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comparison variant_validate.xml @ 15:01ff8dd37d4d draft default tip

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author lz_hust
date Sat, 01 Jun 2019 07:20:41 -0400
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14:68426930d59c 15:01ff8dd37d4d
1 <tool id="gatk2_variant_validate" name="Validate Variants" version="@VERSION@.0">
2 <description></description>
3 <macros>
4 <import>gatk2_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
8 <command interpreter="python">
9 gatk2_wrapper.py
10 --stdout "${output_log}"
11 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
12 -p '
13 @JAR_PATH@
14 -T "ValidateVariants"
15
16 \$GATK2_SITE_OPTIONS
17
18 #if $reference_source.reference_source_selector != "history":
19 -R "${reference_source.ref_file.fields.path}"
20 #end if
21 ${warn_on_errors}
22 ${do_not_validate_filtered_records}
23 '
24 @DBSNP_OPTIONS@
25
26 #include source=$standard_gatk_options#
27 </command>
28 <inputs>
29
30 <conditional name="reference_source">
31 <expand macro="reference_source_selector_param" />
32 <when value="cached">
33 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
34 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
35 <options from_data_table="gatk2_picard_indexes">
36 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
37 </options>
38 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
39 </param>
40 </when>
41 <when value="history"> <!-- FIX ME!!!! -->
42 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
43 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
44 </when>
45 </conditional>
46 <expand macro="dbsnp_param" />
47
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"/>
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"/>
50
51 <expand macro="gatk_param_type_conditional" />
52
53 </inputs>
54 <outputs>
55 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
56 </outputs>
57 <tests>
58 <test>
59 <param name="reference_source_selector" value="history" />
60 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
61 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
62 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
63 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
64 <param name="dbsnp_rod_name" value="dbsnp" />
65 <param name="warn_on_errors" value="True"/>
66 <param name="do_not_validate_filtered_records" />
67 <param name="gatk_param_type_selector" value="basic" />
68 <output name="output_log" file="gatk/gatk_validate_variants/gatk_validate_variants_out_1.log.contains" compare="contains" />
69 </test>
70 </tests>
71 <help>
72 **What it does**
73
74 Validates a variants file.
75
76 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;`_.
77
78 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;`_.
79
80 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
81
82 ------
83
84 **Inputs**
85
86 GenomeAnalysisTK: ValidateVariants accepts variant files as input.
87
88
89 **Outputs**
90
91 The output is a log of variant validation.
92
93
94 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
95
96 -------
97
98 **Settings**::
99
100 doNotValidateFilteredRecords should we skip validation on filtered records?
101 warnOnErrors should we just emit warnings on errors instead of terminating the run?
102
103 @CITATION_SECTION@
104 </help>
105 <expand macro="citations" />
106 </tool>