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1 <tool id="gatk2_variant_validate" name="Validate Variants" version="@VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>gatk2_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command interpreter="python">
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9 gatk2_wrapper.py
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10 --stdout "${output_log}"
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11 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
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12 -p '
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13 @JAR_PATH@
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14 -T "ValidateVariants"
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15
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16 \$GATK2_SITE_OPTIONS
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17
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18 #if $reference_source.reference_source_selector != "history":
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19 -R "${reference_source.ref_file.fields.path}"
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20 #end if
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21 ${warn_on_errors}
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22 ${do_not_validate_filtered_records}
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23 '
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24 @DBSNP_OPTIONS@
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25
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26 #include source=$standard_gatk_options#
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27 </command>
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28 <inputs>
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29
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30 <conditional name="reference_source">
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31 <expand macro="reference_source_selector_param" />
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32 <when value="cached">
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33 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &lt;variant&gt;" />
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34 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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35 <options from_data_table="gatk2_picard_indexes">
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36 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
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37 </options>
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38 <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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39 </param>
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40 </when>
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41 <when value="history"> <!-- FIX ME!!!! -->
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42 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &lt;variant&gt;" />
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43 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
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44 </when>
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45 </conditional>
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46 <expand macro="dbsnp_param" />
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47
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48 <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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49 <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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50
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51 <expand macro="gatk_param_type_conditional" />
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52
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53 </inputs>
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54 <outputs>
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55 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="reference_source_selector" value="history" />
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60 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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61 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
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62 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
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63 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
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64 <param name="dbsnp_rod_name" value="dbsnp" />
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65 <param name="warn_on_errors" value="True"/>
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66 <param name="do_not_validate_filtered_records" />
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67 <param name="gatk_param_type_selector" value="basic" />
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68 <output name="output_log" file="gatk/gatk_validate_variants/gatk_validate_variants_out_1.log.contains" compare="contains" />
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69 </test>
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70 </tests>
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71 <help>
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72 **What it does**
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73
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74 Validates a variants file.
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75
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76 For more information on using the ValidateVariants module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_ValidateVariants.html>`_.
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77
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78 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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79
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80 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_.
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81
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82 ------
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83
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84 **Inputs**
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85
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86 GenomeAnalysisTK: ValidateVariants accepts variant files as input.
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87
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88
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89 **Outputs**
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90
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91 The output is a log of variant validation.
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92
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93
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94 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats.
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95
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96 -------
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97
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98 **Settings**::
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99
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100 doNotValidateFilteredRecords should we skip validation on filtered records?
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101 warnOnErrors should we just emit warnings on errors instead of terminating the run?
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102
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103 @CITATION_SECTION@
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104 </help>
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105 <expand macro="citations" />
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106 </tool>
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