Mercurial > repos > jjohnson > gatk2
annotate variant_filtration.xml @ 35:a29c7d7d962d draft
Fix default read filter screening
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 01 Mar 2013 07:52:02 -0600 |
| parents | b99c25b0ad4d |
| children | 14d47237bb0a |
| rev | line source |
|---|---|
| 34 | 1 <tool id="gatk2_variant_filtration" name="Variant Filtration" version="0.0.7"> |
| 0 | 2 <description>on VCF files</description> |
| 3 <requirements> | |
|
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Update tool_dependencies to GATK v 2.3
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4 <requirement type="package" version="2.3">gatk</requirement> |
| 0 | 5 </requirements> |
| 6 <command interpreter="python">gatk2_wrapper.py | |
| 7 #from binascii import hexlify | |
| 8 --max_jvm_heap_fraction "1" | |
| 9 --stdout "${output_log}" | |
| 10 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" | |
| 11 -p 'java | |
| 12 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" | |
| 13 -T "VariantFiltration" | |
| 14 \$GATK2_SITE_OPTIONS | |
|
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6ef8eb568700
Move GATK tool_dependency to a repository dependency, use 2 env vars: GATK2_NUM_THREADS and GATK2_NUM_CPU_THREADS for site threading values
Jim Johnson <jj@umn.edu>
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diff
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15 \$GATK2_NUM_THREADS |
| 0 | 16 ##--num_threads 4 ##hard coded, for now |
| 17 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home | |
| 18 -o "${output_vcf}" | |
| 19 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout | |
| 20 #if $reference_source.reference_source_selector != "history": | |
| 21 -R "${reference_source.ref_file.fields.path}" | |
| 22 #end if | |
| 23 ' | |
| 24 #for $variant_filter in $variant_filters: | |
| 25 #set $variant_filter = "--%sExpression '%s' --%sName '%s'" % ( str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_expression ), str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_name ) ) | |
| 26 -o '${ hexlify( $variant_filter ) }' | |
| 27 #end for | |
| 28 | |
| 29 #if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask': | |
| 30 -d "--mask:${mask_rod_bind_type.mask_rod_name},%(file_type)s" "${mask_rod_bind_type.input_mask_rod}" "${mask_rod_bind_type.input_mask_rod.ext}" "input_mask_${mask_rod_bind_type.mask_rod_name}" | |
| 31 -p ' | |
| 32 --maskExtension "${mask_rod_bind_type.mask_extension}" | |
| 33 --maskName "${mask_rod_bind_type.mask_rod_name}" | |
| 34 ' | |
| 35 #end if | |
| 36 | |
| 37 ##start standard gatk options | |
| 38 #if $gatk_param_type.gatk_param_type_selector == "advanced": | |
| 39 #for $pedigree in $gatk_param_type.pedigree: | |
| 40 -p '--pedigree "${pedigree.pedigree_file}"' | |
| 41 #end for | |
| 42 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: | |
| 43 -p '--pedigreeString "${pedigree_string.pedigree_string}"' | |
| 44 #end for | |
| 45 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' | |
| 35 | 46 #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] |
| 0 | 47 #for $read_filter in $gatk_param_type.read_filter: |
|
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76f8ca47b810
Omit --read_filter param included by default
Jim Johnson <jj@umn.edu>
parents:
28
diff
changeset
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48 -p ' |
| 35 | 49 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters: |
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76f8ca47b810
Omit --read_filter param included by default
Jim Johnson <jj@umn.edu>
parents:
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diff
changeset
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50 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" |
|
76f8ca47b810
Omit --read_filter param included by default
Jim Johnson <jj@umn.edu>
parents:
28
diff
changeset
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51 #end_if |
| 0 | 52 #for $name, $param in $read_filter.read_filter_type.iteritems(): |
| 53 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: | |
| 54 #if hasattr( $param.input, 'truevalue' ): | |
| 55 ${param} | |
| 56 #else: | |
| 57 --${name} "${param}" | |
| 58 #end if | |
| 59 #end if | |
| 60 #end for | |
| 61 ' | |
| 62 #end for | |
| 63 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): | |
| 64 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" | |
| 65 #end for | |
| 66 | |
| 67 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): | |
| 68 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" | |
| 69 #end for | |
| 70 | |
| 71 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"' | |
| 72 | |
