Mercurial > repos > iuc > gatk2
comparison variant_select.xml @ 0:340633249b3d draft
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author | bgruening |
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date | Mon, 02 Dec 2013 06:18:36 -0500 |
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children | f244b8209eb8 |
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-1:000000000000 | 0:340633249b3d |
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1 <tool id="gatk2_variant_select" name="Select Variants" version="0.0.7"> | |
2 <description>from VCF files</description> | |
3 <expand macro="requirements" /> | |
4 <macros> | |
5 <import>gatk2_macros.xml</import> | |
6 </macros> | |
7 <command interpreter="python"> | |
8 #from binascii import hexlify | |
9 | |
10 gatk2_wrapper.py | |
11 --stdout "${output_log}" | |
12 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" | |
13 -p ' | |
14 @JAR_PATH@ | |
15 -T "SelectVariants" | |
16 \$GATK2_SITE_OPTIONS | |
17 | |
18 @THREADS@ | |
19 -o "${output_vcf}" | |
20 | |
21 #if $reference_source.reference_source_selector != "history": | |
22 -R "${reference_source.ref_file.fields.path}" | |
23 #end if | |
24 ' | |
25 -p ' | |
26 #if $input_concordance: | |
27 --concordance "${input_concordance}" | |
28 #end if | |
29 #if $input_discordance: | |
30 --discordance "${input_discordance}" | |
31 #end if | |
32 | |
33 #for $exclude_sample_name in $exclude_sample_name_repeat: | |
34 --exclude_sample_name "${exclude_sample_name.exclude_sample_name}" | |
35 #end for | |
36 | |
37 ${exclude_filtered} | |
38 | |
39 #for $sample_name in $sample_name_repeat: | |
40 --sample_name "${sample_name.sample_name}" | |
41 #end for | |
42 ' | |
43 | |
44 #for $select_expressions in $select_expressions_repeat: | |
45 #set $select_expression = "--select_expressions '%s'" % ( str( $select_expressions.select_expressions ) ) | |
46 -o '${ hexlify( $select_expression ) }' | |
47 #end for | |
48 | |
49 ##start tool specific options | |
50 #if str( $analysis_param_type.analysis_param_type_selector ) == 'advanced': | |
51 -p ' | |
52 #for $exclude_sample_file in $analysis_param_type.exclude_sample_file_repeat: | |
53 --exclude_sample_file "${exclude_sample_file.exclude_sample_file}" | |
54 #end for | |
55 | |
56 #for $sample_file in $analysis_param_type.sample_file_repeat: | |
57 --sample_file "${ample_file.sample_file}" | |
58 #end for | |
59 | |
60 #if $analysis_param_type.input_keep_ids: | |
61 --keepIDs "${analysis_param_type.input_keep_ids}" | |
62 #end if | |
63 | |
64 ${analysis_param_type.keep_original_AC} | |
65 | |
66 ${analysis_param_type.mendelian_violation} | |
67 | |
68 --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}" | |
69 | |
70 --remove_fraction_genotypes "${analysis_param_type.remove_fraction_genotypes}" | |
71 | |
72 --restrictAllelesTo "${analysis_param_type.restrict_alleles_to}" | |
73 | |
74 #if str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_fraction': | |
75 --select_random_fraction "${analysis_param_type.select_random_type.select_random_fraction}" | |
76 #elif str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_number': | |
77 --select_random_number "${analysis_param_type.select_random_type.select_random_number}" | |
78 #end if | |
79 | |
80 #if $analysis_param_type.select_type_to_include: | |
81 #for $type_to_include in str( $analysis_param_type.select_type_to_include ).split( ',' ): | |
82 --selectTypeToInclude "${type_to_include}" | |
83 #end for | |
84 #end if | |
85 | |
86 ${analysis_param_type.exclude_non_variants} | |
87 ' | |
88 | |
89 #for $sample_expressions in $analysis_param_type.sample_expressions_repeat: | |
90 #set $sample_expression = "--sample_expressions '%s'" % ( str( $sample_expressions.sample_expressions ) ) | |
91 -o '${ hexlify( $sample_expression ) }' | |
92 #end for | |
93 | |
94 #end if | |
95 ##end tool specific options | |
96 | |
97 #include source=$standard_gatk_options# | |
98 | |
99 | |
100 </command> | |
101 <inputs> | |
102 <conditional name="reference_source"> | |
103 <expand macro="reference_source_selector_param" /> | |
104 <when value="cached"> | |
105 <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &lt;variant&gt;" /> | |
106 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
107 <options from_data_table="gatk2_picard_indexes"> | |
108 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> | |
109 </options> | |
110 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
111 </param> | |
112 </when> | |
113 <when value="history"> <!-- FIX ME!!!! --> | |
114 <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &lt;variant&gt;" /> | |
115 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | |
116 </when> | |
117 </conditional> | |
118 | |
119 <repeat name="select_expressions_repeat" title="Criteria to use when selecting the data" help="-select,--select_expressions &lt;select_expressions&gt;"> | |
120 <param name="select_expressions" type="text" label="JEXL expression"> | |
121 <sanitizer> | |
122 <valid initial="string.printable"> | |
123 <remove value="'"/> | |
