Mercurial > repos > jjohnson > snpeff
annotate snpEff.xml @ 9:937367efb1da default tip
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 18 Sep 2013 10:49:56 -0500 |
| parents | 13b6ad2ddace |
| children |
| rev | line source |
|---|---|
| 8 | 1 <tool id="snpEff" name="SnpEff" version="3.2"> |
| 0 | 2 <description>Variant effect and annotation</description> |
| 3 <!-- | |
| 4 You will need to change the path to wherever your installation is. | |
| 5 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
| 6 <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> | |
| 8 | 7 Options: |
| 8 -a , -around : Show N codons and amino acids around change (only in coding regions). Default is 0 codons. | |
| 9 -i <format> : Input format [ vcf, txt, pileup, bed ]. Default: VCF. | |
| 10 -o <format> : Ouput format [ txt, vcf, gatk, bed, bedAnn ]. Default: VCF. | |
| 11 -interval : Use a custom interval file (you may use this option many times) | |
| 12 -chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output. | |
| 13 -s, -stats : Name of stats file (summary). Default is 'snpEff_summary.html' | |
| 14 -t : Use multiple threads (implies '-noStats'). Default 'off' | |
| 15 | |
| 16 Sequence change filter options: | |
| 17 -del : Analyze deletions only | |
| 18 -ins : Analyze insertions only | |
| 19 -hom : Analyze homozygous variants only | |
| 20 -het : Analyze heterozygous variants only | |
| 21 -minQ X, -minQuality X : Filter out variants with quality lower than X | |
| 22 -maxQ X, -maxQuality X : Filter out variants with quality higher than X | |
| 23 -minC X, -minCoverage X : Filter out variants with coverage lower than X | |
| 24 -maxC X, -maxCoverage X : Filter out variants with coverage higher than X | |
| 25 -nmp : Only MNPs (multiple nucleotide polymorphisms) | |
| 26 -snp : Only SNPs (single nucleotide polymorphisms) | |
| 27 | |
| 28 Results filter options: | |
| 29 -fi <bedFile> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times) | |
| 30 -no-downstream : Do not show DOWNSTREAM changes | |
| 31 -no-intergenic : Do not show INTERGENIC changes | |
| 32 -no-intron : Do not show INTRON changes | |
| 33 -no-upstream : Do not show UPSTREAM changes | |
| 34 -no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes | |
| 35 | |
| 36 Annotations options: | |
| 37 -cancer : Perform 'cancer' comparissons (Somatic vs Germline). Default: false | |
| 38 -canon : Only use canonical transcripts. | |
| 39 -geneId : Use gene ID instead of gene name (VCF output). Default: false | |
| 40 -hgvs : Use HGVS annotations for amino acid sub-field. Default: false | |
| 41 -lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags. | |
| 42 -reg <name> : Regulation track to use (this option can be used add several times). | |
| 43 -oicr : Add OICR tag in VCF file. Default: false | |
| 44 -onlyReg : Only use regulation tracks. | |
| 45 -onlyTr <file.txt> : Only use the transcripts in this file. Format: One transcript ID per line. | |
| 46 -sequenceOntolgy : Use Sequence Ontolgy terms. Default: false | |
| 47 -ss, -spliceSiteSize <int> : Set size for splice sites (donor and acceptor) in bases. Default: 2 | |
| 48 -ud, -upDownStreamLen <int> : Set upstream downstream interval length (in bases) | |
| 49 | |
| 50 Generic options: | |
| 51 -0 : File positions are zero-based (same as '-inOffset 0 -outOffset 0') | |
| 52 -1 : File positions are one-based (same as '-inOffset 1 -outOffset 1') | |
| 53 -c , -config : Specify config file | |
| 54 -h , -help : Show this help and exit | |
| 55 -if, -inOffset : Offset input by a number of bases. E.g. '-inOffset 1' for one-based input files | |
| 56 -of, -outOffset : Offset output by a number of bases. E.g. '-outOffset 1' for one-based output files | |
| 57 -noLog : Do not report usage statistics to server | |
| 58 -noStats : Do not create stats (summary) file | |
| 59 -q , -quiet : Quiet mode (do not show any messages or errors) | |
| 60 -v , -verbose : Verbose mode | |
| 61 | |
| 0 | 62 --> |
| 63 <requirements> | |
| 8 | 64 <requirement type="package" version="3.2">snpEff</requirement> |
| 0 | 65 </requirements> |
| 66 <command> | |
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9
937367efb1da
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
Jim Johnson <jj@umn.edu>
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67 SNPEFF_DATA_DIR=`grep '^data_dir' \$SNPEFF_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`; |
| 3 | 68 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ; |
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9
937367efb1da
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
Jim Johnson <jj@umn.edu>
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69 then java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config $genomeVersion ; |
| 3 | 70 fi"; |
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937367efb1da
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
Jim Johnson <jj@umn.edu>
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71 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength |
| 8 | 72 #if $spliceSiteSize and $spliceSiteSize.__str__ != '': |
| 73 -spliceSiteSize $spliceSiteSize | |
| 74 #end if | |
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75 #if $filterIn and $filterIn.__str__ != 'no_filter': |
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76 -$filterIn |
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77 #end if |
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78 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': |
