Mercurial > repos > jjohnson > snpeff

comparison snpEff.xml @ 18:36f3c82323e6

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file
author Jim Johnson <jj@umn.edu>
date Tue, 13 Jan 2015 13:36:11 -0600
parents 13d81e5226cd
children 2e37b58fc24d
comparison
equal deleted inserted replaced
17:13d81e5226cd 18:36f3c82323e6
1 <tool id="snpEff" name="SnpEff" version="4.0.1"> 1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.2">
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
30 #end if 31 #end if
31 #if str( $intervals ) != 'None': ### fix this for multiple dataset input 32 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
32 -interval $intervals 33 -interval $intervals
33 #end if 34 #end if
34 #if $statsFile: 35 #if $statsFile:
35 -stats snpeff_report 36 -stats $statsFile
36 #end if 37 #end if
37 #if $offset.__str__ != 'default': 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() != '':
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 ;
70 #if $statsFile: 71 #if $statsFile:
71 &amp;&amp; mkdir $statsFile.extra_files_path &amp;&amp; cp snpeff_report.genes.txt $statsFile.extra_files_path 72 #import os
72 #end if 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 ]]>
73 </command> 83 </command>
74 <inputs> 84 <inputs>
75 <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)"/>
76 86
77 <param name="inputFormat" type="select" label="Input format"> 87 <param name="inputFormat" type="select" label="Input format">
79 <option value="txt">Tabular (Deprecated)</option> 89 <option value="txt">Tabular (Deprecated)</option>
80 <option value="pileup">Pileup (Deprecated)</option> 90 <option value="pileup">Pileup (Deprecated)</option>
81 <option value="bed">BED (Deprecated)</option> 91 <option value="bed">BED (Deprecated)</option>
82 </param> 92 </param>
83 93
84 <param name="outputFormat" type="select" label="Output format"> 94 <conditional name="outputConditional">
85 <option value="vcf" selected="true">VCF (only if input is VCF)</option> 95 <param name="outputFormat" type="select" label="Output format">
86 <option value="txt">Tabular</option> 96 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
87 <option value="bed">BED</option> 97 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
88 <option value="bedAnn">BED Annotations</option> 98 <option value="txt">Tabular</option>
89 </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>
90 110
91 <conditional name="snpDb"> 111 <conditional name="snpDb">
92 <param name="genomeSrc" type="select" label="Genome source"> 112 <param name="genomeSrc" type="select" label="Genome source">
93 <option value="cached">Locally installed reference genome</option> 113 <option value="cached">Locally installed reference genome</option>
94 <option value="history">Reference genome from your history</option> 114 <option value="history">Reference genome from your history</option>
95 <option value="named">Named on demand</option> 115 <option value="named">Named on demand</option>
96 </param> 116 </param>
97 <when value="cached"> 117 <when value="cached">
98 <param name="genomeVersion" type="select" label="Genome"> 118 <param name="genomeVersion" type="select" label="Genome">
99 <!--GENOME DESCRIPTION--> 119 <!--GENOME DESCRIPTION-->
100 <options from_data_table="snpeff4_genomedb"> 120 <options from_data_table="snpeffv_genomedb">
101 <filter type="unique_value" column="0" /> 121 <filter type="static_value" name="snpeff_version" value="SnpEff4.1" column="1"/>
122 <filter type="unique_value" column="2" />
102 </options> 123 </options>
103 </param> 124 </param>
104 <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">
105 <help>These are available for only a few genomes</help> 126 <help>These are available for only a few genomes</help>
106 <options from_data_table="snpeff4_annotations"> 127 <options from_data_table="snpeffv_annotations">
107 <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> 128 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
108 <filter type="unique_value" column="1" /> 129 <filter type="unique_value" column="1" />
109 </options> 130 </options>
110 </param> 131 </param>
111 <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">
112 <help>These are available for only a few genomes</help> 133 <help>These are available for only a few genomes</help>
113 <options from_data_table="snpeff4_regulationdb"> 134 <options from_data_table="snpeffv_regulationdb">
114 <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> 135 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
115 <filter type="unique_value" column="1" /> 136 <filter type="unique_value" column="1" />
116 </options> 137 </options>
117 </param> 138 </param>
118 </when> 139 </when>
119 <when value="history"> 140 <when value="history">
120 <param format="snpeffdbv4" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/> 141 <param format="snpeffdbv41" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/>
121 <!-- From metadata --> 142 <!-- From metadata -->
122 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> 143 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
123 <help>These are available for only a few genomes</help> 144 <help>These are available for only a few genomes</help>
124 <options> 145 <options>
125 <filter type="data_meta" ref="snpeff_db" key="annotation" /> 146 <filter type="data_meta" ref="snpeff_db" key="annotation" />
126 </options> 147 </options>
127 </param> 148 </param>
128 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation"> 149 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
129 <help>These are available for only a few genomes</help> 150 <help>These are available for only a few genomes</help>
130 <options> 151 <options>
131 <filter type="data_meta" ref="snpeff_db" key="regulation" /> 152 <filter type="data_meta" ref="snpeff_db" key="regulation" />
132 </options> 153 </options>
133 </param> 154 </param>
134 </when> 155 </when>
135 <when value="named"> 156 <when value="named">
136 <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> 157 <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
137 <help>http://sourceforge.net/projects/snpeff/files/databases/v4_0/</help> 158 <help>@SNPEFF_DATABASE_URL@</help>