124 </valid> | |
125 <mapping initial="none"/> | |
126 </sanitizer> | |
127 </param> | |
128 </repeat> | |
129 | |
130 <param name="input_concordance" type="data" format="vcf" label="Output variants that were also called in this comparison track" optional="True" help="-conc,--concordance &lt;concordance&gt;"/> | |
131 <param name="input_discordance" type="data" format="vcf" label="Output variants that were not called in this comparison track" optional="True" help="-disc,--discordance &lt;discordance&gt;"/> | |
132 | |
133 <repeat name="sample_name_repeat" title="Include Samples by name" help="-sn,--sample_name &lt;sample_name&gt;"> | |
134 <param name="sample_name" type="text" label="Include genotypes from this sample"/> | |
135 </repeat> | |
136 | |
137 <repeat name="exclude_sample_name_repeat" title="Exclude Samples by name" help="-xl_sn,--exclude_sample_name &lt;exclude_sample_name&gt;"> | |
138 <param name="exclude_sample_name" type="text" label="Exclude genotypes from this sample"/> | |
139 </repeat> | |
140 | |
141 <param name="exclude_filtered" type="boolean" truevalue="--excludeFiltered" falsevalue="" label="Don't include filtered loci in the analysis" help="-ef,--excludeFiltered" /> | |
142 | |
143 <expand macro="gatk_param_type_conditional" /> | |
144 | |
145 | |
146 <expand macro="analysis_type_conditional"> | |
147 | |
148 <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file" help="-xl_sf,--exclude_sample_file &lt;exclude_sample_file&gt;"> | |
149 <param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/> | |
150 </repeat> | |
151 | |
152 <repeat name="sample_file_repeat" title="Samples by file" help="-sf,--sample_file &lt;sample_file&gt;"> | |
153 <param name="sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to include" /> | |
154 </repeat> | |
155 | |
156 <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &lt;keepIDs&gt;"/> | |
157 | |
158 <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" help="-keepOriginalAC,--keepOriginalAC" /> | |
159 | |
160 <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" help="-mv,--mendelianViolation" /> | |
161 | |
162 <param name="mendelian_violation_qual_threshold" type="float" label="Minimum genotype QUAL score for each trio member required to accept a site as a mendelian violation" value="0" help="-mvq,--mendelianViolationQualThreshold &lt;mendelianViolationQualThreshold&gt;" /> | |
163 | |
164 <param name="remove_fraction_genotypes" type="float" label="Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall" value="0" min="0" max="1" help="-fractionGenotypes,--remove_fraction_genotypes &lt;remove_fraction_genotypes&gt;" /> | |
165 | |
166 <param name="restrict_alleles_to" type="select" label="Select only variants of a particular allelicity" help="-restrictAllelesTo,--restrictAllelesTo &lt;restrictAllelesTo&gt;"> | |
167 <option value="ALL" selected="True">ALL</option> | |
168 <option value="MULTIALLELIC">MULTIALLELIC</option> | |
169 <option value="BIALLELIC">BIALLELIC</option> | |
170 </param> | |
171 | |
172 <repeat name="sample_expressions_repeat" title="Regular expression to select many samples from the ROD tracks provided" help="-se,--sample_expressions &lt;sample_expressions&gt;"> | |
173 <param name="sample_expressions" type="text" label="Regular expression"> | |
174 <sanitizer> | |
175 <valid initial="string.printable"> | |
176 <remove value="'"/> | |
177 </valid> | |
178 <mapping initial="none"/> | |
179 </sanitizer> | |
180 </param> | |
181 </repeat> | |
182 | |
183 <conditional name="select_random_type"> | |
184 <param name="select_random_type_selector" type="select" label="Select a random subset of variants"> | |
185 <option value="select_all" selected="True">Use all variants</option> | |
186 <option value="select_random_fraction">Select random fraction</option> | |
187 <option value="select_random_number">Select random number</option> | |
188 </param> | |
189 <when value="select_all"> | |
190 <!-- Do nothing here --> | |
191 </when> | |
192 <when value="select_random_fraction"> | |
193 <param name="select_random_fraction" type="float" value="0" label="Fraction" min="0" max="1" help="-fraction,--select_random_fraction &lt;select_random_fraction&gt;"/> | |
194 </when> | |
195 <when value="select_random_number"> | |
196 <param name="select_random_number" type="integer" value="0" label="Count" help="-number,--select_random_number &lt;select_random_number&gt;" /> | |
197 </when> | |
198 </conditional> | |
199 | |
200 <param name="exclude_non_variants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the subsetting procedure" help="-env,--excludeNonVariants" /> | |
201 | |
202 <param name="select_type_to_include" type="select" label="Select only a certain type of variants from the input file" multiple="True" display="checkboxes" help="-selectType,--selectTypeToInclude &lt;selectTypeToInclude&gt;"> | |
203 <option value="INDEL">INDEL</option> | |
204 <option value="SNP">SNP</option> | |
205 <option value="MIXED">MIXED</option> | |
206 <option value="MNP">MNP</option> | |
207 <option value="SYMBOLIC">SYMBOLIC</option> | |
