Mercurial > repos > devteam > variant_select
annotate variant_select.xml @ 1:96de2494d113 draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:48:40 -0400 |
| parents | 0ac94ceefd33 |
| children |
| rev | line source |
|---|---|
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96de2494d113
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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1 <tool id="gatk_variant_select" name="Select Variants" version="0.0.3"> |
| 0 | 2 <description>from VCF files</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 #from binascii import hexlify | |
| 11 --max_jvm_heap_fraction "1" | |
| 12 --stdout "${output_log}" | |
| 13 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" | |
| 14 -p 'java | |
| 15 -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar" | |
| 16 -T "SelectVariants" | |
| 17 --num_threads \${GALAXY_SLOTS:-4} | |
| 18 -et "NO_ET" ##ET no phone home | |
| 19 -o "${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 | |
| 45 #for $select_expressions in $select_expressions_repeat: | |
| 46 #set $select_expression = "--select_expressions '%s'" % ( str( $select_expressions.select_expressions ) ) | |
| 47 -o '${ hexlify( $select_expression ) }' | |
| 48 #end for | |
| 49 | |
| 50 ##start tool specific options | |
| 51 #if str( $analysis_param_type.analysis_param_type_selector ) == 'advanced': | |
| 52 -p ' | |
| 53 #for $exclude_sample_file in $analysis_param_type.exclude_sample_file_repeat: | |
| 54 --exclude_sample_file "${exclude_sample_file.exclude_sample_file}" | |
| 55 #end for | |
| 56 | |
| 57 #for $sample_file in $analysis_param_type.sample_file_repeat: | |
| 58 --sample_file "${ample_file.sample_file}" | |
| 59 #end for | |
| 60 | |
| 61 #if $analysis_param_type.input_keep_ids: | |
| 62 --keepIDs "${analysis_param_type.input_keep_ids}" | |
| 63 #end if | |
| 64 | |
| 65 ${analysis_param_type.keep_original_AC} | |
| 66 | |
| 67 ${analysis_param_type.mendelian_violation} | |
| 68 | |
| 69 --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}" | |
| 70 | |
| 71 --remove_fraction_genotypes "${analysis_param_type.remove_fraction_genotypes}" | |
| 72 | |
| 73 --restrictAllelesTo "${analysis_param_type.restrict_alleles_to}" | |
| 74 | |
| 75 #if str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_fraction': | |
| 76 --select_random_fraction "${analysis_param_type.select_random_type.select_random_fraction}" | |
| 77 #elif str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_number': | |
| 78 --select_random_number "${analysis_param_type.select_random_type.select_random_number}" | |
| 79 #end if | |
| 80 | |
| 81 #if $analysis_param_type.select_type_to_include: | |
| 82 #for $type_to_include in str( $analysis_param_type.select_type_to_include ).split( ',' ): | |
| 83 --selectTypeToInclude "${type_to_include}" | |
| 84 #end for | |
| 85 #end if | |
| 86 | |
| 87 ${analysis_param_type.exclude_non_variants} | |
| 88 ' | |
| 89 | |
| 90 #for $sample_expressions in $analysis_param_type.sample_expressions_repeat: | |
| 91 #set $sample_expression = "--sample_expressions '%s'" % ( str( $sample_expressions.sample_expressions ) ) | |
| 92 -o '${ hexlify( $sample_expression ) }' | |
| 93 #end for | |
| 94 | |
| 95 #end if | |
| 96 ##end tool specific options | |
| 97 | |
| 98 #include source=$standard_gatk_options# | |
| 99 | |
| 100 | |
| 101 </command> | |
| 102 <inputs> | |
| 103 <conditional name="reference_source"> | |
| 104 <expand macro="reference_source_selector_param" /> | |
| 105 <when value="cached"> | |
| 106 <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &lt;variant&gt;" /> | |
| 107 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
| 108 <options from_data_table="gatk_picard_indexes"> | |
| 109 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> | |
| 110 </options> | |
| 111 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 112 </param> | |
| 113 </when> | |
| 114 <when value="history"> <!-- FIX ME!!!! --> | |
| 115 <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &lt;variant&gt;" /> | |
| 116 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | |
| 117 </when> | |
| 118 </conditional> | |
| 119 | |
| 120 <repeat name="select_expressions_repeat" title="Criteria to use when selecting the data" help="-select,--select_expressions &lt;select_expressions&gt;"> | |
| 121 <param name="select_expressions" type="text" label="JEXL expression"> | |
