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comparison snpEff.xml @ 1:500832f27cbc draft

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Uploaded
author iuc
date Thu, 22 Jan 2015 08:28:37 -0500
parents e8adfc4c0a6b
children e09ce114d240
comparison
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0:e8adfc4c0a6b 1:500832f27cbc
1 <tool id="snpEff" name="SnpEff" version="3.4"> 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 $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
13 #end if 14 #end if
14 #if $filterIn and $filterIn.__str__ != 'no_filter': 15 #if $filterIn and $filterIn.__str__ != 'no_filter':
15 $filterIn 16 $filterIn
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
64 ${snpDb.snpeff_db.metadata.genome_version} 65 ${snpDb.snpeff_db.metadata.genome_version}
65 #else 66 #else
66 -download 67 -download
67 $snpDb.genome_version 68 $snpDb.genome_version
68 #end if 69 #end if
69 $input > $snpeff_output 70 $input > $snpeff_output ;
71 #if $statsFile:
72 #import os
73 #set $genes_file = str($statsFile) + '.genes.txt'
74 #set $genes_file_name = os.path.split($genes_file)[-1]
75 mkdir $statsFile.files_path;
76 mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#;
77 #end if
78 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
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]"
80 sed -i 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output
81 #end if
82 ]]>
70 </command> 83 </command>
71 <inputs> 84 <inputs>
72 <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)"/>
73 86
74 <param name="inputFormat" type="select" label="Input format"> 87 <param name="inputFormat" type="select" label="Input format">
76 <option value="txt">Tabular (Deprecated)</option> 89 <option value="txt">Tabular (Deprecated)</option>
77 <option value="pileup">Pileup (Deprecated)</option> 90 <option value="pileup">Pileup (Deprecated)</option>
78 <option value="bed">BED (Deprecated)</option> 91 <option value="bed">BED (Deprecated)</option>
79 </param> 92 </param>
80 93
81 <param name="outputFormat" type="select" label="Output format"> 94 <conditional name="outputConditional">
82 <option value="vcf" selected="true">VCF (only if input is VCF)</option> 95 <param name="outputFormat" type="select" label="Output format">
83 <option value="txt">Tabular</option> 96 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
84 <option value="bed">BED</option> 97 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
85 <option value="bedAnn">BED Annotations</option> 98 <option value="txt">Tabular</option>
86 </param> 99 <option value="bed">BED</option>
100 <option value="bedAnn">BED annotations</option>
101 </param>
102 <when value="vcf" />
103 <when value="gatk">
104 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
105 </when>
106 <when value="txt" />
107 <when value="bed" />
108 <when value="bedAnn" />
109 </conditional>
87 110
88 <conditional name="snpDb"> 111 <conditional name="snpDb">
89 <param name="genomeSrc" type="select" label="Genome source"> 112 <param name="genomeSrc" type="select" label="Genome source">
90 <option value="cached">Locally installed reference genome</option> 113 <option value="cached">Locally installed reference genome</option>
91 <option value="history">Reference genome from your history</option> 114 <option value="history">Reference genome from your history</option>
92 <option value="named">Named on demand</option> 115 <option value="named">Named on demand</option>
93 </param> 116 </param>
94 <when value="cached"> 117 <when value="cached">
95 <param name="genomeVersion" type="select" label="Genome"> 118 <param name="genomeVersion" type="select" label="Genome">
96 <!--GENOME DESCRIPTION--> 119 <!--GENOME DESCRIPTION-->
97 <options from_data_table="snpeff_genomedb"> 120 <options from_data_table="snpeffv_genomedb">
98 <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" />
99 </options> 123 </options>
100 </param> 124 </param>
101 <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">
102 <help>These are available for only a few genomes</help> 126 <help>These are available for only a few genomes</help>
103 <options from_data_table="snpeff_annotations"> 127 <options from_data_table="snpeffv_annotations">
104 <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> 128 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
105 <filter type="unique_value" column="1" /> 129 <filter type="unique_value" column="3" />
106 </options> 130 </options>
107 </param> 131 </param>
108 <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">
109 <help>These are available for only a few genomes</help> 133 <help>These are available for only a few genomes</help>
110 <options from_data_table="snpeff_regulationdb"> 134 <options from_data_table="snpeffv_regulationdb">
111 <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> 135 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
112 <filter type="unique_value" column="1" /> 136 <filter type="unique_value" column="3" />
113 </options> 137 </options>
114 </param> 138 </param>
115 </when> 139 </when>
116 <when value="history"> 140 <when value="history">
117 <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>
118 <!-- From metadata --> 147 <!-- From metadata -->
119 <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">
120 <help>These are available for only a few genomes</help> 149 <help>These are available for only a few genomes</help>
121 <options> 150 <options>
122 <filter type="data_meta" ref="snpeff_db" key="annotation" /> 151 <filter type="data_meta" ref="snpeff_db" key="annotation" />
123 </options> 152 </options>
124 </param> 153 </param>
125 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation"> 154 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
126 <help>These are available for only a few genomes</help> 155 <help>These are available for only a few genomes</help>
127 <options> 156 <options>
128 <filter type="data_meta" ref="snpeff_db" key="regulation" /> 157 <filter type="data_meta" ref="snpeff_db" key="regulation" />
129 </options> 158 </options>
130 </param> 159 </param>
131 </when> 160 </when>
132 <when value="named"> 161 <when value="named">
133 <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>
134 </when> 166 </when>
135 </conditional> 167 </conditional>
136 168
137 <param name="udLength" type="select" label="Upstream / Downstream length"> 169 <param name="udLength" type="select" label="Upstream / Downstream length">
138 <option value="0">No upstream / downstream intervals (0 bases)</option> 170 <option value="0">No upstream / downstream intervals (0 bases)</option>
145 <option value="20000">20000 bases</option> 177 <option value="20000">20000 bases</option>
