Mercurial > repos > iuc > gatk2
annotate variant_eval.xml @ 15:a3247b69fa59 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 898393cb5c244c8fab2e965f003ae3991bcb655e
| author | iuc |
|---|---|
| date | Mon, 04 Apr 2016 06:33:05 -0400 |
| parents | 669a23f1f4b5 |
| children |
| rev | line source |
|---|---|
|
13
669a23f1f4b5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents:
11
diff
changeset
|
1 <tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.1"> |
| 0 | 2 <description></description> |
| 3 <macros> | |
| 4 <import>gatk2_macros.xml</import> | |
| 5 </macros> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
6 <expand macro="requirements" /> |
|
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
7 <expand macro="version_command" /> |
| 1 | 8 <command interpreter="python"> |
| 0 | 9 #from binascii import hexlify |
| 1 | 10 |
| 11 gatk2_wrapper.py | |
| 0 | 12 --stdout "${output_log}" |
|
13
669a23f1f4b5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents:
11
diff
changeset
|
13 #for $var_count, $variant in enumerate( $reference_source.input_variants ): |
|
669a23f1f4b5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents:
11
diff
changeset
|
14 -d "--eval:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}" |
| 1 | 15 #end for |
| 16 -p ' | |
| 17 @JAR_PATH@ | |
| 0 | 18 -T "VariantEval" |
| 19 --out "${output_report}" | |
| 20 \$GATK2_SITE_OPTIONS | |
| 21 | |
| 22 @THREADS@ | |
| 23 | |
| 24 #if $reference_source.reference_source_selector != "history": | |
| 25 -R "${reference_source.ref_file.fields.path}" | |
| 26 #end if | |
| 27 ' | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
28 |
| 0 | 29 #for $rod_binding in $comp_rod_bind: |
| 30 -d "--comp:${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}" | |
| 31 #if str( $rod_binding.comp_known_names ): | |
| 32 -p '--known_names "${rod_binding.comp_rod_name}"' | |
| 33 #end if | |
| 34 #end for | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
35 |
| 4 | 36 #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp' |
| 0 | 37 -d "--dbsnp:${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}" |
| 4 | 38 #if $dbsnp_rod_bind_type.dbsnp_known_names |
| 0 | 39 -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"' |
| 40 #end if | |
| 41 #end if | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
42 |
| 0 | 43 #include source=$standard_gatk_options# |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
44 |
| 0 | 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 ' | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
52 |
| 0 | 53 #for $sample in $analysis_param_type.samples: |
| 54 --sample "${sample.sample}" | |
| 55 #end for | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
56 |
| 0 | 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 | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
62 |
| 0 | 63 ${analysis_param_type.do_not_use_all_standard_stratifications} |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
64 |
| 0 | 65 #for $variant_type in $analysis_param_type.only_variants_of_type: |
| 66 --onlyVariantsOfType "${variant_type.variant_type}" | |
| 67 #end for | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
68 |
| 0 | 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 | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
74 |
| 0 | 75 ${analysis_param_type.do_not_use_all_standard_modules} |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
76 |
| 0 | 77 #if str( $analysis_param_type.num_samples ) != "0": |
| 78 --numSamples "${analysis_param_type.num_samples}" | |
| 79 #end if | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
80 |
| 0 | 81 --minPhaseQuality "${analysis_param_type.min_phase_quality}" |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
82 |
| 0 | 83 --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}" |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
84 |
| 0 | 85 #if str( $analysis_param_type.ancestral_alignments ) != "None": |
| 86 --ancestralAlignments "${analysis_param_type.ancestral_alignments}" | |
| 87 #end if | |
| 88 ' | |
| 89 #if str( $analysis_param_type.known_cnvs ) != "None": | |
| 90 -d "--knownCNVs" "${analysis_param_type.known_cnvs}" "${analysis_param_type.known_cnvs.ext}" "input_known_cnvs" | |
| 91 #end if | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
92 |
| 0 | 93 #if str( $analysis_param_type.strat_intervals ) != "None": |
| 94 -d "--stratIntervals" "${analysis_param_type.strat_intervals}" "${analysis_param_type.strat_intervals.ext}" "input_strat_intervals" | |
| 95 #end if | |
| 96 #end if | |
| 97 </command> | |
| 98 <inputs> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
99 |
| 0 | 100 <conditional name="reference_source"> |
