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comparison snpEff.xml @ 30:0c8a8cd9dd5b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd
author iuc
date Sat, 28 Sep 2024 16:27:42 +0000
parents 4c790901c495
children b7029a54f73e
comparison
equal deleted inserted replaced
29:030fe29d4c47 30:0c8a8cd9dd5b
1 <tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy1"> 1 <tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy2">
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 </requirements> 8 </requirements>
9 <expand macro="stdio" /> 9 <expand macro="stdio" />
10 <expand macro="version_command" /> 10 <expand macro="version_command" />
11 <command><![CDATA[ 11 <command><![CDATA[
12 #if $intervals
13 ln -s '${intervals}' intervals.bed &&
14 #end if
12 snpEff @JAVA_OPTIONS@ eff 15 snpEff @JAVA_OPTIONS@ eff
13 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength 16 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
14 #if $spliceSiteSize and str($spliceSiteSize) != '': 17 #if $spliceSiteSize and str($spliceSiteSize) != '':
15 -spliceSiteSize "$spliceSiteSize" 18 -spliceSiteSize "$spliceSiteSize"
16 #end if 19 #end if
40 #end if 43 #end if
41 #if $transcripts 44 #if $transcripts
42 -onlyTr '$transcripts' 45 -onlyTr '$transcripts'
43 #end if 46 #end if
44 #if $intervals ### fix this for multiple dataset input 47 #if $intervals ### fix this for multiple dataset input
45 -interval '$intervals' 48 -interval intervals.bed
46 #end if 49 #end if
47 #if $statsFile: 50 #if $statsFile:
48 -stats '$statsFile' 51 -stats '$statsFile'
49 #end if 52 #end if
50 #if $csvStats: 53 #if $csvStats:
154 </param> 157 </param>
155 </section> 158 </section>
156 </when> 159 </when>
157 <when value="history"> 160 <when value="history">
158 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> 161 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
159 <options options_filter_attribute="metadata.snpeff_version" >
160 <filter type="add_value" value="@SNPEFF_VERSION@" />
161 </options>
162 <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> 162 <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>
163 </param> 163 </param>
164 <section name="reg_section" expanded="false" title="Regulation options"> 164 <section name="reg_section" expanded="false" title="Regulation options">
165 <!-- From metadata --> 165 <!-- From metadata -->
166 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes"> 166 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes">
176 <validator type="empty_field" message="A genome version name is required" /> 176 <validator type="empty_field" message="A genome version name is required" />
177 </param> 177 </param>
178 </when> 178 </when>
179 <when value="custom"> 179 <when value="custom">
180 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> 180 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
181 <options options_filter_attribute="metadata.snpeff_version" >
182 <filter type="add_value" value="@SNPEFF_VERSION@" />
183 </options>
184 <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> 181 <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>
185 </param> 182 </param>
186 <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"> 183 <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">
187 <option selected="true" value="Standard">Standard</option> 184 <option selected="true" value="Standard">Standard</option>
188 <option value="Vertebrate_Mitochondrial">Vertebrate_Mitochondrial</option> 185 <option value="Vertebrate_Mitochondrial">Vertebrate_Mitochondrial</option>
359 <when input="outputConditional.outputFormat" value="bed" format="bed" /> 356 <when input="outputConditional.outputFormat" value="bed" format="bed" />
360 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> 357 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
361 </change_format> 358 </change_format>
362 </data> 359 </data>
363 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats"> 360 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats">
364 <filter>generate_stats == True</filter> 361 <filter>generate_stats</filter>
365 </data> 362 </data>
366 <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats"> 363 <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats">
367 <filter>csvStats == True</filter> 364 <filter>csvStats</filter>
368 </data> 365 </data>
369 </outputs> 366 </outputs>
370 <tests> 367 <tests>
371 <test> 368 <test expect_num_outputs="2">
372 <param name="input" ftype="vcf" value="input.vcf"/> 369 <param name="input" ftype="vcf" value="input.vcf"/>
373 <param name="inputFormat" value="vcf"/> 370 <param name="inputFormat" value="vcf"/>
374 <param name="outputFormat" value="vcf"/> 371 <param name="outputFormat" value="vcf"/>
375 <param name="genomeSrc" value="named"/> 372 <param name="genomeSrc" value="named"/>
376 <param name="genome_version" value="ebola_zaire"/> 373 <param name="genome_version" value="ebola_zaire"/>
377 <param name="udLength" value="0"/> 374 <param name="udLength" value="0"/>
378 <param name="generate_stats" value="false"/> 375 <param name="generate_stats" value="true"/>
379 <output name="snpeff_output"> 376 <output name="snpeff_output">
380 <assert_contents> 377 <assert_contents>
381 <has_text_matching expression="KJ660346\t572\t.*missense_variant" /> 378 <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
382 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" /> 379 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
383 </assert_contents> 380 </assert_contents>
384 </output> 381 </output>
382 <output name="statsFile">
383 <assert_contents>
384 <has_text text="&lt;b&gt;"/>
385 </assert_contents>
386 </output>
387 </test>
388 <!-- Test interval option-->
389 <test expect_num_outputs="2">
390 <param name="input" ftype="vcf" value="input.vcf"/>
391 <param name="inputFormat" value="vcf"/>
392 <param name="outputFormat" value="vcf"/>
393 <param name="genomeSrc" value="named"/>
394 <param name="interval" value="intervals.bed"/>
395 <param name="genome_version" value="ebola_zaire"/>
396 <param name="udLength" value="0"/>
397 <param name="generate_stats" value="false"/>
398 <param name="csvStats" value="true"/>
399 <output name="snpeff_output">
400 <assert_contents>
401 <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
402 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
403 </assert_contents>
404 </output>
405 <output name="csvFile">
406 <assert_contents>
407 <has_n_lines n="185"/>
408 <has_n_columns n="1" sep=","/>
409 </assert_contents>
410 </output>
385 </test> 411 </test>
386 </tests> 412 </tests>
387 <help><![CDATA[ 413 <help><![CDATA[
388 **What it does** 414 **What it does**
389 415