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comparison bcftools_view.xml @ 25:2a7d7ee53975 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 08:15:36 +0000
parents 1a2ef636f48e
children
comparison
equal deleted inserted replaced
24:1a2ef636f48e 25:2a7d7ee53975
12 </macros> 12 </macros>
13 <expand macro="bio_tools" /> 13 <expand macro="bio_tools" />
14 <expand macro="requirements" /> 14 <expand macro="requirements" />
15 <expand macro="version_command" /> 15 <expand macro="version_command" />
16 <command detect_errors="aggressive"><![CDATA[ 16 <command detect_errors="aggressive"><![CDATA[
17 @PREPARE_ENV@
18 @PREPARE_INPUT_FILE@ 17 @PREPARE_INPUT_FILE@
19 #set $section = $sec_restrict 18 #set $section = $sec_restrict
20 @PREPARE_TARGETS_FILE@ 19 @PREPARE_TARGETS_FILE@
21 @PREPARE_REGIONS_FILE@ 20 @PREPARE_REGIONS_FILE@
22 21
100 </command> 99 </command>
101 <inputs> 100 <inputs>
102 <expand macro="macro_input" /> 101 <expand macro="macro_input" />
103 <section name="sec_restrict" expanded="false" title="Restrict to"> 102 <section name="sec_restrict" expanded="false" title="Restrict to">
104 <expand macro="macro_apply_filters" /> 103 <expand macro="macro_apply_filters" />
105 <expand macro="macro_restrict" /> 104 <expand macro="macro_region_restrict" />
106 <expand macro="macro_restrict" type="target" label_type="Target" /> 105 <expand macro="macro_target_restrict" />
107 <expand macro="macro_include" /> 106 <expand macro="macro_include" />
108 <expand macro="macro_exclude" /> 107 <expand macro="macro_exclude" />
109 </section> 108 </section>
110 <section name="sec_subset" expanded="false" title="Subset Options"> 109 <section name="sec_subset" expanded="false" title="Subset Options">
111 <expand macro="macro_samples" /> 110 <expand macro="macro_samples" />
199 <option value="--no-header">(-h) no-header</option> 198 <option value="--no-header">(-h) no-header</option>
200 <option value="--header-only">(-H) header-only</option> 199 <option value="--header-only">(-H) header-only</option>
201 </param> 200 </param>
202 <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" optional="True" 201 <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" optional="True"
203 help="Compression level: 0 uncompressed, 1 best speed, 9 best compression" /> 202 help="Compression level: 0 uncompressed, 1 best speed, 9 best compression" />
204 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets File"
205 help="Inverts the query/filtering applied by Targets File" />
206 </section> 203 </section>
207 <expand macro="macro_select_output_type" /> 204 <expand macro="macro_select_output_type" />
208 </inputs> 205 </inputs>
209 <outputs> 206 <outputs>
210 <expand macro="macro_vcf_output" /> 207 <expand macro="macro_vcf_output" />
211 </outputs> 208 </outputs>
212 <tests> 209 <tests>
213 <test> 210 <test>
214 <param name="input_file" ftype="vcf" value="view.vcf" /> 211 <param name="input_file" ftype="vcf" value="view.vcf" />
215 <param name="min_ac" value="1" /> 212 <section name="sec_filter">
216 <param name="max_ac" value="1" /> 213 <param name="min_ac" value="1" />
217 <param name="samples" value="NA00002" /> 214 <param name="max_ac" value="1" />
218 <param name="types" value="snps" /> 215 <param name="types" value="snps" />
216 </section>
217 <section name="sec_subset">
218 <param name="samples" value="NA00002" />
219 </section>
219 <param name="output_type" value="v" /> 220 <param name="output_type" value="v" />
220 <output name="output_file"> 221 <output name="output_file">
221 <assert_contents> 222 <assert_contents>
222 <has_text text="rs2298108" /> 223 <has_text text="rs2298108" />
223 <not_has_text text="rs6111385" /> 224 <not_has_text text="rs6111385" />
224 </assert_contents> 225 </assert_contents>
225 </output> 226 </output>
226 </test> 227 </test>
227 <test> 228 <test>
228 <param name="input_file" ftype="bcf" value="view.bcf" /> 229 <param name="input_file" ftype="bcf" value="view.bcf" />
229 <param name="min_ac" value="1" /> 230 <section name="sec_filter">
230 <param name="max_ac" value="1" /> 231 <param name="min_ac" value="1" />
