression" help="JEXL formatted expressions (-filter,--filterExpression &lt;filterExpression&gt;)">
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70 <sanitizer>
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71 <valid initial="string.printable">
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72 <remove value="'"/>
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73 </valid>
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74 <mapping initial="none"/>
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75 </sanitizer>
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76 </param>
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77 <param name="filter_name" value="custom_filter" type="text" label="Filter name" help="-filterName,--filterName &lt;filterName&gt;"/>
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78 <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" help="Use -G_filter,--genotypeFilterExpression &lt;genotypeFilterExpression&gt; and -G_filterName,--genotypeFilterName &lt;genotypeFilterName&gt; for filter type" />
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79 </repeat>
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80
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81
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82
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83 <conditional name="mask_rod_bind_type">
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84 <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file">
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85 <option value="set_mask" selected="True">Set maskP</option>
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86 <option value="exclude_mask">Don't set mask</option>
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87 </param>
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88 <when value="exclude_mask">
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89 <!-- Do nothing here -->
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90 </when>
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91 <when value="set_mask">
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92 <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" help="--mask &lt;mask&gt;" />
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93 <param name="mask_rod_name" type="text" value="Mask" label="Mask Name" help="-maskName,--maskName &lt;maskName&gt;"/>
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94 <param name="mask_extension" type="integer" value="0" label="Mask Extension" help="-maskExtend,--maskExtension &lt;maskExtension&gt;"/>
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95 </when>
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96 </conditional>
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97
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98
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99 <expand macro="gatk_param_type_conditional" />
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100
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101 <conditional name="cluster_snp_type">
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102 <param name="cluster_snp_type_selector" type="select" label="Cluster SNPs">
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103 <option value="cluster_snp">Cluster SNPs</option>
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104 <option value="do_not_cluster_snp" selected="True">Do not cluster SNPs</option>
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105 </param>
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106 <when value="do_not_cluster_snp">
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107 <!-- Do nothing here -->
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108 </when>
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109 <when value="cluster_snp">
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110 <param name="cluster_size" type="integer" value="3" label="The number of SNPs which make up a cluster" help="-cluster,--clusterSize &lt;clusterSize&gt;"/>
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111 <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs" help="-window,--clusterWindowSize &lt;clusterWindowSize&gt;"/>
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112 </when>
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113 </conditional>
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114
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115 <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" help="--missingValuesInExpressionsShouldEvaluateAsFailing" />
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116
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117 </inputs>
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118 <outputs>
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119 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
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120 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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121 </outputs>
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122 <tests>
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123 <test>
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124 <param name="reference_source_selector" value="history" />
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125 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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126 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
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127 <param name="filter_expression" value="MQ < 37.74 || MQ0 > 50" />
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128 <param name="filter_name" value="Galaxy_filter" />
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129 <param name="is_genotype_filter" />
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130 <param name="mask_rod_bind_type_selector" value="set_mask" />
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131 <param name="input_mask_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
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132 <param name="mask_rod_name" value="." />
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133 <param name="mask_extension" value="0" />
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134 <param name="gatk_param_type_selector" value="basic" />
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135 <param name="cluster_snp_type_selector" value="do_not_cluster_snp" />
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136 <param name="missing_values_in_expressions_should_evaluate_as_failing" />
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137 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" />
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138 <output name="output_log" file="gatk/gatk_variant_filtration/gatk_variant_filtration_out_1.log.contains" compare="contains" />
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139 </test>
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140 </tests>
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141 <help>
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142 **What it does**
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143
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144 Filters variant calls using a number of user-selectable, parameterizable criteria.
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145
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146 For more information on using the VariantFiltration module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/VariantFiltrationWalker>`_.
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147
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148 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_.
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149
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150 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_.
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151
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152 ------
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153
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154 **Inputs**
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155
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156 GenomeAnalysisTK: VariantFiltration accepts a VCF input file.
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157
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158
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159 **Outputs**
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160
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161 The output is in VCF format.
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162
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163
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164 Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats.
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165
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166 -------
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167
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168 **Settings**::
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169
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170
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171 filterExpression One or more expression used with INFO fields to filter (see wiki docs for more info)
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172 filterName Names to use for the list of filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered
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173 genotypeFilterExpression One or more expression used with FORMAT (sample/genotype-level) fields to filter (see wiki docs for more info)
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174 genotypeFilterName Names to use for the list of sample/genotype filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered
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175 clusterSize The number of SNPs which make up a cluster (see also --clusterWindowSize); [default:3]
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176 clusterWindowSize The window size (in bases) in which to evaluate clustered SNPs (to disable the clustered SNP filter, set this value to less than 1); [default:0]
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177 maskName The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask']
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178 missingValuesInExpressionsShouldEvaluateAsFailing When evaluating the JEXL expressions, should missing values be considered failing the expression (by default they are considered passing)?
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179
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180 @CITATION_SECTION@
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181 </help>
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182 </tool>
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