138 <validator type="regex" message="A genome version name is required">\S+</validator> 159 <validator type="regex" message="A genome version name is required">\S+</validator>
139 </param> 160 </param>
140 </when> 161 </when>
141 </conditional> 162 </conditional>
142 163
151 <option value="20000">20000 bases</option> 172 <option value="20000">20000 bases</option>
152 </param> 173 </param>
153 174
154 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2"> 175 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2">
155 <option value="1">1 base</option> 176 <option value="1">1 base</option>
156 <option value="2">2 bases</option> 177 <option value="2" selected="true">2 bases</option>
157 <option value="3">3 bases</option> 178 <option value="3">3 bases</option>
158 <option value="4">4 bases</option> 179 <option value="4">4 bases</option>
159 <option value="5">5 bases</option> 180 <option value="5">5 bases</option>
160 <option value="6">6 bases</option> 181 <option value="6">6 bases</option>
161 <option value="7">7 bases</option> 182 <option value="7">7 bases</option>
163 <option value="9">9 bases</option> 184 <option value="9">9 bases</option>
164 </param> 185 </param>
165 186
166 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes"> 187 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
167 <option value="no_filter" selected="true">No filter (analyze everything)</option> 188 <option value="no_filter" selected="true">No filter (analyze everything)</option>
168 <option value="-hom">Analyze homozygous sequence changes only </option> 189 <option value="-hom">Analyze homozygous sequence changes only</option>
169 <option value="-het">Analyze heterozygous sequence changes only </option> 190 <option value="-het">Analyze heterozygous sequence changes only</option>
170 </param> 191 </param>
171 192
172 <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation --> 193 <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation -->
173 <param name="filterIn" type="select" display="radio" label="Filter sequence changes"> 194 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
174 <option value="no_filter" selected="true">No filter (analyze everything)</option> 195 <option value="no_filter" selected="true">No filter (analyze everything)</option>
175 <option value="-del">Analyze deletions only </option> 196 <option value="-del">Analyze deletions only</option>
176 <option value="-ins">Analyze insertions only </option> 197 <option value="-ins">Analyze insertions only</option>
177 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms) </option> 198 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms)</option>
178 <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option> 199 <option value="-snp">Only SNPs (single nucleotide polymorphisms)</option>
179 </param> 200 </param>
180 201
181 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> 202 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
182 <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline)</option> 203 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
183 <option value="-canon">Only use canonical transcripts</option> 204 <option value="-canon">Only use canonical transcripts</option>
184 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> 205 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
185 <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option> 206 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
186 <option value="-oicr">Add OICR tag in VCF file</option> 207 <option value="-oicr">Add OICR tag in VCF file</option>
187 <option value="-onlyReg">Only use regulation tracks</option> 208 <option value="-onlyReg">Only use regulation tracks</option>
188 <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> 209 <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>
189 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option> 210 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
190 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option> 211 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
215 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/> 236 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
216 </inputs> 237 </inputs>
217 <outputs> 238 <outputs>
218 <data format="vcf" name="snpeff_output" > 239 <data format="vcf" name="snpeff_output" >
219 <change_format> 240 <change_format>
220 <when input="outputFormat" value="vcf" format="vcf" /> 241 <when input="outputConditional.outputFormat" value="txt" format="tabular" />
221 <when input="outputFormat" value="txt" format="tabular" /> 242 <when input="outputConditional.outputFormat" value="bed" format="bed" />
222 <when input="outputFormat" value="bed" format="bed" /> 243 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
223 <when input="outputFormat" value="bedAnn" format="bed" />
224 </change_format> 244 </change_format>
225 </data> 245 </data>
226 <data format="html" name="statsFile" label="{tool.name} on ${on_string} Summary Report" from_work_dir="snpeff_report"> 246 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">
227 <filter>generate_stats == True</filter> 247 <filter>generate_stats == True</filter>
228 </data> 248 </data>
229 </outputs> 249 </outputs>
230 <expand macro="stdio" /> 250 <expand macro="stdio" />
231 <tests> 251 <tests>
285 <param name="outputFormat" value="vcf"/> 305 <param name="outputFormat" value="vcf"/>
286 <param name="genomeSrc" value="named"/> 306 <param name="genomeSrc" value="named"/>
287 <param name="genome_version" value="testCase"/> 307 <param name="genome_version" value="testCase"/>
288 <param name="udLength" value="0"/> 308 <param name="udLength" value="0"/>
289 <param name="filterHomHet" value="no_filter"/> 309 <param name="filterHomHet" value="no_filter"/>
290 <param name="filterIn" value="del"/> 310 <param name="filterIn" value="+-del"/>
291 <!-- 311 <!--
292 <param name="filterOut" value=""/> 312 <param name="filterOut" value=""/>
293 --> 313 -->
294 <param name="generate_stats" value="False"/> 314 <param name="generate_stats" value="False"/>
295 <output name="snpeff_output"> 315 <output name="snpeff_output">
331 @EXTERNAL_DOCUMENTATION@ 351 @EXTERNAL_DOCUMENTATION@
332 352
333 @CITATION_SECTION@ 353 @CITATION_SECTION@
334 354
335 </help> 355 </help>
356 <expand macro="citations" />
336 </tool> 357 </tool>
337 358