231 <param name="samples" value="NA00002" /> 232 <param name="max_ac" value="1" />
232 <param name="types" value="snps" /> 233 <param name="types" value="snps" />
234 </section>
235 <section name="sec_subset">
236 <param name="samples" value="NA00002" />
237 </section>
233 <param name="output_type" value="v" /> 238 <param name="output_type" value="v" />
234 <output name="output_file"> 239 <output name="output_file">
235 <assert_contents> 240 <assert_contents>
236 <has_text text="rs2298108" /> 241 <has_text text="rs2298108" />
237 <not_has_text text="rs6111385" /> 242 <not_has_text text="rs6111385" />
238 </assert_contents> 243 </assert_contents>
239 </output> 244 </output>
240 </test> 245 </test>
241 <test> 246 <test>
242 <param name="input_file" ftype="vcf" value="view.vcf" /> 247 <param name="input_file" ftype="vcf" value="view.vcf" />
243 <param name="known_or_novel" value="--novel" /> 248 <section name="sec_filter">
244 <param name="private" value="--exclude-private" /> 249 <param name="known_or_novel" value="--novel" />
245 <param name="samples" value="NA00003" /> 250 <param name="private" value="--exclude-private" />
251 </section>
252 <section name="sec_subset">
253 <param name="samples" value="NA00003" />
254 </section>
246 <section name="sec_restrict"> 255 <section name="sec_restrict">
247 <conditional name="regions"> 256 <conditional name="regions">
248 <param name="regions_src" value="regions"/> 257 <param name="regions_src" value="regions"/>
249 <repeat name="regions"> 258 <repeat name="region_specs">
250 <param name="chrom" value="Y" /> 259 <param name="chrom" value="Y" />
251 <param name="start" value="20" /> 260 <param name="start" value="20" />
252 </repeat> 261 </repeat>
253 </conditional> 262 </conditional>
254 </section> 263 </section>
263 <has_text text="--regions 'Y:20-'"/> 272 <has_text text="--regions 'Y:20-'"/>
264 </assert_command> 273 </assert_command>
265 </test> 274 </test>
266 <test> 275 <test>
267 <param name="input_file" ftype="vcf" value="view.vcf" /> 276 <param name="input_file" ftype="vcf" value="view.vcf" />
268 <param name="known_or_novel" value="--known" /> 277 <section name="sec_filter">
269 <param name="private" value="--exclude-private" /> 278 <param name="known_or_novel" value="--known" />
270 <param name="apply_filters" value="PASS" /> 279 <param name="private" value="--exclude-private" />
271 <param name="samples" value="NA00003" /> 280 </section>
281 <section name="sec_subset">
282 <param name="samples" value="NA00003" />
283 </section>
272 <section name="sec_restrict"> 284 <section name="sec_restrict">
285 <param name="apply_filters" value="PASS" />
273 <conditional name="regions"> 286 <conditional name="regions">
274 <param name="regions_src" value="regions"/> 287 <param name="regions_src" value="regions"/>
275 <repeat name="regions"> 288 <repeat name="region_specs">
276 <param name="chrom" value="Y" /> 289 <param name="chrom" value="Y" />
277 <param name="start" value="20" /> 290 <param name="start" value="20" />
278 </repeat> 291 </repeat>
279 </conditional> 292 </conditional>
280 </section> 293 </section>
286 </assert_contents> 299 </assert_contents>
287 </output> 300 </output>
288 </test> 301 </test>
289 <test> 302 <test>
290 <param name="input_file" ftype="vcf" value="view.vcf" /> 303 <param name="input_file" ftype="vcf" value="view.vcf" />
291 <param name="private" value="--private" /> 304 <section name="sec_filter">
292 <param name="samples" value="NA00003" /> 305 <param name="private" value="--private" />
306 </section>
307 <section name="sec_subset">
308 <param name="samples" value="NA00003" />
309 </section>
293 <param name="output_type" value="v" /> 310 <param name="output_type" value="v" />
294 <output name="output_file"> 311 <output name="output_file">
295 <assert_contents> 312 <assert_contents>
296 <has_text text="rs62584840" /> 313 <has_text text="rs62584840" />
297 <not_has_text text="8657215" /> 314 <not_has_text text="8657215" />
298 </assert_contents> 315 </assert_contents>
299 </output> 316 </output>
300 </test> 317 </test>
301 <test> 318 <test>
