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comparison variants_validate.xml @ 0:7e1ecaa64370 draft default tip

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author devteam
date Tue, 01 Apr 2014 10:49:56 -0400
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1 <tool id="gatk_validate_variants" name="Validate Variants" version="0.0.4">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="1.4">gatk</requirement>
5 </requirements>
6 <macros>
7 <import>gatk_macros.xml</import>
8 </macros>
9 <command interpreter="python">gatk_wrapper.py
10 --max_jvm_heap_fraction "1"
11 --stdout "${output_log}"
12 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
13 -p 'java
14 -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar"
15 -T "ValidateVariants"
16
17 -et "NO_ET" ##ET no phone home
18 ##--num_threads 4 ##hard coded, for now
19 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
20 #if $reference_source.reference_source_selector != "history":
21 -R "${reference_source.ref_file.fields.path}"
22 #end if
23 ${warn_on_errors}
24 ${do_not_validate_filtered_records}
25 '
26
27 #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
28 -d "--dbsnp:${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_${dbsnp_rod_bind_type.dbsnp_rod_name}"
29 #end if
30
31 #include source=$standard_gatk_options#
32 </command>
33 <inputs>
34
35 <conditional name="reference_source">
36 <expand macro="reference_source_selector_param" />
37 <when value="cached">
38 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
39 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
40 <options from_data_table="gatk_picard_indexes">
41 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
42 </options>
43 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
44 </param>
45 </when>
46 <when value="history"> <!-- FIX ME!!!! -->
47 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
48 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
49 </when>
50 </conditional>
51
52 <conditional name="dbsnp_rod_bind_type">
53 <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
54 <option value="set_dbsnp" selected="True">Set dbSNP</option>
55 <option value="exclude_dbsnp">Don't set dbSNP</option>
56 </param>
57 <when value="exclude_dbsnp">
58 <!-- Do nothing here -->
59 </when>
60 <when value="set_dbsnp">
61 <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
62 <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/>
63 </when>
64 </conditional>
65
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"/>
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"/>
68
69 <expand macro="gatk_param_type_conditional" />
70
71 </inputs>
72 <outputs>
73 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
74 </outputs>
75 <tests>
76 <test>
77 <param name="reference_source_selector" value="history" />
78 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
79 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
80 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
81 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
82 <param name="warn_on_errors" value="True"/>
83 <param name="do_not_validate_filtered_records" />
84 <param name="gatk_param_type_selector" value="basic" />
85 <output name="output_log" file="gatk/gatk_validate_variants/gatk_validate_variants_out_1.log.contains" compare="contains" />
86 </test>
87 </tests>
88 <help>
89 **What it does**
90
91 Validates a variants file.
92
93 For more information on using the ValidateVariants module, see this `tool specific page &lt;http://www.broadinstitute.org/gsa/wiki/index.php/VariantValidator&gt;`_.
94
95 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3&gt;`_.
96
97 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions&gt;`_.
98
99 ------
100
101 **Inputs**
102
103 GenomeAnalysisTK: ValidateVariants accepts variant files as input.
104
105
106 **Outputs**
107
108 The output is a log of variant validation.
109
110
111 Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK&gt;`_ for details on GATK file formats.
112
113 -------
114
115 **Settings**::
116
117 doNotValidateFilteredRecords should we skip validation on filtered records?
118 warnOnErrors should we just emit warnings on errors instead of terminating the run?
119
120 @CITATION_SECTION@
121 </help>
122 </tool>