Mercurial > repos > iuc > gatk2
comparison variant_eval.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 | 8bcc13094767 |
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-1:000000000000 | 0:340633249b3d |
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1 <tool id="gatk2_variant_eval" name="Eval 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"> | |
8 #from binascii import hexlify | |
9 | |
10 gatk2_wrapper.py | |
11 --stdout "${output_log}" | |
12 #for $var_count, $variant in enumerate( $reference_source.variants ): | |
13 -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}" | |
14 #end for | |
15 -p ' | |
16 @JAR_PATH@ | |
17 -T "VariantEval" | |
18 --out "${output_report}" | |
19 \$GATK2_SITE_OPTIONS | |
20 | |
21 @THREADS@ | |
22 | |
23 #if $reference_source.reference_source_selector != "history": | |
24 -R "${reference_source.ref_file.fields.path}" | |
25 #end if | |
26 ' | |
27 | |
28 #for $rod_binding in $comp_rod_bind: | |
29 -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}" | |
30 #if str( $rod_binding.comp_known_names ): | |
31 -p '--known_names "${rod_binding.comp_rod_name}"' | |
32 #end if | |
33 #end for | |
34 | |
35 #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp': | |
36 -d "--dbsnp:${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}" | |
37 #if str( $dbsnp_rod_bind_type.dbsnp_known_names ): | |
38 -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"' | |
39 #end if | |
40 #end if | |
41 | |
42 #include source=$standard_gatk_options# | |
43 | |
44 | |
45 ##start analysis specific options | |
46 #if $analysis_param_type.analysis_param_type_selector == "advanced": | |
47 #for $stratification in $analysis_param_type.stratifications: | |
48 #set $select_string = "--select_exps '%s' --select_names '%s'" % ( str( $stratification.select_exps ), str( $stratification.select_name ) ) | |
49 -o '${ hexlify( $select_string ) }' | |
50 #end for | |
51 -p ' | |
52 | |
53 #for $sample in $analysis_param_type.samples: | |
54 --sample "${sample.sample}" | |
55 #end for | |
56 | |
57 #if str( $analysis_param_type.stratification_modules ) != "None": | |
58 #for $stratification_module in str( $analysis_param_type.stratification_modules).split( ',' ): | |
59 --stratificationModule "${stratification_module}" | |
60 #end for | |
61 #end if | |
62 | |
63 ${analysis_param_type.do_not_use_all_standard_stratifications} | |
64 | |
65 #for $variant_type in $analysis_param_type.only_variants_of_type: | |
66 --onlyVariantsOfType "${variant_type.variant_type}" | |
67 #end for | |
68 | |
69 #if str( $analysis_param_type.eval_modules ) != "None": | |
70 #for $eval_module in str( $analysis_param_type.eval_modules).split( ',' ): | |
71 --evalModule "${eval_module}" | |
72 #end for | |
73 #end if | |
74 | |
75 ${analysis_param_type.do_not_use_all_standard_modules} | |
76 | |
77 #if str( $analysis_param_type.num_samples ) != "0": | |
78 --numSamples "${analysis_param_type.num_samples}" | |
79 #end if | |
80 | |
81 --minPhaseQuality "${analysis_param_type.min_phase_quality}" | |
82 | |
83 #if str( $analysis_param_type.family ): | |
84 --family_structure "${analysis_param_type.family}" | |
85 #end if | |
86 | |
87 --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}" | |
88 | |
89 #if str( $analysis_param_type.ancestral_alignments ) != "None": | |
90 --ancestralAlignments "${analysis_param_type.ancestral_alignments}" | |
91 #end if | |
92 ' | |
93 #if str( $analysis_param_type.known_cnvs ) != "None": | |
94 -d "--knownCNVs" "${analysis_param_type.known_cnvs}" "${analysis_param_type.known_cnvs.ext}" "input_known_cnvs" | |
95 #end if | |
96 | |
97 #if str( $analysis_param_type.strat_intervals ) != "None": | |
98 -d "--stratIntervals" "${analysis_param_type.strat_intervals}" "${analysis_param_type.strat_intervals.ext}" "input_strat_intervals" | |
99 #end if | |
100 #end if | |
101 </command> | |
102 <inputs> | |
103 | |
104 <conditional name="reference_source"> | |
105 <expand macro="reference_source_selector_param" /> | |
106 <when value="cached"> | |
107 <repeat name="variants" title="Variant" min="1" help="-eval,--eval &lt;eval&gt;"> | |
108 <param name="input_variant" type="data" format="vcf" label="Input variant file" /> | |
109 </repeat> | |
110 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
111 <options from_data_table="gatk2_picard_indexes"> | |
112 <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> --> | |
113 </options> | |
114 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
115 </param> | |
116 </when> | |
117 <when value="history"> <!-- FIX ME!!!! --> | |
