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comparison snpEff.xml @ 2:114f423f99c0 draft

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author iuc
date Tue, 07 Apr 2015 10:54:12 -0400
parents 39bac90c773d
children 92b80578fa22
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1:1938721334b3 2:114f423f99c0
1 <tool id="snpEff" name="SnpEff" version="3.6"> 1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0">
2 <description>Variant effect and annotation</description> 2 <description>Variant effect and annotation</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <macros> 4 <macros>
5 <import>snpEff_macros.xml</import> 5 <import>snpEff_macros.xml</import>
6 </macros> 6 </macros>
7 <command> 7 <command>
8 <![CDATA[
8 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff 9 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff
9 -c \$SNPEFF_JAR_PATH/snpEff.config 10 -c \$SNPEFF_JAR_PATH/snpEff.config
10 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength 11 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
11 #if $spliceSiteSize and $spliceSiteSize.__str__ != '': 12 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
12 -spliceSiteSize $spliceSiteSize 13 -spliceSiteSize $spliceSiteSize
32 -interval $intervals 33 -interval $intervals
33 #end if 34 #end if
34 #if $statsFile: 35 #if $statsFile:
35 -stats $statsFile 36 -stats $statsFile
36 #end if 37 #end if
37 #if $offset.__str__ != '': 38 #if $offset.__str__ != 'default':
38 ${offset} 39 ${offset}
39 #end if 40 #end if
40 #if $chr.__str__.strip() != '': 41 #if $chr.__str__.strip() != '':
41 -chr "$chr" 42 -chr "$chr"
42 #end if 43 #end if
50 #if $snpDb.regulation and $snpDb.regulation.__str__ != '': 51 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
51 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))# 52 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
52 #end if 53 #end if
53 $snpDb.genomeVersion 54 $snpDb.genomeVersion
54 #elif $snpDb.genomeSrc == 'history': 55 #elif $snpDb.genomeSrc == 'history':
55 -dataDir ${snpDb.snpeff_db.files_path} 56 -dataDir ${snpDb.snpeff_db.extra_files_path}
56 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': 57 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
57 #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',') 58 #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
58 #echo " " 59 #echo " "
59 #echo ' -'.join($xannotations) 60 #echo ' -'.join($xannotations)
60 #end if 61 #end if
74 mkdir $statsFile.files_path; 75 mkdir $statsFile.files_path;
75 mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#; 76 mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#;
76 #end if 77 #end if
77 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 78 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
78 ## 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]" 79 ## 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]"
79 sed -i 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output 80 sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output
80 #end if 81 #end if
82 ]]>
81 </command> 83 </command>
82 <inputs> 84 <inputs>
83 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> 85 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
84 86
85 <param name="inputFormat" type="select" label="Input format"> 87 <param name="inputFormat" type="select" label="Input format">
113 <option value="named">Named on demand</option> 115 <option value="named">Named on demand</option>
114 </param> 116 </param>
115 <when value="cached"> 117 <when value="cached">
116 <param name="genomeVersion" type="select" label="Genome"> 118 <param name="genomeVersion" type="select" label="Genome">
117 <!--GENOME DESCRIPTION--> 119 <!--GENOME DESCRIPTION-->
118 <options from_data_table="snpeff_genomedb"> 120 <options from_data_table="snpeffv_genomedb">
119 <filter type="unique_value" column="0" /> 121 <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/>
122 <filter type="unique_value" column="2" />
120 </options> 123 </options>
121 </param> 124 </param>
122 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> 125 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
123 <help>These are available for only a few genomes</help> 126 <help>These are available for only a few genomes</help>
124 <options from_data_table="snpeff_annotations"> 127 <options from_data_table="snpeffv_annotations">
125 <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> 128 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
126 <filter type="unique_value" column="1" /> 129 <filter type="unique_value" column="3" />
127 </options> 130 </options>
128 </param> 131 </param>
129 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation"> 132 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
130 <help>These are available for only a few genomes</help> 133 <help>These are available for only a few genomes</help>
131 <options from_data_table="snpeff_regulationdb"> 134 <options from_data_table="snpeffv_regulationdb">
132 <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> 135 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
133 <filter type="unique_value" column="1" /> 136 <filter type="unique_value" column="3" />
134 </options> 137 </options>
135 </param> 138 </param>
136 </when> 139 </when>
137 <when value="history"> 140 <when value="history">
138 <param format="snpeffdb" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/> 141 <param format="snpeffdb" name="snpeff_db" type="data" label="@SNPEFF_VERSION@ Genome Data">
142 <options options_filter_attribute="metadata.snpeff_version" >
143 <filter type="add_value" value="@SNPEFF_VERSION@" />
144 </options>
145 <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>
146 </param>
139 <!-- From metadata --> 147 <!-- From metadata -->