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79 -$filterHomHet |
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80 #end if |
| 8 | 81 #if $annotations and $annotations.__str__ != '': |
| 82 -#slurp | |
| 83 #echo ' -'.join($annotations.__str__.split(',')) | |
| 84 #end if | |
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85 #if $filterOut and $filterOut.__str__ != '': |
| 8 | 86 -#slurp |
| 87 #echo ' -'.join($filterOut.__str__.split(',')) | |
| 88 #end if | |
| 89 #if str( $transcripts ) != 'None': | |
| 90 -onlyTr $transcripts | |
| 91 #end if | |
| 92 #if str( $intervals ) != 'None': ### fix this for multiple dataset input | |
| 93 -interval $intervals | |
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94 #end if |
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95 #if $statsFile: |
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96 -stats $statsFile |
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97 #end if |
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98 #if $offset.__str__ != '': |
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99 -${offset} |
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100 #end if |
| 8 | 101 #if $chr.__str__.strip() != '': |
| 102 -chr "$chr" | |
| 103 #end if | |
| 104 $noLog $genomeVersion $input > $snpeff_output | |
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105 </command> |
| 0 | 106 <inputs> |
| 107 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> | |
| 108 | |
| 109 <param name="inputFormat" type="select" label="Input format"> | |
| 8 | 110 <option value="vcf" selected="true">VCF</option> |
| 111 <option value="txt">Tabular (Deprecated)</option> | |
| 112 <option value="pileup">Pileup (Deprecated)</option> | |
| 113 <option value="bed">BED (Deprecated)</option> | |
| 0 | 114 </param> |
| 115 | |
| 116 <param name="outputFormat" type="select" label="Output format"> | |
| 8 | 117 <option value="vcf" selected="true">VCF (only if input is VCF)</option> |
| 0 | 118 <option value="txt">Tabular</option> |
| 119 <option value="bed">BED</option> | |
| 120 <option value="bedAnn">BED Annotations</option> | |
| 121 </param> | |
| 122 | |
| 123 <param name="genomeVersion" type="select" label="Genome"> | |
| 8 | 124 <!--GENOME DESCRIPTION--> |
| 0 | 125 <options from_file="snpeffect_genomedb.loc"> |
| 126 <column name="name" index="1"/> | |
| 127 <column name="value" index="0"/> | |
| 128 </options> | |
| 129 </param> | |
| 130 | |
| 131 <param name="udLength" type="select" label="Upstream / Downstream length"> | |
| 132 <option value="0">No upstream / downstream intervals (0 bases)</option> | |
| 133 <option value="200">200 bases</option> | |
| 134 <option value="500">500 bases</option> | |
| 135 <option value="1000">1000 bases</option> | |
| 136 <option value="2000">2000 bases</option> | |
| 137 <option value="5000" selected="true">5000 bases</option> | |
| 138 <option value="10000">10000 bases</option> | |
| 139 <option value="20000">20000 bases</option> | |
| 140 </param> | |
| 141 | |
| 8 | 142 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases. Default: 2"> |
| 143 <option value="1">1 base</option> | |
| 144 <option value="2">2 bases</option> | |
| 145 <option value="3">3 bases</option> | |
| 146 <option value="4">4 bases</option> | |
| 147 <option value="5">5 bases</option> | |
| 148 <option value="6">6 bases</option> | |
| 149 <option value="7">7 bases</option> | |
| 150 <option value="8">8 bases</option> | |
| 151 <option value="9">9 bases</option> | |
| 152 </param> | |
| 153 | |
| 154 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes"> | |
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155 <option value="no_filter" selected="true">No filter (analyze everything)</option> |
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156 <option value="hom">Analyze homozygous sequence changes only </option> |
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157 <option value="het">Analyze heterozygous sequence changes only </option> |
| 8 | 158 </param> |
| 0 | 159 |
| 8 | 160 <!-- The tool testing code can not handle select,radio,checkbox values that start with '-', so the '-' is added in the command generation --> |
| 161 <param name="filterIn" type="select" display="radio" label="Filter sequence changes"> | |
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162 <option value="no_filter" selected="true">No filter (analyze everything)</option> |
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163 <option value="del">Analyze deletions only </option> |
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164 <option value="ins">Analyze insertions only </option> |
| 8 | 165 <option value="mnp">Only MNPs (multiple nucleotide polymorphisms) </option> |
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166 <option value="snp">Only SNPs (single nucleotide polymorphisms) </option> |
| 8 | 167 </param> |
| 168 | |
| 169 <param name="annotations" type="select" display="checkboxes" multiple="true" optional="true" label="Annotation options"> | |
| 170 <option value="cancer">Perform 'cancer' comparissons (Somatic vs Germline). Default: false</option> | |
| 171 <option value="canon">Only use canonical transcripts.</option> | |
| 172 <option value="geneId">Use gene ID instead of gene name (VCF output). Default: false</option> | |
| 173 <option value="hgvs">Use HGVS annotations for amino acid sub-field. Default: false</option> | |
| 174 <option value="lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.</option> | |
