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comparison variant_validate.xml @ 0:9ad15075b9fa draft

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author iuc
date Mon, 25 Nov 2013 14:23:47 -0500
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1 <tool id="gatk2_variant_validate" name="Validate Variants" version="0.0.7">
2 <description></description>
3 <expand macro="requirements" />
4 <macros>
5 <import>gatk2_macros.xml</import>
6 </macros>
7 <command interpreter="python">gatk2_wrapper.py
8 ##--max_jvm_heap_fraction "1"
9 --stdout "${output_log}"
10 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
11 -p '
12 @JAR_PATH@
13 -T "ValidateVariants"
14
15 \$GATK2_SITE_OPTIONS
16
17 @THREADS@
18 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
19 #if $reference_source.reference_source_selector != "history":
20 -R "${reference_source.ref_file.fields.path}"
21 #end if
22 ${warn_on_errors}
23 ${do_not_validate_filtered_records}
24 '
25
26 #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
27 -d "--dbsnp:${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_${dbsnp_rod_bind_type.dbsnp_rod_name}"
28 #end if
29
30 #include source=$standard_gatk_options#
31 </command>
32 <inputs>
33
34 <conditional name="reference_source">
35 <expand macro="reference_source_selector_param" />
36 <when value="cached">
37 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
38 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
39 <options from_data_table="gatk2_picard_indexes">
40 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
41 </options>
42 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
43 </param>
44 </when>
45 <when value="history"> <!-- FIX ME!!!! -->
46 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
47 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
48 </when>
49 </conditional>
50
51 <conditional name="dbsnp_rod_bind_type">
52 <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;">
53 <option value="set_dbsnp" selected="True">Set dbSNP</option>
54 <option value="exclude_dbsnp">Don't set dbSNP</option>
55 </param>
56 <when value="exclude_dbsnp">
57 <!-- Do nothing here -->
58 </when>
59 <when value="set_dbsnp">
60 <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
61 <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/>
62 </when>
63 </conditional>
64
65 <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"/>
66 <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"/>
67
68 <expand macro="gatk_param_type_conditional" />
69
70 </inputs>
71 <outputs>
72 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
73 </outputs>
74 <tests>
75 <test>
76 <param name="reference_source_selector" value="history" />
77 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
78 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
79 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
80 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
81 <param name="warn_on_errors" value="True"/>
82 <param name="do_not_validate_filtered_records" />
83 <param name="gatk_param_type_selector" value="basic" />
84 <output name="output_log" file="gatk/gatk_validate_variants/gatk_validate_variants_out_1.log.contains" compare="contains" />
85 </test>
86 </tests>
87 <help>
88 **What it does**
89
90 Validates a variants file.
91
92 For more information on using the ValidateVariants module, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_ValidateVariants.html&gt;`_.
93
94 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
95
96 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
97
98 ------
99
100 **Inputs**
101
102 GenomeAnalysisTK: ValidateVariants accepts variant files as input.
103
104
105 **Outputs**
106
107 The output is a log of variant validation.
108
109
110 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
111
112 -------
113
114 **Settings**::
115
116 doNotValidateFilteredRecords should we skip validation on filtered records?
117 warnOnErrors should we just emit warnings on errors instead of terminating the run?
118
119 @CITATION_SECTION@
120 </help>
121 </tool>