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comparison snpEff.xml @ 28:6322be79bd8e 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 16:27:56 +0000
parents 5b80f544c67f
children ca2b512e8d7c
comparison
equal deleted inserted replaced
27:9473cd297a76 28:6322be79bd8e
157 </param> 157 </param>
158 </section> 158 </section>
159 </when> 159 </when>
160 <when value="history"> 160 <when value="history">
161 <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">
162 <options options_filter_attribute="metadata.snpeff_version" >
163 <filter type="add_value" value="@SNPEFF_VERSION@" />
164 </options>
165 <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>
166 </param> 163 </param>
167 <section name="reg_section" expanded="false" title="Regulation options"> 164 <section name="reg_section" expanded="false" title="Regulation options">
168 <!-- From metadata --> 165 <!-- From metadata -->
169 <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">
179 <validator type="empty_field" message="A genome version name is required" /> 176 <validator type="empty_field" message="A genome version name is required" />
180 </param> 177 </param>
181 </when> 178 </when>
182 <when value="custom"> 179 <when value="custom">
183 <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">
184 <options options_filter_attribute="metadata.snpeff_version" >
185 <filter type="add_value" value="@SNPEFF_VERSION@" />
186 </options>
187 <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>
188 </param> 182 </param>
189 <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">
190 <option selected="true" value="Standard">Standard</option> 184 <option selected="true" value="Standard">Standard</option>
191 <option value="Vertebrate_Mitochondrial">Vertebrate_Mitochondrial</option> 185 <option value="Vertebrate_Mitochondrial">Vertebrate_Mitochondrial</option>
362 <when input="outputConditional.outputFormat" value="bed" format="bed" /> 356 <when input="outputConditional.outputFormat" value="bed" format="bed" />
363 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> 357 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
364 </change_format> 358 </change_format>
365 </data> 359 </data>
366 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats"> 360 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats">
367 <filter>generate_stats == True</filter> 361 <filter>generate_stats</filter>
368 </data> 362 </data>
369 <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats"> 363 <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats">
370 <filter>csvStats == True</filter> 364 <filter>csvStats</filter>
371 </data> 365 </data>
372 </outputs> 366 </outputs>
373 <tests> 367 <tests>
374 <test> 368 <test expect_num_outputs="2">
375 <param name="input" ftype="vcf" value="input.vcf"/> 369 <param name="input" ftype="vcf" value="input.vcf"/>
376 <param name="inputFormat" value="vcf"/> 370 <param name="inputFormat" value="vcf"/>
377 <param name="outputFormat" value="vcf"/> 371 <param name="outputFormat" value="vcf"/>
378 <param name="genomeSrc" value="named"/> 372 <param name="genomeSrc" value="named"/>
379 <param name="genome_version" value="ebola_zaire"/> 373 <param name="genome_version" value="ebola_zaire"/>
380 <param name="udLength" value="0"/> 374 <param name="udLength" value="0"/>
381 <param name="generate_stats" value="false"/> 375 <param name="generate_stats" value="true"/>
382 <output name="snpeff_output"> 376 <output name="snpeff_output">
383 <assert_contents> 377 <assert_contents>
384 <has_text_matching expression="KJ660346\t572\t.*missense_variant" /> 378 <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
385 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" /> 379 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
386 </assert_contents> 380 </assert_contents>
387 </output> 381 </output>
382 <output name="statsFile">
383 <assert_contents>
384 <has_text text="&lt;b&gt;"/>
385 </assert_contents>
386 </output>
388 </test> 387 </test>
389 <!-- Test interval option--> 388 <!-- Test interval option-->
390 <test> 389 <test expect_num_outputs="2">
391 <param name="input" ftype="vcf" value="input.vcf"/> 390 <param name="input" ftype="vcf" value="input.vcf"/>
392 <param name="inputFormat" value="vcf"/> 391 <param name="inputFormat" value="vcf"/>
393 <param name="outputFormat" value="vcf"/> 392 <param name="outputFormat" value="vcf"/>
394 <param name="genomeSrc" value="named"/> 393 <param name="genomeSrc" value="named"/>
395 <param name="interval" value="intervals.bed"/> 394 <param name="interval" value="intervals.bed"/>
396 <param name="genome_version" value="ebola_zaire"/> 395 <param name="genome_version" value="ebola_zaire"/>
397 <param name="udLength" value="0"/> 396 <param name="udLength" value="0"/>
398 <param name="generate_stats" value="false"/> 397 <param name="generate_stats" value="false"/>
398 <param name="csvStats" value="true"/>
399 <output name="snpeff_output"> 399 <output name="snpeff_output">
400 <assert_contents> 400 <assert_contents>
401 <has_text_matching expression="KJ660346\t572\t.*missense_variant" /> 401 <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
402 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" /> 402 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
403 </assert_contents> 403 </assert_contents>
404 </output> 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>
405 </test> 411 </test>
406 </tests> 412 </tests>
407 <help><![CDATA[ 413 <help><![CDATA[
408 **What it does** 414 **What it does**
409 415