| 73 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' | |
| 74 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": | |
| 75 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' | |
| 76 #end if | |
| 77 -p ' | |
| 78 --baq "${gatk_param_type.baq}" | |
| 79 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}" | |
| 80 ${gatk_param_type.use_original_qualities} | |
| 81 --defaultBaseQualities "${gatk_param_type.default_base_qualities}" | |
| 82 --validation_strictness "${gatk_param_type.validation_strictness}" | |
| 83 --interval_merging "${gatk_param_type.interval_merging}" | |
| 84 ${gatk_param_type.disable_experimental_low_memory_sharding} | |
|
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7533db8dfb5b
Update tool_dependencies to GATK v 2.3
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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85 ${gatk_param_type.fix_misencoded_quality_scores} |
| 0 | 86 ${gatk_param_type.non_deterministic_random_seed} |
| 87 ' | |
| 88 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): | |
| 89 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": | |
| 90 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" | |
| 91 #else | |
| 92 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' | |
| 93 #end if | |
| 94 #end for | |
| 95 #end if | |
| 96 | |
| 97 #if str( $reference_source.reference_source_selector ) == "history": | |
| 98 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" | |
| 99 #end if | |
| 100 ##end standard gatk options | |
| 101 | |
| 102 ##start analysis specific options | |
| 103 #if $cluster_snp_type.cluster_snp_type_selector == "cluster_snp": | |
| 104 -p ' | |
| 105 --clusterSize "${cluster_snp_type.cluster_size}" | |
| 106 --clusterWindowSize "${cluster_snp_type.cluster_window_size}" | |
| 107 ' | |
| 108 #end if | |
| 109 -p '${missing_values_in_expressions_should_evaluate_as_failing}' | |
| 110 </command> | |
| 111 <inputs> | |
| 112 <conditional name="reference_source"> | |
| 113 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> | |
| 114 <option value="cached">Locally cached</option> | |
| 115 <option value="history">History</option> | |
| 116 </param> | |
| 117 <when value="cached"> | |
| 118 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;" /> | |
| 119 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
| 120 <options from_data_table="gatk2_picard_indexes"> | |
| 121 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> | |
| 122 </options> | |
| 123 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 124 </param> | |
| 125 </when> | |
| 126 <when value="history"> <!-- FIX ME!!!! --> | |
| 127 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;" /> | |
| 128 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | |
| 129 </when> | |
| 130 </conditional> | |
| 131 | |
| 132 | |
| 133 <repeat name="variant_filters" title="Variant Filters"> | |
| 134 <param name="filter_expression" value="AB < 0.2 || MQ0 > 50" type="text" label="Filter expression" help="JEXL formatted expressions (-filter,--filterExpression &lt;filterExpression&gt;)"> | |
| 135 <sanitizer> | |
| 136 <valid initial="string.printable"> | |
| 137 <remove value="'"/> | |
| 138 </valid> | |
| 139 <mapping initial="none"/> | |
| 140 </sanitizer> | |
| 141 </param> | |
| 142 <param name="filter_name" value="custom_filter" type="text" label="Filter name" help="-filterName,--filterName &lt;filterName&gt;"/> | |
| 143 <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" help="Use -G_filter,--genotypeFilterExpression &lt;genotypeFilterExpression&gt; and -G_filterName,--genotypeFilterName &lt;genotypeFilterName&gt; for filter type" /> | |
| 144 </repeat> | |
| 145 | |
| 146 | |
| 147 | |
| 148 <conditional name="mask_rod_bind_type"> | |
| 149 <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file"> | |
| 150 <option value="set_mask" selected="True">Set maskP</option> | |
| 151 <option value="exclude_mask">Don't set mask</option> | |
| 152 </param> | |
| 153 <when value="exclude_mask"> | |
| 154 <!-- Do nothing here --> | |
| 155 </when> | |
| 156 <when value="set_mask"> | |
| 157 <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" help="--mask &lt;mask&gt;" /> | |
| 158 <param name="mask_rod_name" type="text" value="Mask" label="Mask Name" help="-maskName,--maskName &lt;maskName&gt;"/> | |
| 159 <param name="mask_extension" type="integer" value="0" label="Mask Extension" help="-maskExtend,--maskExtension &lt;maskExtension&gt;"/> | |
| 160 </when> | |
| 161 </conditional> | |
| 162 | |
| 163 | |
| 164 <conditional name="gatk_param_type"> | |
| 165 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"> | |
| 166 <option value="basic" selected="True">Basic</option> | |
