Mercurial > repos > iuc > snpeff

comparison snpEff.xml @ 33:94653948fdb9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5
author iuc
date Sat, 04 Oct 2025 17:00:46 +0000
parents ebe9fd7e5bd1
children
comparison
equal deleted inserted replaced
32:ebe9fd7e5bd1 33:94653948fdb9
2 <description> annotate variants</description> 2 <description> annotate variants</description>
3 <macros> 3 <macros>
4 <import>snpEff_macros.xml</import> 4 <import>snpEff_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <expand macro="requirement" /> 7 <expand macro="requirement">
8 <requirement type="package" version="9.5">coreutils</requirement>
9 </expand>
8 </requirements> 10 </requirements>
9 <expand macro="stdio" /> 11 <expand macro="stdio" />
10 <expand macro="version_command" /> 12 <expand macro="version_command" />
11 <command><![CDATA[ 13 <command><![CDATA[
12 #if $intervals 14 #if $intervals
45 -onlyTr '$transcripts' 47 -onlyTr '$transcripts'
46 #end if 48 #end if
47 #if $intervals ### fix this for multiple dataset input 49 #if $intervals ### fix this for multiple dataset input
48 -interval intervals.bed 50 -interval intervals.bed
49 #end if 51 #end if
50 #if $statsFile:
51 -stats '$statsFile'
52 #end if
53 #if $csvStats:
54 -csvStats '$csvFile'
55 #end if
56 #if str($chr).strip() != '': 52 #if str($chr).strip() != '':
57 -chr '$chr' 53 -chr '$chr'
54 #end if
55 #if $generate_stats or $generate_gene_stats or $csvStats:
56 #if $csvStats:
57 $csvStats snpeff_stats.csv
58 #end if
59 #if $generate_stats or ($generate_gene_stats and not $csvStats):
60 ## the base name passed in via the -csvStats or the -s option also determines the name of the genes.txt file
61 ## so in the absence of the first we need the second to have a consistent name of the genes.txt file
62 -s snpeff_stats.html
63 #end if
64 #else:
65 ## when no stats output is requested by the user, we can make things a little more efficient
66 ## by telling snpEff that it doesn't have to write even the default (html and genes.txt) ones.
67 -noStats
58 #end if 68 #end if
59 $noLog 69 $noLog
60 ## Regulation names can include parentheses: H3K4me3-MSC_(VB)_enriched_sites 70 ## Regulation names can include parentheses: H3K4me3-MSC_(VB)_enriched_sites
61 ## Enclose them in in single and double quotes, as the conda snpEff bash script will remove outer quotes 71 ## Enclose them in in single and double quotes, as the conda snpEff bash script will remove outer quotes
62 #if $snpDb.genomeSrc == 'cached': 72 #if $snpDb.genomeSrc == 'cached':
86 -dataDir "\$PWD/temp" 96 -dataDir "\$PWD/temp"
87 -download 97 -download
88 '$snpDb.genome_version' 98 '$snpDb.genome_version'
89 #end if 99 #end if
90 '$input' > '$snpeff_output' 100 '$input' > '$snpeff_output'
91 #if $statsFile: 101 #if $generate_gene_stats:
92 && 102 ## remove the first, unnecessary comment line from the output
93 #import os 103 && tail -n+2 snpeff_stats.genes.txt > genes.txt
94 #if $csvStats: 104 #end if
95 #set $genes_file = str($csvFile) + '.genes.txt' 105 #if $generate_stats:
96 #else 106 ## independently of whether the user asked for the gene.txt file,
97 #set $genes_file = str($statsFile) + '.genes.txt' 107 ## we need to add it to files_path because the stats html report links to it.