| 122 <sanitizer> | |
| 123 <valid initial="string.printable"> | |
| 124 <remove value="'"/> | |
| 125 </valid> | |
| 126 <mapping initial="none"/> | |
| 127 </sanitizer> | |
| 128 </param> | |
| 129 </repeat> | |
| 130 | |
| 131 <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;"/> | |
| 132 <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;"/> | |
| 133 | |
| 134 <repeat name="sample_name_repeat" title="Include Samples by name" help="-sn,--sample_name &lt;sample_name&gt;"> | |
| 135 <param name="sample_name" type="text" label="Include genotypes from this sample"/> | |
| 136 </repeat> | |
| 137 | |
| 138 <repeat name="exclude_sample_name_repeat" title="Exclude Samples by name" help="-xl_sn,--exclude_sample_name &lt;exclude_sample_name&gt;"> | |
| 139 <param name="exclude_sample_name" type="text" label="Exclude genotypes from this sample"/> | |
| 140 </repeat> | |
| 141 | |
| 142 <param name="exclude_filtered" type="boolean" truevalue="--excludeFiltered" falsevalue="" label="Don't include filtered loci in the analysis" help="-ef,--excludeFiltered" /> | |
| 143 | |
| 144 <expand macro="gatk_param_type_conditional" /> | |
| 145 | |
| 146 | |
| 147 <expand macro="analysis_type_conditional"> | |
| 148 | |
| 149 <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file" help="-xl_sf,--exclude_sample_file &lt;exclude_sample_file&gt;"> | |
| 150 <param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/> | |
| 151 </repeat> | |
| 152 | |
| 153 <repeat name="sample_file_repeat" title="Samples by file" help="-sf,--sample_file &lt;sample_file&gt;"> | |
| 154 <param name="sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to include" /> | |
| 155 </repeat> | |
| 156 | |
|
1
96de2494d113
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
157 <param name="input_keep_ids" type="data" format="txt" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &lt;keepIDs&gt;"/> |
| 0 | 158 |
| 159 <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" /> | |
| 160 | |
| 161 <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" help="-mv,--mendelianViolation" /> | |
| 162 | |
| 163 <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;" /> | |
| 164 | |
| 165 <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;" /> | |
| 166 | |
| 167 <param name="restrict_alleles_to" type="select" label="Select only variants of a particular allelicity" help="-restrictAllelesTo,--restrictAllelesTo &lt;restrictAllelesTo&gt;"> | |
| 168 <option value="ALL" selected="True">ALL</option> | |
| 169 <option value="MULTIALLELIC">MULTIALLELIC</option> | |
| 170 <option value="BIALLELIC">BIALLELIC</option> | |
| 171 </param> | |
| 172 | |
| 173 <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;"> | |
| 174 <param name="sample_expressions" type="text" label="Regular expression"> | |
| 175 <sanitizer> | |
| 176 <valid initial="string.printable"> | |
| 177 <remove value="'"/> | |
| 178 </valid> | |
| 179 <mapping initial="none"/> | |
| 180 </sanitizer> | |
| 181 </param> | |
| 182 </repeat> | |
| 183 | |
| 184 <conditional name="select_random_type"> | |
| 185 <param name="select_random_type_selector" type="select" label="Select a random subset of variants"> | |
| 186 <option value="select_all" selected="True">Use all variants</option> | |
| 187 <option value="select_random_fraction">Select random fraction</option> | |
| 188 <option value="select_random_number">Select random number</option> | |
| 189 </param> | |
| 190 <when value="select_all"> | |
| 191 <!-- Do nothing here --> | |
| 192 </when> | |
| 193 <when value="select_random_fraction"> | |
| 194 <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;"/> | |
| 195 </when> | |
| 196 <when value="select_random_number"> | |
| 197 <param name="select_random_number" type="integer" value="0" label="Count" help="-number,--select_random_number &lt;select_random_number&gt;" /> | |
| 198 </when> | |
| 199 </conditional> | |
| 200 | |
| 201 <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" /> | |
| 202 | |
| 203 <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;"> | |
| 204 <option value="INDEL">INDEL</option> | |
| 205 <option value="SNP">SNP</option> | |
| 206 <option value="MIXED">MIXED</option> | |
| 207 <option value="MNP">MNP</option> | |
| 208 <option value="SYMBOLIC">SYMBOLIC</option> | |
| 209 <option value="NO_VARIATION">NO_VARIATION</option> | |
| 210 </param> | |