| 101 <expand macro="reference_source_selector_param" /> | |
| 102 <when value="cached"> | |
|
13
669a23f1f4b5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents:
11
diff
changeset
|
103 <expand macro="input_variants" help="-eval,--eval &lt;eval&gt;"/> |
| 0 | 104 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> |
| 105 <options from_data_table="gatk2_picard_indexes"> | |
| 106 <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> --> | |
| 107 </options> | |
| 108 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 109 </param> | |
| 110 </when> | |
| 111 <when value="history"> <!-- FIX ME!!!! --> | |
|
13
669a23f1f4b5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents:
11
diff
changeset
|
112 <expand macro="input_variants" help="-eval,--eval &lt;eval&gt;" /> |
| 0 | 113 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> |
| 114 </when> | |
| 115 </conditional> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
116 |
| 4 | 117 <repeat name="comp_rod_bind" title="Comparison Reference-Ordered Data (ROD) file" help="-comp,--comp &lt;comp&gt;"> |
| 0 | 118 <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" /> |
| 4 | 119 <param name="comp_rod_name" type="text" value="" label="Comparison ROD name"> |
| 120 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator> | |
| 121 </param> | |
| 122 <param name="comp_known_names" type="boolean" label="Use comparison ROD file as known_names" help="-knownName,--known_names &lt;known_names&gt;"/> | |
| 0 | 123 </repeat> |
| 124 <conditional name="dbsnp_rod_bind_type"> | |
| 4 | 125 <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP Reference-Ordered Data (ROD) file" help="-D,--dbsnp &lt;dbsnp&gt;"> |
| 0 | 126 <option value="set_dbsnp" selected="True">Set dbSNP</option> |
| 127 <option value="exclude_dbsnp">Don't set dbSNP</option> | |
| 128 </param> | |
| 4 | 129 <when value="exclude_dbsnp" /> |
| 0 | 130 <when value="set_dbsnp"> |
| 131 <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" /> | |
| 4 | 132 <param name="dbsnp_rod_name" type="text" value="dbsnp" label="dbsnp ROD name"> |
| 133 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator> | |
| 134 </param> | |
| 135 <param name="dbsnp_known_names" type="boolean" label="Use dbSNP ROD file as known_names" help="-knownName,--known_names &lt;known_names&gt;" /> | |
| 0 | 136 </when> |
| 137 </conditional> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
138 |
| 0 | 139 <expand macro="gatk_param_type_conditional" /> |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
140 |
| 0 | 141 <expand macro="analysis_type_conditional"> |
| 142 <repeat name="stratifications" title="Stratification"> | |
| 143 <param name="select_exps" value="" type="text" label="Stratification Expression" help="-select,--select_exps &lt;select_exps&gt;"> | |
| 144 <sanitizer> | |
| 145 <valid initial="string.printable"> | |
| 146 <remove value="'"/> | |
| 147 </valid> | |
| 148 <mapping initial="none"/> | |
| 149 </sanitizer> | |
| 150 </param> | |
| 151 <param name="select_name" value="" type="text" label="Name" help="-selectName,--select_names &lt;select_names&gt;"/> | |
| 152 </repeat> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
153 |
| 0 | 154 <repeat name="samples" title="Sample" help="-sn,--sample &lt;sample&gt;"> |
| 155 <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"/> | |
| 156 </repeat> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
157 |
| 0 | 158 <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;" > |
| 6 | 159 <option value="AlleleCount" /> |
| 0 | 160 <option value="AlleleFrequency" /> |
| 161 <option value="CompRod" /> | |
| 162 <option value="Contig" /> | |
| 163 <option value="CpG" /> | |
| 164 <option value="Degeneracy" /> | |
| 165 <option value="EvalRod" /> | |
| 166 <option value="Filter" /> | |
| 167 <option value="FunctionalClass" /> | |
| 6 | 168 <option value="IndelSize" /> |
| 169 <option value="IntervalStratification" /> | |
| 0 | 170 <option value="JexlExpression" /> |
| 6 | 171 <option value="Novelty" /> |
| 172 <option value="OneBPIndel" /> | |
| 0 | 173 <option value="Sample" /> |
| 6 | 174 <option value="SnpEffPositionModifier" /> |
| 175 <option value="TandemRepeat" /> | |
| 176 <option value="VariantType" /> | |
| 0 | 177 </param> |
| 178 <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" /> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
179 |
| 0 | 180 <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType"> |
| 181 <param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/> | |
| 182 </repeat> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
183 |
| 0 | 184 <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;" > |
