Mercurial > repos > devteam > variants_validate

comparison variants_validate.xml @ 0:79b091e42374 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Imported from capsule None
author devteam
date Tue, 01 Apr 2014 09:12:17 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:79b091e42374
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>