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1 <tool id="gatk_validate_variants" name="Validate Variants" version="0.0.4">
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2 <description></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 --max_jvm_heap_fraction "1"
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11 --stdout "${output_log}"
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12 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
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13 -p 'java
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14 -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar"
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15 -T "ValidateVariants"
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16
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17 -et "NO_ET" ##ET no phone home
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18 ##--num_threads 4 ##hard coded, for now
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19 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
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20 #if $reference_source.reference_source_selector != "history":
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21 -R "${reference_source.ref_file.fields.path}"
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22 #end if
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23 ${warn_on_errors}
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24 ${do_not_validate_filtered_records}
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25 '
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26
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27 #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
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28 -d "--dbsnp:${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_${dbsnp_rod_bind_type.dbsnp_rod_name}"
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29 #end if
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30
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31 #include source=$standard_gatk_options#
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32 </command>
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33 <inputs>
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34
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35 <conditional name="reference_source">
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36 <expand macro="reference_source_selector_param" />
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37 <when value="cached">
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38 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &lt;variant&gt;" />
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39 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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40 <options from_data_table="gatk_picard_indexes">
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41 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
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42 </options>
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43 <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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44 </param>
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45 </when>
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46 <when value="history"> <!-- FIX ME!!!! -->
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47 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &lt;variant&gt;" />
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48 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
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49 </when>
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50 </conditional>
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51
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52 <conditional name="dbsnp_rod_bind_type">
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53 <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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54 <option value="set_dbsnp" selected="True">Set dbSNP</option>
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55 <option value="exclude_dbsnp">Don't set dbSNP</option>
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56 </param>
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57 <when value="exclude_dbsnp">
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58 <!-- Do nothing here -->
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59 </when>
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60 <when value="set_dbsnp">
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61 <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
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62 <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/>
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63 </when>
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64 </conditional>
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65
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66 <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen." help="-warnOnErrors,--warnOnErrors"/>
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67 <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed." help="-doNotValidateFilteredRecords,--doNotValidateFilteredRecords"/>
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68
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69 <expand macro="gatk_param_type_conditional" />
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70
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71 </inputs>
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72 <outputs>
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73 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="reference_source_selector" value="history" />
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78 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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79 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
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80 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
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81 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
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82 <param name="warn_on_errors" value="True"/>
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83 <param name="do_not_validate_filtered_records" />
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84 <param name="gatk_param_type_selector" value="basic" />
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85 <output name="output_log" file="gatk/gatk_validate_variants/gatk_validate_variants_out_1.log.contains" compare="contains" />
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86 </test>
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87 </tests>
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88 <help>
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89 **What it does**
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90
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91 Validates a variants file.
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92
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93 For more information on using the ValidateVariants module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/VariantValidator>`_.
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94
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95 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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96
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97 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_.
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98
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99 ------
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100
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101 **Inputs**
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102
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103 GenomeAnalysisTK: ValidateVariants accepts variant files as input.
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104
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105
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106 **Outputs**
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107
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108 The output is a log of variant validation.
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109
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110
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111 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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112
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113 -------
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114
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115 **Settings**::
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116
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117 doNotValidateFilteredRecords should we skip validation on filtered records?
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118 warnOnErrors should we just emit warnings on errors instead of terminating the run?
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119
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120 @CITATION_SECTION@
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121 </help>
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122 </tool>
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