98 #end if 108 && mkdir '$statsFile.files_path' &&
99 #set $genes_file_name = os.path.split($genes_file)[-1] 109 mv snpeff_stats.genes.txt $statsFile.files_path
100 mkdir '$statsFile.files_path' &&
101 mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#'
102 #end if 110 #end if
103 ]]></command> 111 ]]></command>
104 <inputs> 112 <inputs>
105 <param name="input" type="data" format="vcf,bed" label="Sequence changes (SNPs, MNPs, InDels)"/> 113 <param name="input" type="data" format="vcf,bed" label="Sequence changes (SNPs, MNPs, InDels)"/>
106 <param argument="-i" name="inputFormat" type="select" label="Input format" help="Specify the format of input dataset(s)"> 114 <param argument="-i" name="inputFormat" type="select" label="Input format" help="Specify the format of input dataset(s)">
112 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option> 120 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
113 <option value="bed">BED</option> 121 <option value="bed">BED</option>
114 <option value="bedAnn">BED annotations</option> 122 <option value="bedAnn">BED annotations</option>
115 </param> 123 </param>
116 <param argument="-csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report?" help="Useful for downstream analyses and report generation" /> 124 <param argument="-csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report?" help="Useful for downstream analyses and report generation" />
117 <param argument="-noStats" name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats?" help="Generates an HTML summary of results"/> 125 <param name="generate_stats" type="boolean" checked="true" label="Produce Summary Stats?" help="Generates an HTML summary of results"/>
126 <param name="generate_gene_stats" type="boolean" label="Produce Gene Statistics output?" help="Generates a table of effects per gene as an extra output"/>
118 <conditional name="snpDb"> 127 <conditional name="snpDb">
119 <param name="genomeSrc" type="select" label="Genome source"> 128 <param name="genomeSrc" type="select" label="Genome source">
120 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well --> 129 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well -->
121 <option value="cached">Locally installed snpEff database</option> 130 <option value="cached">Locally installed snpEff database</option>
122 <option value="history">Downloaded snpEff database in your history</option> 131 <option value="history">Downloaded snpEff database in your history</option>
125 </param> 134 </param>
126 <when value="cached"> 135 <when value="cached">
127 <param name="genomeVersion" type="select" label="Genome"> 136 <param name="genomeVersion" type="select" label="Genome">
128 <!--GENOME DESCRIPTION--> 137 <!--GENOME DESCRIPTION-->
129 <options from_data_table="snpeffv_genomedb"> 138 <options from_data_table="snpeffv_genomedb">
130 <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/> 139 <filter type="regexp" column="1" value="@COMPATIBLE_DB_VERSIONS_REGEX@" />
131 <filter type="unique_value" column="2" /> 140 <filter type="unique_value" column="2" />
132 </options> 141 </options>
133 </param> 142 </param>
134 <section name="reg_section" expanded="false" title="Regulation options"> 143 <section name="reg_section" expanded="false" title="Regulation options">
135 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes"> 144 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes">
136 <options from_data_table="snpeffv_regulationdb"> 145 <options from_data_table="snpeffv_regulationdb">
137 <filter type="param_value" ref="genomeVersion" key="genome" column="2" /> 146 <filter type="regexp" column="1" value="@COMPATIBLE_DB_VERSIONS_REGEX@" />
147 <filter type="param_value" ref="genomeVersion" column="2" />
138 <filter type="unique_value" column="3" /> 148 <filter type="unique_value" column="3" />
139 </options> 149 </options>
140 </param> 150 </param>
141 </section> 151 </section>
142 </when> 152 </when>
143 <when value="history"> 153 <when value="history">
144 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> 154 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
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> 155 <validator type="expression" message="This version of SnpEff will only work with @COMPATIBLE_DB_VERSIONS_STRING@ genome databases">value.metadata.snpeff_version in @COMPATIBLE_DB_VERSIONS@</validator>