| 167 <option value="advanced">Advanced</option> | |
| 168 </param> | |
| 169 <when value="basic"> | |
| 170 <!-- Do nothing here --> | |
| 171 </when> | |
| 172 <when value="advanced"> | |
| 173 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"> | |
| 174 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/> | |
| 175 </repeat> | |
| 176 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"> | |
| 177 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/> | |
| 178 </repeat> | |
| 179 <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"> | |
| 180 <option value="STRICT" selected="True">STRICT</option> | |
| 181 <option value="SILENT">SILENT</option> | |
| 182 </param> | |
| 183 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"> | |
| 184 <conditional name="read_filter_type"> | |
| 185 <param name="read_filter_type_selector" type="select" label="Read Filter Type"> | |
| 186 <option value="BadCigar">BadCigar</option> | |
| 187 <option value="BadMate">BadMate</option> | |
| 188 <option value="DuplicateRead">DuplicateRead</option> | |
| 189 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> | |
| 190 <option value="MalformedRead">MalformedRead</option> | |
| 191 <option value="MappingQuality">MappingQuality</option> | |
| 192 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> | |
| 193 <option value="MappingQualityZero">MappingQualityZero</option> | |
| 194 <option value="MateSameStrand">MateSameStrand</option> | |
| 195 <option value="MaxInsertSize">MaxInsertSize</option> | |
| 196 <option value="MaxReadLength" selected="True">MaxReadLength</option> | |
| 197 <option value="MissingReadGroup">MissingReadGroup</option> | |
| 198 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> | |
| 199 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> | |
| 200 <option value="Platform454">Platform454</option> | |
| 201 <option value="Platform">Platform</option> | |
| 202 <option value="PlatformUnit">PlatformUnit</option> | |
| 203 <option value="ReadGroupBlackList">ReadGroupBlackList</option> | |
| 204 <option value="ReadName">ReadName</option> | |
| 205 <option value="ReadStrand">ReadStrand</option> | |
| 206 <option value="ReassignMappingQuality">ReassignMappingQuality</option> | |
| 207 <option value="Sample">Sample</option> | |
| 208 <option value="SingleReadGroup">SingleReadGroup</option> | |
| 209 <option value="UnmappedRead">UnmappedRead</option> | |
| 210 </param> | |
| 211 <when value="BadCigar"> | |
| 212 <!-- no extra options --> | |
| 213 </when> | |
| 214 <when value="BadMate"> | |
| 215 <!-- no extra options --> | |
| 216 </when> | |
| 217 <when value="DuplicateRead"> | |
| 218 <!-- no extra options --> | |
| 219 </when> | |
| 220 <when value="FailsVendorQualityCheck"> | |
| 221 <!-- no extra options --> | |
| 222 </when> | |
| 223 <when value="MalformedRead"> | |
| 35 | 224 <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/> |
| 0 | 225 </when> |
| 226 <when value="MappingQuality"> | |
| 227 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> | |
| 228 </when> | |
| 229 <when value="MappingQualityUnavailable"> | |
| 230 <!-- no extra options --> | |
| 231 </when> | |
| 232 <when value="MappingQualityZero"> | |
| 233 <!-- no extra options --> | |
| 234 </when> | |
| 235 <when value="MateSameStrand"> | |
| 236 <!-- no extra options --> | |
| 237 </when> | |
| 238 <when value="MaxInsertSize"> | |
| 239 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> | |
| 240 </when> | |
| 241 <when value="MaxReadLength"> | |
| 242 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> | |
| 243 </when> | |
| 244 <when value="MissingReadGroup"> | |
| 245 <!-- no extra options --> | |
| 246 </when> | |
| 247 <when value="NoOriginalQualityScores"> | |
| 248 <!-- no extra options --> | |
| 249 </when> | |
| 250 <when value="NotPrimaryAlignment"> | |
| 251 <!-- no extra options --> | |
| 252 </when> | |
| 253 <when value="Platform454"> | |
| 254 <!-- no extra options --> | |
| 255 </when> | |
| 256 <when value="Platform"> | |
| 257 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> | |
| 258 </when> | |
| 259 <when value="PlatformUnit"> | |
| 260 <!-- no extra options --> | |
| 261 </when> | |
| 262 <when value="ReadGroupBlackList"> | |
| 263 <!-- no extra options --> | |
| 264 </when> | |
| 265 <when value="ReadName"> | |
| 266 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> | |
| 267 </when> | |
| 268 <when value="ReadStrand"> | |
| 269 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> | |
| 270 </when> | |
| 271 <when value="ReassignMappingQuality"> | |
| 272 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> | |
| 273 </when> | |