118 <repeat name="variants" title="Variant" min="1" help="-eval,--eval &lt;eval&gt;"> | |
119 <param name="input_variant" type="data" format="vcf" label="Input variant file" /> | |
120 </repeat> | |
121 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | |
122 </when> | |
123 </conditional> | |
124 | |
125 <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &lt;comp&gt;"> | |
126 <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" /> | |
127 <param name="comp_rod_name" type="text" value="Unnamed" label="Comparison ROD Name"/> | |
128 <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" help="-knownName,--known_names &lt;known_names&gt;"/> | |
129 </repeat> | |
130 | |
131 <conditional name="dbsnp_rod_bind_type"> | |
132 <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &lt;dbsnp&gt;"> | |
133 <option value="set_dbsnp" selected="True">Set dbSNP</option> | |
134 <option value="exclude_dbsnp">Don't set dbSNP</option> | |
135 </param> | |
136 <when value="exclude_dbsnp"> | |
137 <!-- Do nothing here --> | |
138 </when> | |
139 <when value="set_dbsnp"> | |
140 <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" /> | |
141 <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="dbSNP ROD Name"/> | |
142 <param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" help="-knownName,--known_names &lt;known_names&gt;" /> | |
143 </when> | |
144 </conditional> | |
145 | |
146 <expand macro="gatk_param_type_conditional" /> | |
147 | |
148 | |
149 <expand macro="analysis_type_conditional"> | |
150 <repeat name="stratifications" title="Stratification"> | |
151 <param name="select_exps" value="" type="text" label="Stratification Expression" help="-select,--select_exps &lt;select_exps&gt;"> | |
152 <sanitizer> | |
153 <valid initial="string.printable"> | |
154 <remove value="'"/> | |
155 </valid> | |
156 <mapping initial="none"/> | |
157 </sanitizer> | |
158 </param> | |
159 <param name="select_name" value="" type="text" label="Name" help="-selectName,--select_names &lt;select_names&gt;"/> | |
160 </repeat> | |
161 | |
162 <repeat name="samples" title="Sample" help="-sn,--sample &lt;sample&gt;"> | |
163 <param name="sample" value="" type="text" label="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context"/> | |
164 </repeat> | |
165 | |
166 <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" help="-ST,--stratificationModule &lt;stratificationModule&gt;" > | |
167 <!-- do these need individual options also? gatk wiki has little info --> | |
168 <option value="AlleleFrequency" /> | |
169 <option value="AlleleCount" /> | |
170 <option value="CompRod" /> | |
171 <option value="Contig" /> | |
172 <option value="CpG" /> | |
173 <option value="Degeneracy" /> | |
174 <option value="EvalRod" /> | |
175 <option value="Filter" /> | |
176 <option value="FunctionalClass" /> | |
177 <option value="JexlExpression" /> | |
178 <option value="Sample" /> | |
179 <option value="IntervalStratification" /> | |
180 </param> | |
181 <param name="do_not_use_all_standard_stratifications" checked="false" type="boolean" truevalue="--doNotUseAllStandardStratifications" falsevalue="" label="Do not use the standard stratification modules by default" help="-noST,--doNotUseAllStandardStratifications" /> | |
182 | |
183 <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType"> | |
184 <param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/> | |
185 </repeat> | |
186 | |
187 <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" help="-EV,--evalModule &lt;evalModule&gt;" > | |
188 <!-- do these need individual options also? gatk wiki has little info --> | |
189 <option value="ACTransitionTable" /> | |
190 <option value="AlleleFrequencyComparison" /> | |
191 <option value="AminoAcidTransition" /> | |
192 <option value="CompOverlap" /> | |
193 <option value="CountVariants" /> | |
194 <option value="GenotypeConcordance" /> | |
195 <option value="GenotypePhasingEvaluator" /> | |
196 <option value="IndelMetricsByAC" /> | |
197 <option value="IndelStatistics" /> | |
198 <option value="MendelianViolationEvaluator" /> | |
199 <option value="PrintMissingComp" /> | |
200 <option value="PrivatePermutations" /> | |
201 <option value="SimpleMetricsByAC" /> | |
202 <option value="ThetaVariantEvaluator" /> | |
203 <option value="TiTvVariantEvaluator" /> | |
204 <option value="VariantQualityScore" /> | |
205 </param> | |
206 <param name="do_not_use_all_standard_modules" checked="false" type="boolean" truevalue="--doNotUseAllStandardModules" falsevalue="" label="Do not use the standard eval modules by default" help="-noEV,--doNotUseAllStandardModules" /> | |
