Mercurial > repos > devteam > variant_apply_recalibration
comparison variant_apply_recalibration.xml @ 0:c06c30bfcf1b draft default tip
Imported from capsule None
author | devteam |
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date | Tue, 01 Apr 2014 09:11:48 -0400 |
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-1:000000000000 | 0:c06c30bfcf1b |
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1 <tool id="gatk_variant_apply_recalibration" name="Apply Variant Recalibration" 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 #for $var_count, $variant in enumerate( $reference_source.variants ): | |
13 -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}" | |
14 #end for | |
15 -p 'java | |
16 -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar" | |
17 -T "ApplyRecalibration" | |
18 ##--num_threads 4 ##hard coded, for now | |
19 -et "NO_ET" ##ET no phone home | |
20 #if $reference_source.reference_source_selector != "history": | |
21 -R "${reference_source.ref_file.fields.path}" | |
22 #end if | |
23 --recal_file "${reference_source.input_recal}" | |
24 --tranches_file "${reference_source.input_tranches}" | |
25 --out "${output_variants}" | |
26 ' | |
27 | |
28 #include source=$standard_gatk_options# | |
29 | |
30 ##start analysis specific options | |
31 -p ' | |
32 --mode "${mode}" | |
33 | |
34 #for $ignore_filter in $ignore_filters: | |
35 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector ) | |
36 #if $ignore_filter_name == "custom": | |
37 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name ) | |
38 #end if | |
39 --ignore_filter "${ignore_filter_name}" | |
40 #end for | |
41 --ts_filter_level "${ts_filter_level}" | |
42 ' | |
43 </command> | |
44 <inputs> | |
45 <conditional name="reference_source"> | |
46 <expand macro="reference_source_selector_param" /> | |
47 <when value="cached"> | |
48 <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"> | |
49 <param name="input_variants" type="data" format="vcf" label="Variant file to annotate"/> | |
50 </repeat> | |
51 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" /> | |
52 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" /> | |
53 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
54 <options from_data_table="gatk_picard_indexes"> | |
55 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --> | |
56 </options> | |
57 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
58 </param> | |
59 </when> | |
60 <when value="history"> <!-- FIX ME!!!! --> | |
61 <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"> | |
62 <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" /> | |
63 </repeat> | |
64 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" /> | |
65 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" /> | |
66 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | |
67 </when> | |
68 </conditional> | |
69 | |
70 <expand macro="gatk_param_type_conditional" /> | |
71 | |
72 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &lt;mode&gt;"> | |
73 <option value="SNP" selected="True">SNP</option> | |
74 <option value="INDEL">INDEL</option> | |
75 <option value="BOTH">BOTH</option> | |
76 </param> | |
77 <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &lt;ignore_filter&gt;"> | |
78 <conditional name="ignore_filter_type"> | |
79 <param name="ignore_filter_type_selector" type="select" label="Filter Type"> | |
80 <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option> | |
81 <option value="LowQual" >LowQual</option> | |
82 <option value="custom" selected="True">Other</option> | |
83 </param> | |
84 <when value="custom"> | |
85 <param name="filter_name" type="text" value="" label="Filter name"/> | |
86 </when> | |
87 <when value="HARD_TO_VALIDATE" /> | |
88 <when value="LowQual" /> | |
89 </conditional> | |
90 </repeat> | |
91 <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &lt;ts_filter_level&gt;"/> | |
92 </inputs> | |
93 <outputs> | |
94 <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (Variants File)" /> | |
95 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
96 </outputs> | |
97 <tests> | |
98 <!-- ADD TESTS --> | |
99 </tests> | |
100 <help> | |
101 **What it does** | |
102 | |
103 Applies cuts to the input vcf file (by adding filter lines) to achieve the desired novel FDR levels which were specified during VariantRecalibration | |
104 | |
105 For more information on using the ApplyRecalibration module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration>`_. | |
106 | |
107 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_. | |
108 | |
109 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_. | |
110 | |
111 ------ | |
112 | |
113 **Inputs** | |
114 | |
115 GenomeAnalysisTK: ApplyRecalibration accepts a variant input file, a recalibration file and a tranches file. | |
116 | |
117 | |
118 **Outputs** | |
119 | |
120 The output is in VCF format. | |
121 | |
122 | |
123 Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats. | |
124 | |
125 ------- | |
126 | |
127 **Settings**:: | |
128 | |
129 | |
130 recal_file The output recal file used by ApplyRecalibration | |
131 tranches_file The input tranches file describing where to cut the data | |
132 out The output filtered, recalibrated VCF file | |
133 ts_filter_level The truth sensitivity level at which to start filtering | |
134 ignore_filter If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file | |
135 mode Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously. (SNP|INDEL|BOTH) | |
136 | |
137 @CITATION_SECTION@ | |
138 </help> | |
139 </tool> |