| 211 </expand> | |
| 212 | |
| 213 </inputs> | |
| 214 <outputs> | |
| 215 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> | |
| 216 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
| 217 </outputs> | |
| 218 <tests> | |
| 219 <test> | |
| 220 <param name="reference_source_selector" value="history" /> | |
| 221 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
| 222 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> | |
| 223 <param name="select_expressions_repeat" value="0" /> | |
| 224 <param name="input_concordance" /> | |
| 225 <param name="input_discordance" /> | |
| 226 <param name="exclude_sample_name_repeat" value="0" /> | |
| 227 <param name="exclude_filtered" /> | |
| 228 <param name="sample_name_repeat" value="0" /> | |
| 229 <param name="gatk_param_type_selector" value="basic" /> | |
| 230 <param name="analysis_param_type_selector" value="basic" /> | |
| 231 <output name="output_vcf" file="gatk/gatk_variant_select/gatk_variant_select_out_1.vcf" lines_diff="4" /> | |
| 232 <output name="output_log" file="gatk/gatk_variant_select/gatk_variant_select_out_1.log.contains" compare="contains" /> | |
| 233 </test> | |
| 234 </tests> | |
| 235 <help> | |
| 236 **What it does** | |
| 237 | |
| 238 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://www.broadinstitute.org/gsa/wiki/index.php/Using_JEXL_expressions). One can optionally include concordance or discordance tracks for use in selecting overlapping variants. | |
| 239 | |
| 240 For more information on using the SelectVariants module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/SelectVariants>`_. | |
| 241 | |
| 242 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>`_. | |
| 243 | |
| 244 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_. | |
| 245 | |
| 246 ------ | |
| 247 | |
| 248 **Inputs** | |
| 249 | |
| 250 GenomeAnalysisTK: SelectVariants accepts a VCF input file. | |
| 251 | |
| 252 | |
| 253 **Outputs** | |
| 254 | |
| 255 The output is in VCF format. | |
| 256 | |
| 257 | |
| 258 Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats. | |
| 259 | |
| 260 ------- | |
| 261 | |
| 262 **Settings**:: | |
| 263 | |
| 264 | |
| 265 out VCFWriter stdout File to which variants should be written | |
| 266 variant RodBinding[VariantContext] NA Input VCF file | |
| 267 concordance RodBinding[VariantContext] none Output variants that were also called in this comparison track | |
| 268 discordance RodBinding[VariantContext] none Output variants that were not called in this comparison track | |
| 269 exclude_sample_file Set[File] [] File containing a list of samples (one per line) to exclude. Can be specified multiple times | |
| 270 exclude_sample_name Set[String] [] Exclude genotypes from this sample. Can be specified multiple times | |
| 271 excludeFiltered boolean false Don't include filtered loci in the analysis | |
| 272 excludeNonVariants boolean false Don't include loci found to be non-variant after the subsetting procedure | |
| 273 keepIDs File NA Only emit sites whose ID is found in this file (one ID per line) | |
| 274 keepOriginalAC boolean false Don't update the AC, AF, or AN values in the INFO field after selecting | |
| 275 mendelianViolation Boolean false output mendelian violation sites only | |
| 276 mvq double 0.0 Minimum genotype QUAL score for each trio member required to accept a site as a violation | |
| 277 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 | |
| 278 restrictAllelesTo NumberAlleleRestriction ALL Select only variants of a particular allelicity. Valid options are ALL (default), MULTIALLELIC or BIALLELIC | |
| 279 sample_expressions Set[String] NA Regular expression to select many samples from the ROD tracks provided. Can be specified multiple times | |
| 280 sample_file Set[File] NA File containing a list of samples (one per line) to include. Can be specified multiple times | |
| 281 sample_name Set[String] [] Include genotypes from this sample. Can be specified multiple times | |
| 282 select_expressions ArrayList[String] [] One or more criteria to use when selecting the data | |
| 283 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 | |
| 284 select_random_number int 0 Selects a number of variants at random from the variant track | |
| 285 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 | |
| 286 | |
| 287 @CITATION_SECTION@ | |
| 288 </help> | |
| 289 </tool> |