Mercurial > repos > iuc > snpeff
annotate snpEff.xml @ 5:92b80578fa22 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
| author | iuc |
|---|---|
| date | Mon, 04 May 2015 22:37:25 -0400 |
| parents | 114f423f99c0 |
| children | 9ec1cb6f760d |
| rev | line source |
|---|---|
| 2 | 1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0"> |
| 0 | 2 <description>Variant effect and annotation</description> |
| 3 <macros> | |
| 4 <import>snpEff_macros.xml</import> | |
| 5 </macros> | |
|
5
92b80578fa22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
2
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changeset
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6 <expand macro="requirements" /> |
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92b80578fa22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
2
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changeset
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7 <expand macro="stdio" /> |
| 0 | 8 <command> |
| 2 | 9 <![CDATA[ |
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92b80578fa22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
2
diff
changeset
|
10 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff |
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92b80578fa22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
2
diff
changeset
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11 -c \$SNPEFF_JAR_PATH/snpEff.config |
| 0 | 12 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength |
| 13 #if $spliceSiteSize and $spliceSiteSize.__str__ != '': | |
| 14 -spliceSiteSize $spliceSiteSize | |
| 15 #end if | |
| 16 #if $filterIn and $filterIn.__str__ != 'no_filter': | |
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5
92b80578fa22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
2
diff
changeset
|
17 $filterIn |
| 0 | 18 #end if |
| 19 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter': | |
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5
92b80578fa22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
2
diff
changeset
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20 $filterHomHet |
| 0 | 21 #end if |
| 22 #if $annotations and $annotations.__str__ != '': | |
| 23 #echo " " | |
| 24 #echo ' '.join($annotations.__str__.split(',')) | |
| 25 #end if | |
| 26 #if $filterOut and $filterOut.__str__ != '': | |
| 27 #echo " " | |
| 28 #echo ' '.join($filterOut.__str__.split(',')) | |
| 29 #end if | |
| 30 #if str( $transcripts ) != 'None': | |
| 31 -onlyTr $transcripts | |
| 32 #end if | |
| 33 #if str( $intervals ) != 'None': ### fix this for multiple dataset input | |
| 34 -interval $intervals | |
| 35 #end if | |
| 36 #if $statsFile: | |
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5
92b80578fa22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
2
diff
changeset
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37 -stats $statsFile |
| 0 | 38 #end if |
| 2 | 39 #if $offset.__str__ != 'default': |
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5
92b80578fa22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
2
diff
changeset
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40 ${offset} |
| 0 | 41 #end if |
| 42 #if $chr.__str__.strip() != '': | |
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5
92b80578fa22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
2
diff
changeset
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43 -chr "$chr" |
| 0 | 44 #end if |
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5
92b80578fa22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
2
diff
changeset
|
45 $noLog |
| 0 | 46 #if $snpDb.genomeSrc == 'cached': |
| 47 -dataDir ${snpDb.genomeVersion.fields.path} | |
| 48 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': | |
| 49 #echo " " | |
| 50 #echo ' '.join($snpDb.extra_annotations.__str__.split(',')) | |
| 51 #end if | |
| 52 #if $snpDb.regulation and $snpDb.regulation.__str__ != '': | |
| 53 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# | |
| 54 #end if | |
| 55 $snpDb.genomeVersion | |
| 56 #elif $snpDb.genomeSrc == 'history': | |
| 2 | 57 -dataDir ${snpDb.snpeff_db.extra_files_path} |
| 0 | 58 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': |
| 59 #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',') | |
| 60 #echo " " | |
| 61 #echo ' -'.join($xannotations) | |
| 62 #end if | |
| 63 #if $snpDb.regulation and $snpDb.regulation.__str__ != '': | |
| 64 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# | |
| 65 #end if | |
| 66 ${snpDb.snpeff_db.metadata.genome_version} | |