| 175 <option value="oicr">Add OICR tag in VCF file. Default: false</option> | |
| 176 <option value="onlyReg">Only use regulation tracks.</option> | |
| 177 <option value="sequenceOntolgy">Use Sequence Ontolgy terms. Default: false</option> | |
| 178 </param> | |
| 0 | 179 |
| 8 | 180 <param name="regulation" type="select" display="checkboxes" multiple="true" optional="true" label="Non-coding and regulatory Annotation"> |
| 181 <help>These are available for only a few genomes</help> | |
| 182 <!--GENOME REG_NAME --> | |
| 183 <options from_file="snpeffect_regulationdb.loc"> | |
| 184 <column name="name" index="1"/> | |
| 185 <column name="value" index="0"/> | |
| 186 <filter type="param_value" ref="genomeVersion" key="name" column="1" /> | |
| 187 </options> | |
| 188 </param> | |
| 0 | 189 |
| 8 | 190 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/> |
| 191 <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file. Format: One transcript ID per line."/> | |
| 192 | |
| 193 <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="true" label="Filter output"> | |
| 194 <option value="no-downstream">Do not show DOWNSTREAM changes </option> | |
| 195 <option value="no-intergenic">Do not show INTERGENIC changes </option> | |
| 196 <option value="no-intron">Do not show INTRON changes </option> | |
| 197 <option value="no-upstream">Do not show UPSTREAM changes </option> | |
| 198 <option value="no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option> | |
| 199 </param> | |
| 200 | |
| 201 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> | |
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202 <option value="" selected="true">Use default (based on input type)</option> |
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203 <option value="0">Force zero-based positions (both input and output)</option> |
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204 <option value="1">Force one-based positions (both input and output)</option> |
| 0 | 205 </param> |
| 8 | 206 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name" help="By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. You can prepend any string you want to the chromosome name."> |
| 207 <validator type="regex" message="No whitespace allows">^\S*$</validator> | |
| 208 | |
| 209 </param> | |
| 210 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/> | |
| 211 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/> | |
| 0 | 212 </inputs> |
| 213 <outputs> | |
| 8 | 214 <data format="vcf" name="snpeff_output" > |
| 0 | 215 <change_format> |
| 8 | 216 <when input="outputFormat" value="vcf" format="vcf" /> |
| 0 | 217 <when input="outputFormat" value="txt" format="tabular" /> |
| 218 <when input="outputFormat" value="bed" format="bed" /> | |
| 219 <when input="outputFormat" value="bedAnn" format="bed" /> | |
| 220 </change_format> | |
| 221 </data> | |
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222 |
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223 <data format="html" name="statsFile"> |
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224 <filter>generate_stats == True</filter> |
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225 </data> |
| 0 | 226 </outputs> |
| 227 <stdio> | |
| 228 <exit_code range="1:" level="fatal" description="Error" /> | |
| 8 | 229 <exit_code range="-1" level="fatal" description="Error: Cannot open file" /> |
| 0 | 230 </stdio> |
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231 <tests> |
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232 <test> |
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233 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> |
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234 <param name="inputFormat" value="vcf"/> |
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235 <param name="outputFormat" value="vcf"/> |
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236 <param name="genomeVersion" value="testCase"/> |
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237 <param name="udLength" value="0"/> |
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238 <param name="filterHomHet" value="no_filter"/> |
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239 <param name="filterIn" value="no_filter"/> |
| 8 | 240 <param name="generate_stats" value="False"/> |
| 241 <!-- | |
| 242 <param name="filterOut" value="no-upstream"/> | |
| 243 --> | |
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244 <output name="snpeff_output"> |
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245 <assert_contents> |
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246 <!-- Check that an effect was added --> |
| 8 | 247 <has_text text="EFF=" /> |
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248 </assert_contents> |
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249 </output> |
| 8 | 250 <!-- Check for a HTML header indicating that this was successful --> |
| 251 <!-- | |
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252 <output name="statsFile"> |
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253 <assert_contents> |
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254 <has_text text="SnpEff: Variant analysis" /> |
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255 </assert_contents> |
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256 </output> |
| 8 | 257 --> |
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258 </test> |
| 8 | 259 |