| 274 <when value="Sample"> | |
| 275 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> | |
| 276 </when> | |
| 277 <when value="SingleReadGroup"> | |
| 278 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> | |
| 279 </when> | |
| 280 <when value="UnmappedRead"> | |
| 281 <!-- no extra options --> | |
| 282 </when> | |
| 283 </conditional> | |
| 284 </repeat> | |
| 285 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"> | |
| 286 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /> | |
| 287 </repeat> | |
| 288 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"> | |
| 289 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /> | |
| 290 </repeat> | |
| 291 | |
| 292 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"> | |
| 293 <option value="UNION" selected="True">UNION</option> | |
| 294 <option value="INTERSECTION">INTERSECTION</option> | |
| 295 </param> | |
| 296 | |
| 297 <conditional name="downsampling_type"> | |
| 298 <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"> | |
| 299 <option value="NONE" selected="True">NONE</option> | |
| 300 <option value="ALL_READS">ALL_READS</option> | |
| 301 <option value="BY_SAMPLE">BY_SAMPLE</option> | |
| 302 </param> | |
| 303 <when value="NONE"> | |
| 304 <!-- no more options here --> | |
| 305 </when> | |
| 306 <when value="ALL_READS"> | |
| 307 <conditional name="downsample_to_type"> | |
| 308 <param name="downsample_to_type_selector" type="select" label="Downsample method"> | |
| 309 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> | |
| 310 <option value="downsample_to_coverage">Downsample by Coverage</option> | |
| 311 </param> | |
| 312 <when value="downsample_to_fraction"> | |
| 313 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/> | |
| 314 </when> | |
| 315 <when value="downsample_to_coverage"> | |
| 316 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/> | |
| 317 </when> | |
| 318 </conditional> | |
| 319 </when> | |
| 320 <when value="BY_SAMPLE"> | |
| 321 <conditional name="downsample_to_type"> | |
| 322 <param name="downsample_to_type_selector" type="select" label="Downsample method"> | |
| 323 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> | |
| 324 <option value="downsample_to_coverage">Downsample by Coverage</option> | |
| 325 </param> | |
| 326 <when value="downsample_to_fraction"> | |
| 327 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/> | |
| 328 </when> | |
| 329 <when value="downsample_to_coverage"> | |
| 330 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/> | |
| 331 </when> | |
| 332 </conditional> | |
| 333 </when> | |
| 334 </conditional> | |
| 335 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"> | |
| 336 <option value="OFF" selected="True">OFF</option> | |
| 337 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option> | |
| 338 <option value="RECALCULATE">RECALCULATE</option> | |
| 339 </param> | |
| 340 <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /> | |
| 341 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> | |
| 342 <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> | |
| 343 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"> | |
| 344 <option value="STRICT" selected="True">STRICT</option> | |
| 345 <option value="LENIENT">LENIENT</option> | |
| 346 <option value="SILENT">SILENT</option> | |
| 347 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--> | |
| 348 </param> | |
| 349 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"> | |
| 350 <option value="ALL" selected="True">ALL</option> | |
| 351 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option> | |
| 352 </param> | |
| 353 | |
| 354 <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"> | |
| 355 <conditional name="read_group_black_list_type"> | |
| 356 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> | |
| 357 <option value="file" selected="True">Filters in file</option> | |
| 358 <option value="text">Specify filters as a string</option> | |
| 359 </param> | |
| 360 <when value="file"> | |
| 361 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> | |
| 362 </when> | |
| 363 <when value="text"> | |
| 364 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> | |
| 365 </when> | |
| 366 </conditional> | |
| 367 </repeat> | |
| 368 | |
| 369 <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> | |
| 370 <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/> | |
|
18
7533db8dfb5b
Update tool_dependencies to GATK v 2.3
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
371 <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False" help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/> |
| 0 | 372 |
| 373 </when> | |
| 374 </conditional> | |