207 | |
208 <param name="num_samples" type="integer" label="Number of samples (used if no samples are available in the VCF file" value="0" help="-ns,--numSamples &lt;numSamples&gt;"/> | |
209 <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &lt;minPhaseQuality&gt;"/> | |
210 <param name="family" type="text" value="" label="If provided, genotypes in will be examined for mendelian violations: this argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined" help="--family_structure"/> | |
211 <param name="mendelian_violation_qual_threshold" type="integer" label="Minimum genotype QUAL score for each trio member required to accept a site as a violation" value="50" help="-mvq,--mendelianViolationQualThreshold &lt;mendelianViolationQualThreshold&gt;"/> | |
212 <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &lt;ancestralAlignments&gt;" /> | |
213 <param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" help="-knownCNVs,--knownCNVs &lt;knownCNVs&gt;" /> | |
214 <param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" help="-stratIntervals,--stratIntervals &lt;stratIntervals&gt;" /> | |
215 | |
216 </expand> | |
217 | |
218 | |
219 </inputs> | |
220 <outputs> | |
221 <data format="gatk_report" name="output_report" label="${tool.name} on ${on_string} (report)" /> | |
222 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
223 </outputs> | |
224 <tests> | |
225 <test> | |
226 <param name="reference_source_selector" value="history" /> | |
227 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
228 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> | |
229 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" /> | |
230 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> | |
231 <param name="dbsnp_known_names" value="True"/> | |
232 <param name="comp_rod_bind" value="0" /> | |
233 <param name="gatk_param_type_selector" value="basic" /> | |
234 <param name="analysis_param_type_selector" value="basic" /> | |
235 <output name="output_report" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.gatk_report" /> | |
236 <output name="output_log" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.log.contains" compare="contains" /> | |
237 </test> | |
238 </tests> | |
239 <help> | |
240 **What it does** | |
241 | |
242 General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more) | |
243 | |
244 For more information on using the VariantEval module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_varianteval_VariantEval.html>`_. | |
245 | |
246 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
247 | |
248 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
249 | |
250 ------ | |
251 | |
252 **Inputs** | |
253 | |
254 GenomeAnalysisTK: VariantEval accepts variant files as input. | |
255 | |
256 | |
257 **Outputs** | |
258 | |
259 The output is a table of variant evaluation. | |
260 | |
261 | |
262 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
263 | |
264 ------- | |
265 | |
266 **Settings**:: | |
267 | |
268 out An output file presented to the walker. Will overwrite contents if file exists. | |
269 list List the available eval modules and exit | |
270 select_exps One or more stratifications to use when evaluating the data | |
271 select_names Names to use for the list of stratifications (must be a 1-to-1 mapping) | |
272 sample Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context | |
273 known_names Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets | |
274 stratificationModule One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified) | |
275 doNotUseAllStandardStratifications Do not use the standard stratification modules by default (instead, only those that are specified with the -S option) | |
276 onlyVariantsOfType If provided, only variants of these types will be considered during the evaluation, in | |
277 evalModule One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified) | |
278 doNotUseAllStandardModules Do not use the standard modules by default (instead, only those that are specified with the -E option) | |
279 numSamples Number of samples (used if no samples are available in the VCF file | |
280 minPhaseQuality Minimum phasing quality | |
281 family_structure If provided, genotypes in will be examined for mendelian violations: this argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined | |
282 mendelianViolationQualThreshold Minimum genotype QUAL score for each trio member required to accept a site as a violation | |
283 ancestralAlignments Fasta file with ancestral alleles | |
284 | |
285 @CITATION_SECTION@ | |
286 </help> | |
287 </tool> |