| 185 <option value="CompOverlap" /> | |
| 186 <option value="CountVariants" /> | |
| 6 | 187 <option value="IndelLengthHistogram" /> |
| 188 <option value="IndelSummary" /> | |
| 0 | 189 <option value="MendelianViolationEvaluator" /> |
| 6 | 190 <option value="MultiallelicSummary" /> |
| 0 | 191 <option value="PrintMissingComp" /> |
| 192 <option value="ThetaVariantEvaluator" /> | |
| 193 <option value="TiTvVariantEvaluator" /> | |
| 6 | 194 <option value="ValidationReport" /> |
| 195 <option value="VariantSummary" /> | |
| 0 | 196 </param> |
| 197 <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" /> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
198 |
| 0 | 199 <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;"/> |
| 200 <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &lt;minPhaseQuality&gt;"/> | |
| 201 <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;"/> | |
| 202 <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &lt;ancestralAlignments&gt;" /> | |
| 203 <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;" /> | |
| 204 <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;" /> | |
| 205 </expand> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
206 |
| 0 | 207 </inputs> |
| 208 <outputs> | |
| 209 <data format="gatk_report" name="output_report" label="${tool.name} on ${on_string} (report)" /> | |
| 210 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
| 211 </outputs> | |
| 212 <tests> | |
| 213 <test> | |
| 214 <param name="reference_source_selector" value="history" /> | |
| 215 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
| 216 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> | |
| 217 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" /> | |
| 218 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> | |
| 4 | 219 <param name="dbsnp_rod_name" value="dbsnp" /> |
| 0 | 220 <param name="dbsnp_known_names" value="True"/> |
| 221 <param name="comp_rod_bind" value="0" /> | |
| 222 <param name="gatk_param_type_selector" value="basic" /> | |
| 223 <param name="analysis_param_type_selector" value="basic" /> | |
| 224 <output name="output_report" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.gatk_report" /> | |
| 225 <output name="output_log" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.log.contains" compare="contains" /> | |
| 226 </test> | |
| 227 </tests> | |
| 228 <help> | |
| 229 **What it does** | |
| 230 | |
| 231 General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more) | |
| 232 | |
| 233 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>`_. | |
| 234 | |
| 235 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
| 236 | |
| 237 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
| 238 | |
| 239 ------ | |
| 240 | |
| 241 **Inputs** | |
| 242 | |
| 243 GenomeAnalysisTK: VariantEval accepts variant files as input. | |
| 244 | |
| 245 | |
| 246 **Outputs** | |
| 247 | |
| 248 The output is a table of variant evaluation. | |
| 249 | |
| 250 | |
| 251 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
| 252 | |
| 253 ------- | |
| 254 | |
| 255 **Settings**:: | |
| 256 | |
| 257 out An output file presented to the walker. Will overwrite contents if file exists. | |
| 258 list List the available eval modules and exit | |
| 259 select_exps One or more stratifications to use when evaluating the data | |
| 260 select_names Names to use for the list of stratifications (must be a 1-to-1 mapping) | |
| 261 sample Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context | |
| 262 known_names Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets | |
| 263 stratificationModule One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified) | |
| 264 doNotUseAllStandardStratifications Do not use the standard stratification modules by default (instead, only those that are specified with the -S option) | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
265 onlyVariantsOfType If provided, only variants of these types will be considered during the evaluation, in |
| 0 | 266 evalModule One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified) |
| 267 doNotUseAllStandardModules Do not use the standard modules by default (instead, only those that are specified with the -E option) | |
| 268 numSamples Number of samples (used if no samples are available in the VCF file | |
| 269 minPhaseQuality Minimum phasing quality | |
| 270 mendelianViolationQualThreshold Minimum genotype QUAL score for each trio member required to accept a site as a violation | |
| 271 ancestralAlignments Fasta file with ancestral alleles | |
| 272 | |
| 273 @CITATION_SECTION@ | |
| 274 </help> | |
| 6 | 275 <expand macro="citations" /> |
| 0 | 276 </tool> |