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260 <test> |
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261 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> |
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262 <param name="inputFormat" value="vcf"/> |
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263 <param name="outputFormat" value="vcf"/> |
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264 <param name="genomeVersion" value="testCase"/> |
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265 <param name="udLength" value="0"/> |
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266 <param name="filterHomHet" value="het"/> |
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267 <param name="filterIn" value="no_filter"/> |
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268 <!-- |
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269 <param name="filterOut" value=""/> |
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270 --> |
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271 <param name="generate_stats" value="False"/> |
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272 <output name="snpeff_output"> |
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273 <assert_contents> |
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274 <!-- Check that NO effects were added since -het is set --> |
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275 <not_has_text text="EFF=NON_SYNONYMOUS_CODING" /> |
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276 </assert_contents> |
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277 </output> |
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278 </test> |
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279 <test> |
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280 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> |
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281 <param name="inputFormat" value="vcf"/> |
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282 <param name="outputFormat" value="vcf"/> |
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283 <param name="genomeVersion" value="testCase"/> |
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284 <param name="udLength" value="0"/> |
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285 <param name="filterHomHet" value="no_filter"/> |
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286 <param name="filterIn" value="del"/> |
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287 <!-- |
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288 <param name="filterOut" value=""/> |
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289 --> |
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290 <param name="generate_stats" value="False"/> |
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291 <output name="snpeff_output"> |
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292 <assert_contents> |
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293 <!-- Check that deleletions were evaluated --> |
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294 <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" /> |
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295 <!-- Check that insertion on last line was NOT evaluated --> |
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296 <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" /> |
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297 </assert_contents> |
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298 </output> |
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299 </test> |
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300 <test> |
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301 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> |
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302 <param name="inputFormat" value="vcf"/> |
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303 <param name="outputFormat" value="vcf"/> |
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304 <param name="genomeVersion" value="testCase"/> |
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305 <param name="udLength" value="0"/> |
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306 <param name="filterHomHet" value="no_filter"/> |
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307 <param name="filterIn" value="no_filter"/> |
| 8 | 308 <param name="filterOut" value="no-upstream"/> |
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309 <param name="generate_stats" value="False"/> |
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310 <output name="snpeff_output"> |
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311 <assert_contents> |
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312 <!-- Check that NO UPSTREAM effect was added --> |
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313 <not_has_text text="UPSTREAM" /> |
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314 </assert_contents> |
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315 </output> |
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316 </test> |
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317 |
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318 </tests> |
| 0 | 319 <help> |
| 320 | |
| 321 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. | |
| 322 | |
| 323 For details about this tool, please go to http://snpEff.sourceforge.net | |
| 324 | |
| 325 </help> | |
| 326 </tool> | |
| 327 |