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5
92b80578fa22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
2
diff
changeset
|
67 #else |
| 0 | 68 -download |
| 69 $snpDb.genome_version | |
| 70 #end if | |
| 71 $input > $snpeff_output ; | |
| 72 #if $statsFile: | |
| 73 #import os | |
| 74 #set $genes_file = str($statsFile) + '.genes.txt' | |
| 75 #set $genes_file_name = os.path.split($genes_file)[-1] | |
| 76 mkdir $statsFile.files_path; | |
| 77 mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#; | |
| 78 #end if | |
| 79 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 | |
| 80 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]" | |
| 2 | 81 sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output |
| 0 | 82 #end if |
| 2 | 83 ]]> |
| 0 | 84 </command> |
| 85 <inputs> | |
| 86 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> | |
| 87 | |
| 88 <param name="inputFormat" type="select" label="Input format"> | |
| 89 <option value="vcf" selected="true">VCF</option> | |
| 90 <option value="txt">Tabular (Deprecated)</option> | |
| 91 <option value="pileup">Pileup (Deprecated)</option> | |
| 92 <option value="bed">BED (Deprecated)</option> | |
| 93 </param> | |
| 94 | |
| 95 <conditional name="outputConditional"> | |
| 96 <param name="outputFormat" type="select" label="Output format"> | |
| 97 <option value="vcf" selected="true">VCF (only if input is VCF)</option> | |
| 98 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option> | |
| 99 <option value="txt">Tabular</option> | |
| 100 <option value="bed">BED</option> | |
| 101 <option value="bedAnn">BED annotations</option> | |
| 102 </param> | |
| 103 <when value="vcf" /> | |
| 104 <when value="gatk"> | |
| 105 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" /> | |
| 106 </when> | |
| 107 <when value="txt" /> | |
| 108 <when value="bed" /> | |
| 109 <when value="bedAnn" /> | |
| 110 </conditional> | |
| 111 | |
| 112 <conditional name="snpDb"> | |
| 113 <param name="genomeSrc" type="select" label="Genome source"> | |
| 114 <option value="cached">Locally installed reference genome</option> | |
| 115 <option value="history">Reference genome from your history</option> | |
| 116 <option value="named">Named on demand</option> | |
| 117 </param> | |
| 118 <when value="cached"> | |
| 119 <param name="genomeVersion" type="select" label="Genome"> | |
| 120 <!--GENOME DESCRIPTION--> | |
| 2 | 121 <options from_data_table="snpeffv_genomedb"> |
| 122 <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/> | |
| 123 <filter type="unique_value" column="2" /> | |
| 0 | 124 </options> |
| 125 </param> | |
| 126 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> | |
| 127 <help>These are available for only a few genomes</help> | |
| 2 | 128 <options from_data_table="snpeffv_annotations"> |
| 129 <filter type="param_value" ref="genomeVersion" key="genome" column="2" /> | |
| 130 <filter type="unique_value" column="3" /> | |
| 0 | 131 </options> |
| 132 </param> | |
| 133 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation"> | |
| 134 <help>These are available for only a few genomes</help> | |
| 2 | 135 <options from_data_table="snpeffv_regulationdb"> |
| 136 <filter type="param_value" ref="genomeVersion" key="genome" column="2" /> | |
| 137 <filter type="unique_value" column="3" /> | |
| 0 | 138 </options> |
| 139 </param> | |
| 140 </when> | |
| 141 <when value="history"> | |
| 2 | 142 <param format="snpeffdb" name="snpeff_db" type="data" label="@SNPEFF_VERSION@ Genome Data"> |
| 143 <options options_filter_attribute="metadata.snpeff_version" > | |
| 144 <filter type="add_value" value="@SNPEFF_VERSION@" /> | |
| 145 </options> | |
| 146 <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ Genome databases.">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator> | |
| 147 </param> | |
| 0 | 148 <!-- From metadata --> |
| 149 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> | |
| 150 <help>These are available for only a few genomes</help> | |
| 151 <options> | |
| 152 <filter type="data_meta" ref="snpeff_db" key="annotation" /> | |
| 153 </options> | |
| 154 </param> | |
| 155 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation"> | |
| 156 <help>These are available for only a few genomes</help> | |
| 157 <options> | |
| 158 <filter type="data_meta" ref="snpeff_db" key="regulation" /> | |
| 159 </options> | |
| 160 </param> | |
| 161 </when> | |
| 162 <when value="named"> | |
| 2 | 163 <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> |
| 164 <help>@SNPEFF_DATABASE_URL@</help> | |
| 165 <validator type="regex" message="A genome version name is required">\S+</validator> | |