208 <option value="NO_VARIATION">NO_VARIATION</option> | |
209 </param> | |
210 </expand> | |
211 | |
212 </inputs> | |
213 <outputs> | |
214 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> | |
215 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
216 </outputs> | |
217 <tests> | |
218 <test> | |
219 <param name="reference_source_selector" value="history" /> | |
220 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
221 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> | |
222 <param name="select_expressions_repeat" value="0" /> | |
223 <param name="input_concordance" /> | |
224 <param name="input_discordance" /> | |
225 <param name="exclude_sample_name_repeat" value="0" /> | |
226 <param name="exclude_filtered" /> | |
227 <param name="sample_name_repeat" value="0" /> | |
228 <param name="gatk_param_type_selector" value="basic" /> | |
229 <param name="analysis_param_type_selector" value="basic" /> | |
230 <output name="output_vcf" file="gatk/gatk_variant_select/gatk_variant_select_out_1.vcf" lines_diff="4" /> | |
231 <output name="output_log" file="gatk/gatk_variant_select/gatk_variant_select_out_1.log.contains" compare="contains" /> | |
232 </test> | |
233 </tests> | |
234 <help> | |
235 **What it does** | |
236 | |
237 Often, a VCF containing many samples and/or variants will need to be subset in order to facilitate certain analyses (e.g. comparing and contrasting cases vs. controls; extracting variant or non-variant loci that meet certain requirements, displaying just a few samples in a browser like IGV, etc.). SelectVariants can be used for this purpose. Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion, i.e. "DP > 1000" (depth of coverage greater than 1000x), "AF < 0.25" (sites with allele frequency less than 0.25). These JEXL expressions are documented in the `Using JEXL expressions section <http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk>`_. One can optionally include concordance or discordance tracks for use in selecting overlapping variants. | |
238 | |
239 For more information on using the SelectVariants module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_SelectVariants.html>`_. | |
240 | |
241 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
242 | |
243 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
244 | |
245 ------ | |
246 | |
247 **Inputs** | |
248 | |
249 GenomeAnalysisTK: SelectVariants accepts a VCF input file. | |
250 | |
251 | |
252 **Outputs** | |
253 | |
254 The output is in VCF format. | |
255 | |
256 | |
257 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
258 | |
259 ------- | |
260 | |
261 **Settings**:: | |
262 | |
263 | |
264 out VCFWriter stdout File to which variants should be written | |
265 variant RodBinding[VariantContext] NA Input VCF file | |
266 concordance RodBinding[VariantContext] none Output variants that were also called in this comparison track | |
267 discordance RodBinding[VariantContext] none Output variants that were not called in this comparison track | |
268 exclude_sample_file Set[File] [] File containing a list of samples (one per line) to exclude. Can be specified multiple times | |
269 exclude_sample_name Set[String] [] Exclude genotypes from this sample. Can be specified multiple times | |
270 excludeFiltered boolean false Don't include filtered loci in the analysis | |
271 excludeNonVariants boolean false Don't include loci found to be non-variant after the subsetting procedure | |
272 keepIDs File NA Only emit sites whose ID is found in this file (one ID per line) | |
273 keepOriginalAC boolean false Don't update the AC, AF, or AN values in the INFO field after selecting | |
274 mendelianViolation Boolean false output mendelian violation sites only | |
275 mvq double 0.0 Minimum genotype QUAL score for each trio member required to accept a site as a violation | |
276 remove_fraction_genotypes double 0.0 Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall | |
277 restrictAllelesTo NumberAlleleRestriction ALL Select only variants of a particular allelicity. Valid options are ALL (default), MULTIALLELIC or BIALLELIC | |
278 sample_expressions Set[String] NA Regular expression to select many samples from the ROD tracks provided. Can be specified multiple times | |
279 sample_file Set[File] NA File containing a list of samples (one per line) to include. Can be specified multiple times | |
280 sample_name Set[String] [] Include genotypes from this sample. Can be specified multiple times | |
281 select_expressions ArrayList[String] [] One or more criteria to use when selecting the data | |
282 select_random_fraction double 0.0 Selects a fraction (a number between 0 and 1) of the total variants at random from the variant track | |
283 select_random_number int 0 Selects a number of variants at random from the variant track | |
284 selectTypeToInclude List[Type] [] Select only a certain type of variants from the input file. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Can be specified multiple times | |
285 | |
286 @CITATION_SECTION@ | |
287 </help> | |
288 </tool> |