146 </param> 178 </param>
147 179
148 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2"> 180 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2">
149 <option value="1">1 base</option> 181 <option value="1">1 base</option>
150 <option value="2">2 bases</option> 182 <option value="2" selected="true">2 bases</option>
151 <option value="3">3 bases</option> 183 <option value="3">3 bases</option>
152 <option value="4">4 bases</option> 184 <option value="4">4 bases</option>
153 <option value="5">5 bases</option> 185 <option value="5">5 bases</option>
154 <option value="6">6 bases</option> 186 <option value="6">6 bases</option>
155 <option value="7">7 bases</option> 187 <option value="7">7 bases</option>
157 <option value="9">9 bases</option> 189 <option value="9">9 bases</option>
158 </param> 190 </param>
159 191
160 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes"> 192 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
161 <option value="no_filter" selected="true">No filter (analyze everything)</option> 193 <option value="no_filter" selected="true">No filter (analyze everything)</option>
162 <option value="-hom">Analyze homozygous sequence changes only </option> 194 <option value="-hom">Analyze homozygous sequence changes only</option>
163 <option value="-het">Analyze heterozygous sequence changes only </option> 195 <option value="-het">Analyze heterozygous sequence changes only</option>
164 </param> 196 </param>
165 197
166 <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation --> 198 <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation -->
167 <param name="filterIn" type="select" display="radio" label="Filter sequence changes"> 199 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
168 <option value="no_filter" selected="true">No filter (analyze everything)</option> 200 <option value="no_filter" selected="true">No filter (analyze everything)</option>
169 <option value="-del">Analyze deletions only </option> 201 <option value="-del">Analyze deletions only</option>
170 <option value="-ins">Analyze insertions only </option> 202 <option value="-ins">Analyze insertions only</option>
171 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms) </option> 203 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms)</option>
172 <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option> 204 <option value="-snp">Only SNPs (single nucleotide polymorphisms)</option>
173 </param> 205 </param>
174 206
175 <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">
176 <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline)</option> 208 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
177 <option value="-canon">Only use canonical transcripts</option> 209 <option value="-canon">Only use canonical transcripts</option>
178 <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>
179 <option value="-hgvs">Use HGVS annotations for amino acid sub-field</option> 211 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
180 <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option>
181 <option value="-oicr">Add OICR tag in VCF file</option> 212 <option value="-oicr">Add OICR tag in VCF file</option>
182 <option value="-onlyReg">Only use regulation tracks</option> 213 <option value="-onlyReg">Only use regulation tracks</option>
183 <option value="-sequenceOntolgy">Use Sequence Ontolgy 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>
184 </param> 217 </param>
185 <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"/>
186 <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."/>
187 <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">
188 <option value="-no-downstream">Do not show DOWNSTREAM changes</option> 221 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
191 <option value="-no-upstream">Do not show UPSTREAM changes</option> 224 <option value="-no-upstream">Do not show UPSTREAM changes</option>
192 <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>
193 </param> 226 </param>
194 227
195 <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">
196 <option value="" selected="true">Use default (based on input type)</option> 229 <option value="default" selected="true">Use default (based on input type)</option>
197 <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>
198 <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>
199 </param> 232 </param>
200 <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">
201 <help> 234 <help>
208 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/> 241 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
209 </inputs> 242 </inputs>
210 <outputs> 243 <outputs>
211 <data format="vcf" name="snpeff_output" > 244 <data format="vcf" name="snpeff_output" >
212 <change_format> 245 <change_format>
213 <when input="outputFormat" value="vcf" format="vcf" /> 246 <when input="outputConditional.outputFormat" value="txt" format="tabular" />
214 <when input="outputFormat" value="txt" format="tabular" /> 247 <when input="outputConditional.outputFormat" value="bed" format="bed" />
215 <when input="outputFormat" value="bed" format="bed" /> 248 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
216 <when input="outputFormat" value="bedAnn" format="bed" />
217 </change_format> 249 </change_format>
218 </data> 250 </data>
219 <data format="html" name="statsFile"> 251 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">
220 <filter>generate_stats == True</filter> 252 <filter>generate_stats == True</filter>
221 </data> 253 </data>
222 </outputs> 254 </outputs>
223 <expand macro="stdio" /> 255 <expand macro="stdio" />
224 <tests> 256 <tests>
278 <param name="outputFormat" value="vcf"/> 310 <param name="outputFormat" value="vcf"/>
279 <param name="genomeSrc" value="named"/> 311 <param name="genomeSrc" value="named"/>
280 <param name="genome_version" value="testCase"/> 312 <param name="genome_version" value="testCase"/>
281 <param name="udLength" value="0"/> 313 <param name="udLength" value="0"/>
282 <param name="filterHomHet" value="no_filter"/> 314 <param name="filterHomHet" value="no_filter"/>
283 <param name="filterIn" value="del"/> 315 <param name="filterIn" value="+-del"/>
284 <!-- 316 <!--
285 <param name="filterOut" value=""/> 317 <param name="filterOut" value=""/>
286 --> 318 -->
287 <param name="generate_stats" value="False"/> 319 <param name="generate_stats" value="False"/>
288 <output name="snpeff_output"> 320 <output name="snpeff_output">
324 @EXTERNAL_DOCUMENTATION@ 356 @EXTERNAL_DOCUMENTATION@
325 357
326 @CITATION_SECTION@ 358 @CITATION_SECTION@
327 359
328 </help> 360 </help>
361 <expand macro="citations" />
329 </tool> 362 </tool>
330 363