| 166 </param> | |
| 0 | 167 </when> |
| 168 </conditional> | |
| 169 | |
| 170 <param name="udLength" type="select" label="Upstream / Downstream length"> | |
| 171 <option value="0">No upstream / downstream intervals (0 bases)</option> | |
| 172 <option value="200">200 bases</option> | |
| 173 <option value="500">500 bases</option> | |
| 174 <option value="1000">1000 bases</option> | |
| 175 <option value="2000">2000 bases</option> | |
| 176 <option value="5000" selected="true">5000 bases</option> | |
| 177 <option value="10000">10000 bases</option> | |
| 178 <option value="20000">20000 bases</option> | |
| 179 </param> | |
| 180 | |
| 181 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2"> | |
| 182 <option value="1">1 base</option> | |
| 183 <option value="2" selected="true">2 bases</option> | |
| 184 <option value="3">3 bases</option> | |
| 185 <option value="4">4 bases</option> | |
| 186 <option value="5">5 bases</option> | |
| 187 <option value="6">6 bases</option> | |
| 188 <option value="7">7 bases</option> | |
| 189 <option value="8">8 bases</option> | |
| 190 <option value="9">9 bases</option> | |
| 191 </param> | |
| 192 | |
| 193 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes"> | |
| 194 <option value="no_filter" selected="true">No filter (analyze everything)</option> | |
| 195 <option value="-hom">Analyze homozygous sequence changes only</option> | |
| 196 <option value="-het">Analyze heterozygous sequence changes only</option> | |
| 197 </param> | |
| 198 | |
| 2 | 199 <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation --> |
| 0 | 200 <param name="filterIn" type="select" display="radio" label="Filter sequence changes"> |
| 201 <option value="no_filter" selected="true">No filter (analyze everything)</option> | |
| 202 <option value="-del">Analyze deletions only</option> | |
| 203 <option value="-ins">Analyze insertions only</option> | |
| 204 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms)</option> | |
| 205 <option value="-snp">Only SNPs (single nucleotide polymorphisms)</option> | |
| 206 </param> | |
| 207 | |
| 208 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> | |
| 209 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> | |
| 210 <option value="-canon">Only use canonical transcripts</option> | |
| 211 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> | |
| 212 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option> | |
| 213 <option value="-oicr">Add OICR tag in VCF file</option> | |
| 214 <option value="-onlyReg">Only use regulation tracks</option> | |
| 2 | 215 <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option> |
| 216 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option> | |
| 217 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option> | |
| 0 | 218 </param> |
| 219 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/> | |
| 220 <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file." help="Format is one transcript ID per line."/> | |
| 221 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output"> | |
| 222 <option value="-no-downstream">Do not show DOWNSTREAM changes</option> | |
| 223 <option value="-no-intergenic">Do not show INTERGENIC changes</option> | |
| 224 <option value="-no-intron">Do not show INTRON changes</option> | |
| 225 <option value="-no-upstream">Do not show UPSTREAM changes</option> | |
| 226 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option> | |
| 227 </param> | |
| 228 | |
| 229 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> | |
| 2 | 230 <option value="default" selected="true">Use default (based on input type)</option> |
| 0 | 231 <option value="-0">Force zero-based positions (both input and output)</option> |
| 232 <option value="-1">Force one-based positions (both input and output)</option> | |
| 233 </param> | |
| 234 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name"> | |
| 235 <help> | |
| 236 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. | |
| 237 You can prepend any string you want to the chromosome name. | |
| 238 </help> | |
| 239 <validator type="regex" message="No whitespace allowed">^\S*$</validator> | |
| 240 </param> | |
| 241 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/> | |
| 242 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/> | |
| 243 </inputs> | |
| 244 <outputs> | |
| 245 <data format="vcf" name="snpeff_output" > | |
| 246 <change_format> | |
| 247 <when input="outputConditional.outputFormat" value="txt" format="tabular" /> | |
| 248 <when input="outputConditional.outputFormat" value="bed" format="bed" /> | |