| 375 | |
| 376 <conditional name="cluster_snp_type"> | |
| 377 <param name="cluster_snp_type_selector" type="select" label="Cluster SNPs"> | |
| 378 <option value="cluster_snp">Cluster SNPs</option> | |
| 379 <option value="do_not_cluster_snp" selected="True">Do not cluster SNPs</option> | |
| 380 </param> | |
| 381 <when value="do_not_cluster_snp"> | |
| 382 <!-- Do nothing here --> | |
| 383 </when> | |
| 384 <when value="cluster_snp"> | |
| 385 <param name="cluster_size" type="integer" value="3" label="The number of SNPs which make up a cluster" help="-cluster,--clusterSize &lt;clusterSize&gt;"/> | |
| 386 <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs" help="-window,--clusterWindowSize &lt;clusterWindowSize&gt;"/> | |
| 387 </when> | |
| 388 </conditional> | |
| 389 | |
| 390 <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" help="--missingValuesInExpressionsShouldEvaluateAsFailing" /> | |
| 391 | |
| 392 </inputs> | |
| 393 <outputs> | |
| 394 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> | |
| 395 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
| 396 </outputs> | |
| 397 <tests> | |
| 398 <test> | |
| 399 <param name="reference_source_selector" value="history" /> | |
| 400 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
| 401 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> | |
| 402 <param name="filter_expression" value="MQ < 37.74 || MQ0 > 50" /> | |
| 403 <param name="filter_name" value="Galaxy_filter" /> | |
| 404 <param name="is_genotype_filter" /> | |
| 405 <param name="mask_rod_bind_type_selector" value="set_mask" /> | |
| 406 <param name="input_mask_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> | |
| 407 <param name="mask_rod_name" value="." /> | |
| 408 <param name="mask_extension" value="0" /> | |
| 409 <param name="gatk_param_type_selector" value="basic" /> | |
| 410 <param name="cluster_snp_type_selector" value="do_not_cluster_snp" /> | |
| 411 <param name="missing_values_in_expressions_should_evaluate_as_failing" /> | |
| 412 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" /> | |
| 413 <output name="output_log" file="gatk/gatk_variant_filtration/gatk_variant_filtration_out_1.log.contains" compare="contains" /> | |
| 414 </test> | |
| 415 </tests> | |
| 416 <help> | |
| 417 **What it does** | |
| 418 | |
| 419 Filters variant calls using a number of user-selectable, parameterizable criteria. | |
| 420 | |
| 421 For more information on using the VariantFiltration module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_filters_VariantFiltration.html>`_. | |
| 422 | |
| 423 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
| 424 | |
| 425 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
| 426 | |
| 427 ------ | |
| 428 | |
| 429 **Inputs** | |
| 430 | |
| 431 GenomeAnalysisTK: VariantFiltration accepts a VCF input file. | |
| 432 | |
| 433 | |
| 434 **Outputs** | |
| 435 | |
| 436 The output is in VCF format. | |
| 437 | |
| 438 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
| 439 | |
| 440 ------- | |
| 441 | |
| 442 **Settings**:: | |
| 443 | |
| 444 | |
| 445 filterExpression One or more expression used with INFO fields to filter (see wiki docs for more info) | |
| 446 filterName Names to use for the list of filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered | |
| 447 genotypeFilterExpression One or more expression used with FORMAT (sample/genotype-level) fields to filter (see wiki docs for more info) | |
| 448 genotypeFilterName Names to use for the list of sample/genotype filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered | |
| 449 clusterSize The number of SNPs which make up a cluster (see also --clusterWindowSize); [default:3] | |
| 450 clusterWindowSize The window size (in bases) in which to evaluate clustered SNPs (to disable the clustered SNP filter, set this value to less than 1); [default:0] | |
| 451 maskName The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask'] | |
| 452 missingValuesInExpressionsShouldEvaluateAsFailing When evaluating the JEXL expressions, should missing values be considered failing the expression (by default they are considered passing)? | |
| 453 | |
| 454 ------ | |
| 455 | |
| 456 **Citation** | |
| 457 | |
| 458 For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ | |
| 459 | |
| 460 Please also site `McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303. Epub 2010 Jul 19. <http://www.ncbi.nlm.nih.gov/pubmed/20644199>`_ | |
| 461 | |
| 462 If you use this tool in Galaxy, please cite `Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21. <http://www.ncbi.nlm.nih.gov/pubmed/20069535>`_ | |
| 463 | |
| 464 | |
| 465 </help> | |
| 466 </tool> |