146 </param> 156 </param>
147 <section name="reg_section" expanded="false" title="Regulation options"> 157 <section name="reg_section" expanded="false" title="Regulation options">
148 <!-- From metadata --> 158 <!-- From metadata -->
149 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes"> 159 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes">
150 <options> 160 <options>
158 <validator type="empty_field" message="A genome version name is required" /> 168 <validator type="empty_field" message="A genome version name is required" />
159 </param> 169 </param>
160 </when> 170 </when>
161 <when value="custom"> 171 <when value="custom">
162 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> 172 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
163 <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> 173 <validator type="expression" message="This version of SnpEff will only work with @COMPATIBLE_DB_VERSIONS_STRING@ genome databases">value.metadata.snpeff_version in @COMPATIBLE_DB_VERSIONS@</validator>
164 </param> 174 </param>
165 <param name="codon_table" type="select" label="Select genetic code for this sequence" help="If this sequence uses non-standard genetic code, select one from these options"> 175 <param name="codon_table" type="select" label="Select genetic code for this sequence" help="If this sequence uses non-standard genetic code, select one from these options">
166 <option selected="true" value="Standard">Standard</option> 176 <option selected="true" value="Standard">Standard</option>
167 <option value="Vertebrate_Mitochondrial">Vertebrate_Mitochondrial</option> 177 <option value="Vertebrate_Mitochondrial">Vertebrate_Mitochondrial</option>
168 <option value="Yeast_Mitochondrial">Yeast_Mitochondrial</option> 178 <option value="Yeast_Mitochondrial">Yeast_Mitochondrial</option>
186 <option value="Blepharisma_Macronuclear">Blepharisma_Macronuclear</option> 196 <option value="Blepharisma_Macronuclear">Blepharisma_Macronuclear</option>
187 <option value="Chlorophycean_Mitochondrial">Chlorophycean_Mitochondrial</option> 197 <option value="Chlorophycean_Mitochondrial">Chlorophycean_Mitochondrial</option>
188 <option value="Trematode_Mitochondrial">Trematode_Mitochondrial</option> 198 <option value="Trematode_Mitochondrial">Trematode_Mitochondrial</option>
189 <option value="Scenedesmus_obliquus_Mitochondrial">Scenedesmus_obliquus_Mitochondrial</option> 199 <option value="Scenedesmus_obliquus_Mitochondrial">Scenedesmus_obliquus_Mitochondrial</option>
190 <option value="Thraustochytrium_Mitochondrial">Thraustochytrium_Mitochondrial</option> 200 <option value="Thraustochytrium_Mitochondrial">Thraustochytrium_Mitochondrial</option>
191 </param> 201 </param>
192 </when> 202 </when>
193 </conditional> 203 </conditional>
194 <param name="udLength" argument="-ud" type="select" label="Upstream / Downstream length"> 204 <param name="udLength" argument="-ud" type="select" label="Upstream / Downstream length">
195 <option value="0" selected="true">No upstream / downstream intervals (0 bases)</option> 205 <option value="0" selected="true">No upstream / downstream intervals (0 bases)</option>
196 <option value="200">200 bases</option> 206 <option value="200">200 bases</option>
326 <change_format> 336 <change_format>
327 <when input="outputConditional.outputFormat" value="bed" format="bed" /> 337 <when input="outputConditional.outputFormat" value="bed" format="bed" />
328 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> 338 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
329 </change_format> 339 </change_format>
330 </data> 340 </data>
331 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats"> 341 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats" from_work_dir="snpeff_stats.html">
332 <filter>generate_stats</filter> 342 <filter>generate_stats</filter>
333 </data> 343 </data>
334 <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats"> 344 <data name="genes_file" format="tabular" label="${tool.name} on ${on_string} - Gene stats" from_work_dir="genes.txt">
345 <filter>generate_gene_stats</filter>
346 </data>