140 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> 148 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
141 <help>These are available for only a few genomes</help> 149 <help>These are available for only a few genomes</help>
142 <options> 150 <options>
143 <filter type="data_meta" ref="snpeff_db" key="annotation" /> 151 <filter type="data_meta" ref="snpeff_db" key="annotation" />
149 <filter type="data_meta" ref="snpeff_db" key="regulation" /> 157 <filter type="data_meta" ref="snpeff_db" key="regulation" />
150 </options> 158 </options>
151 </param> 159 </param>
152 </when> 160 </when>
153 <when value="named"> 161 <when value="named">
154 <param name="genome_version" type="text" value="GRCh37.68" label="Snpff Version Name"/> 162 <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
163 <help>@SNPEFF_DATABASE_URL@</help>
164 <validator type="regex" message="A genome version name is required">\S+</validator>
165 </param>
155 </when> 166 </when>
156 </conditional> 167 </conditional>
157 168
158 <param name="udLength" type="select" label="Upstream / Downstream length"> 169 <param name="udLength" type="select" label="Upstream / Downstream length">
159 <option value="0">No upstream / downstream intervals (0 bases)</option> 170 <option value="0">No upstream / downstream intervals (0 bases)</option>
182 <option value="no_filter" selected="true">No filter (analyze everything)</option> 193 <option value="no_filter" selected="true">No filter (analyze everything)</option>
183 <option value="-hom">Analyze homozygous sequence changes only</option> 194 <option value="-hom">Analyze homozygous sequence changes only</option>
184 <option value="-het">Analyze heterozygous sequence changes only</option> 195 <option value="-het">Analyze heterozygous sequence changes only</option>
185 </param> 196 </param>
186 197
198 <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation -->
187 <param name="filterIn" type="select" display="radio" label="Filter sequence changes"> 199 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
188 <option value="no_filter" selected="true">No filter (analyze everything)</option> 200 <option value="no_filter" selected="true">No filter (analyze everything)</option>
189 <option value="-del">Analyze deletions only</option> 201 <option value="-del">Analyze deletions only</option>
190 <option value="-ins">Analyze insertions only</option> 202 <option value="-ins">Analyze insertions only</option>
191 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms)</option> 203 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms)</option>
194 206
195 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> 207 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
196 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> 208 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
197 <option value="-canon">Only use canonical transcripts</option> 209 <option value="-canon">Only use canonical transcripts</option>
198 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> 210 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
199 <option value="-hgvs">Use HGVS annotations for amino acid sub-field</option>
200 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option> 211 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
201 <option value="-oicr">Add OICR tag in VCF file</option> 212 <option value="-oicr">Add OICR tag in VCF file</option>
202 <option value="-onlyReg">Only use regulation tracks</option> 213 <option value="-onlyReg">Only use regulation tracks</option>
203 <option value="-sequenceOntolgy">Use Sequence Ontology terms</option> 214 <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>
215 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
216 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
204 </param> 217 </param>
205 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/> 218 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
206 <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."/> 219 <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."/>
207 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output"> 220 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
208 <option value="-no-downstream">Do not show DOWNSTREAM changes</option> 221 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
211 <option value="-no-upstream">Do not show UPSTREAM changes</option> 224 <option value="-no-upstream">Do not show UPSTREAM changes</option>
212 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option> 225 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
213 </param> 226 </param>
214 227
215 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> 228 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
216 <option value="" selected="true">Use default (based on input type)</option> 229 <option value="default" selected="true">Use default (based on input type)</option>
217 <option value="-0">Force zero-based positions (both input and output)</option> 230 <option value="-0">Force zero-based positions (both input and output)</option>
218 <option value="-1">Force one-based positions (both input and output)</option> 231 <option value="-1">Force one-based positions (both input and output)</option>
219 </param> 232 </param>
220 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name"> 233 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
221 <help> 234 <help>
335 </test> 348 </test>
336 --> 349 -->
337 350
338 </tests> 351 </tests>
339 <help> 352 <help>
353
340 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. 354 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
341 355
342 @EXTERNAL_DOCUMENTATION@ 356 @EXTERNAL_DOCUMENTATION@
357
358 @CITATION_SECTION@
343 359
344 </help> 360 </help>
345 <expand macro="citations" /> 361 <expand macro="citations" />
346 </tool> 362 </tool>
347 363