| 249 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> | |
| 250 </change_format> | |
| 251 </data> | |
| 252 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats"> | |
| 253 <filter>generate_stats == True</filter> | |
| 254 </data> | |
| 255 </outputs> | |
| 256 <tests> | |
| 257 <!-- Check that an effect was added in out VCF --> | |
| 258 <!-- Check for a HTML header indicating that this was successful --> | |
| 259 <!-- | |
| 260 <output name="statsFile"> | |
| 261 <assert_contents> | |
| 262 <has_text text="SnpEff: Variant analysis" /> | |
| 263 </assert_contents> | |
| 264 </output> | |
|
5
92b80578fa22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
2
diff
changeset
|
265 --> |
| 0 | 266 <!-- Setting filterOut throws exception in twilltestcase.py |
| 267 <test> | |
| 268 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> | |
| 269 <param name="inputFormat" value="vcf"/> | |
| 270 <param name="outputFormat" value="vcf"/> | |
| 271 <param name="genomeSrc" value="named"/> | |
| 272 <param name="genome_version" value="testCase"/> | |
| 273 <param name="udLength" value="0"/> | |
| 274 <param name="filterHomHet" value="no_filter"/> | |
| 275 <param name="filterIn" value="no_filter"/> | |
| 276 <param name="generate_stats" value="False"/> | |
| 277 <param name="filterOut" value="+-no-upstream"/> | |
| 278 <output name="snpeff_output"> | |
| 279 <assert_contents> | |
| 280 <has_text text="EFF=" /> | |
| 281 </assert_contents> | |
| 282 </output> | |
| 283 </test> | |
|
5
92b80578fa22
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
2
diff
changeset
|
284 --> |
| 0 | 285 |
| 286 <test> | |
| 287 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> | |
| 288 <param name="inputFormat" value="vcf"/> | |
| 289 <param name="outputFormat" value="vcf"/> | |
| 290 <param name="genomeSrc" value="named"/> | |
| 291 <param name="genome_version" value="testCase"/> | |
| 292 <param name="udLength" value="0"/> | |
| 293 <param name="filterHomHet" value="+-het"/> | |
| 294 <param name="filterIn" value="no_filter"/> | |
| 295 <!-- | |
| 296 <param name="filterOut" value=""/> | |
| 297 --> | |
| 298 <param name="generate_stats" value="False"/> | |
| 299 <output name="snpeff_output"> | |
| 300 <assert_contents> | |
| 301 <!-- Check that NO effects were added since -het is set --> | |
| 302 <not_has_text text="EFF=NON_SYNONYMOUS_CODING" /> | |
| 303 </assert_contents> | |
| 304 </output> | |
| 305 </test> | |
| 306 | |
| 307 <test> | |
| 308 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> | |
| 309 <param name="inputFormat" value="vcf"/> | |
| 310 <param name="outputFormat" value="vcf"/> | |
| 311 <param name="genomeSrc" value="named"/> | |
| 312 <param name="genome_version" value="testCase"/> | |
| 313 <param name="udLength" value="0"/> | |
| 314 <param name="filterHomHet" value="no_filter"/> | |
| 315 <param name="filterIn" value="+-del"/> | |
| 316 <!-- | |
| 317 <param name="filterOut" value=""/> | |
| 318 --> | |
| 319 <param name="generate_stats" value="False"/> | |
| 320 <output name="snpeff_output"> | |
| 321 <assert_contents> | |
| 322 <!-- Check that deleletions were evaluated --> | |
| 323 <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" /> | |
| 324 <!-- Check that insertion on last line was NOT evaluated --> | |
| 325 <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" /> | |
| 326 </assert_contents> | |
| 327 </output> | |
| 328 </test> | |
| 329 | |
| 330 <!-- Check that NO UPSTREAM effect was added --> | |
| 331 <!-- Setting filterOut throws exception in twilltestcase.py | |
| 332 <test> | |
| 333 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> | |
| 334 <param name="inputFormat" value="vcf"/> | |
| 335 <param name="outputFormat" value="vcf"/> | |
| 336 <param name="genomeSrc" value="named"/> | |
| 337 <param name="genome_version" value="testCase"/> | |
| 338 <param name="udLength" value="0"/> | |
| 339 <param name="filterHomHet" value="no_filter"/> | |
| 340 <param name="filterIn" value="no_filter"/> | |
| 341 <param name="filterOut" value="+-no-upstream"/> | |
| 342 <param name="generate_stats" value="False"/> | |
| 343 <output name="snpeff_output"> | |
| 344 <assert_contents> | |
| 345 <not_has_text text="UPSTREAM" /> | |
| 346 </assert_contents> | |
| 347 </output> | |
| 348 </test> | |
| 349 --> | |
| 350 | |
| 351 </tests> | |
| 352 <help> | |
| 2 | 353 |
| 0 | 354 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. |
| 355 | |
| 356 @EXTERNAL_DOCUMENTATION@ | |
| 357 | |
| 2 | 358 @CITATION_SECTION@ |
| 359 | |
| 0 | 360 </help> |
| 361 <expand macro="citations" /> | |
| 362 </tool> | |
| 363 |