347 <data name="csvFile" format="txt" label="${tool.name} on ${on_string} - CSV stats" from_work_dir="snpeff_stats.csv">
335 <filter>csvStats</filter> 348 <filter>csvStats</filter>
336 </data> 349 </data>
337 </outputs> 350 </outputs>
338 <tests> 351 <tests>
352 <test expect_num_outputs="1">
353 <param name="input" ftype="vcf" value="input.vcf"/>
354 <param name="inputFormat" value="vcf"/>
355 <param name="outputFormat" value="vcf"/>
356 <conditional name="snpDb">
357 <param name="genomeSrc" value="cached"/>
358 <param name="genomeVersion" value="ebola_zaire"/>
359 </conditional>
360 <param name="udLength" value="0"/>
361 <param name="generate_stats" value="false"/>
362 <output name="snpeff_output">
363 <assert_contents>
364 <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
365 <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
366 </assert_contents>
367 </output>
368 </test>
339 <test expect_num_outputs="2"> 369 <test expect_num_outputs="2">
340 <param name="input" ftype="vcf" value="input.vcf"/> 370 <param name="input" ftype="vcf" value="input.vcf"/>
341 <param name="inputFormat" value="vcf"/> 371 <param name="inputFormat" value="vcf"/>
342 <param name="outputFormat" value="vcf"/> 372 <param name="outputFormat" value="vcf"/>
343 <param name="genomeSrc" value="named"/> 373 <conditional name="snpDb">
344 <param name="genome_version" value="ebola_zaire"/> 374 <param name="genomeSrc" value="cached"/>
375 <param name="genomeVersion" value="ebola_zaire"/>
376 </conditional>
345 <param name="udLength" value="0"/> 377 <param name="udLength" value="0"/>
346 <param name="generate_stats" value="true"/>
347 <output name="snpeff_output"> 378 <output name="snpeff_output">
348 <assert_contents> 379 <assert_contents>
349 <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" /> 380 <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
350 <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" /> 381 <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
351 </assert_contents> 382 </assert_contents>
352 </output> 383 </output>
353 <output name="statsFile"> 384 <output name="statsFile">
354 <assert_contents> 385 <assert_contents>
355 <has_text text="&lt;b&gt;"/> 386 <has_text text="&lt;b&gt;"/>
387 </assert_contents>
388 </output>
389 </test>
390 <test expect_num_outputs="2">
391 <param name="input" ftype="vcf" value="input.vcf"/>
392 <param name="inputFormat" value="vcf"/>
393 <param name="outputFormat" value="vcf"/>
394 <conditional name="snpDb">
395 <param name="genomeSrc" value="cached"/>
396 <param name="genomeVersion" value="ebola_zaire"/>
397 </conditional>
398 <param name="udLength" value="0"/>
399 <param name="generate_stats" value="false"/>
400 <param name="generate_gene_stats" value="true"/>
401 <output name="snpeff_output">
402 <assert_contents>
403 <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
404 <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
405 </assert_contents>
406 </output>
407 <output name="genes_file">
408 <assert_contents>
409 <has_text text="#GeneName"/>
356 </assert_contents> 410 </assert_contents>
357 </output> 411 </output>
358 </test> 412 </test>
359 <!-- Test interval option--> 413 <!-- Test interval option-->
360 <test expect_num_outputs="2"> 414 <test expect_num_outputs="2">
361 <param name="input" ftype="vcf" value="input.vcf"/> 415 <param name="input" ftype="vcf" value="input.vcf"/>
362 <param name="inputFormat" value="vcf"/> 416 <param name="inputFormat" value="vcf"/>
363 <param name="outputFormat" value="vcf"/> 417 <param name="outputFormat" value="vcf"/>
364 <param name="genomeSrc" value="named"/> 418 <conditional name="snpDb">
365 <param name="interval" value="intervals.bed"/> 419 <param name="genomeSrc" value="cached"/>
366 <param name="genome_version" value="ebola_zaire"/> 420 <param name="genomeVersion" value="ebola_zaire"/>
421 </conditional>
422 <param name="intervals" value="intervals.bed"/>
367 <param name="udLength" value="0"/> 423 <param name="udLength" value="0"/>
368 <param name="generate_stats" value="false"/> 424 <param name="generate_stats" value="false"/>
369 <param name="csvStats" value="true"/> 425 <param name="csvStats" value="true"/>
370 <output name="snpeff_output"> 426 <output name="snpeff_output">
371 <assert_contents> 427 <assert_contents>