302 <param name="input_file" ftype="vcf" value="view.vcf" /> 319 <param name="input_file" ftype="vcf" value="view.vcf" />
303 <param name="include" value="QUAL==999 &amp;&amp; (FS&lt;20 || FS&gt;=41.02) &amp;&amp; ICF&gt;-0.1 &amp;&amp; HWE*2&gt;1.2" /> 320 <section name="sec_restrict">
321 <param name="include" value="QUAL==999 &amp;&amp; (FS&lt;20 || FS&gt;=41.02) &amp;&amp; ICF&gt;-0.1 &amp;&amp; HWE*2&gt;1.2" />
322 </section>
304 <param name="output_type" value="v" /> 323 <param name="output_type" value="v" />
305 <output name="output_file"> 324 <output name="output_file">
306 <assert_contents> 325 <assert_contents>
307 <has_text text="rs5939407" /> 326 <has_text text="rs5939407" />
308 <not_has_text text="8657215" /> 327 <not_has_text text="8657215" />
309 </assert_contents> 328 </assert_contents>
310 </output> 329 </output>
311 </test> 330 </test>
312 <test> 331 <test>
313 <param name="input_file" ftype="vcf" value="view.vcf" /> 332 <param name="input_file" ftype="vcf" value="view.vcf" />
314 <param name="phased" value="--phased" /> 333 <section name="sec_filter">
334 <param name="phased" value="--phased" />
335 </section>
315 <param name="output_type" value="v" /> 336 <param name="output_type" value="v" />
316 <output name="output_file"> 337 <output name="output_file">
317 <assert_contents> 338 <assert_contents>
318 <has_text text="rs78249411" /> 339 <has_text text="rs78249411" />
319 <not_has_text text="rs6111385" /> 340 <not_has_text text="rs6111385" />
320 </assert_contents> 341 </assert_contents>
321 </output> 342 </output>
322 </test> 343 </test>
323 <test> 344 <test>
324 <param name="input_file" ftype="vcf" value="view.vcf" /> 345 <param name="input_file" ftype="vcf" value="view.vcf" />
325 <param name="phased" value="--exclude-phased" /> 346 <section name="sec_filter">
347 <param name="phased" value="--exclude-phased" />
348 </section>
326 <param name="output_type" value="v" /> 349 <param name="output_type" value="v" />
327 <output name="output_file"> 350 <output name="output_file">
328 <assert_contents> 351 <assert_contents>
329 <has_text text="rs6111385" /> 352 <has_text text="rs6111385" />
330 <not_has_text text="rs78249411" /> 353 <not_has_text text="rs78249411" />
331 </assert_contents> 354 </assert_contents>
332 </output> 355 </output>
333 </test> 356 </test>
334 <test> 357 <test>
335 <param name="input_file" ftype="vcf" value="view.vcf" /> 358 <param name="input_file" ftype="vcf" value="view.vcf" />
336 <param name="min_alleles" value="2" /> 359 <section name="sec_filter">
337 <param name="max_alleles" value="2" /> 360 <param name="min_alleles" value="2" />
338 <param name="min_af" value="0.3" /> 361 <param name="max_alleles" value="2" />
339 <param name="max_af" value="0.7" /> 362 <param name="min_af" value="0.3" />
340 <param name="header" value="--header-only" /> 363 <param name="max_af" value="0.7" />
364 </section>
365 <section name="sec_output">
366 <param name="header" value="--header-only" />
367 </section>
341 <param name="output_type" value="v" /> 368 <param name="output_type" value="v" />
342 <output name="output_file"> 369 <output name="output_file">
343 <assert_contents> 370 <assert_contents>
344 <has_text text="##bcftools_viewCommand" /> 371 <has_text text="##bcftools_viewCommand" />
345 <not_has_text text="rs78249411" /> 372 <not_has_text text="rs78249411" />
346 </assert_contents> 373 </assert_contents>
347 </output> 374 </output>
348 </test> 375 </test>
349 <test> 376 <test>
350 <param name="input_file" ftype="vcf" value="view.vcf" /> 377 <param name="input_file" ftype="vcf" value="view.vcf" />
351 <param name="uncalled" value="--uncalled" /> 378 <section name="sec_filter">
352 <param name="header" value="--no-header" /> 379 <param name="uncalled" value="--uncalled" />
380 </section>
381 <section name="sec_output">
382 <param name="header" value="--no-header" />
383 </section>
353 <param name="output_type" value="v" /> 384 <param name="output_type" value="v" />
354 <output name="output_file"> 385 <output name="output_file">
355 <assert_contents> 386 <assert_contents>
356 <not_has_text text="##bcftools_viewCommand" /> 387 <not_has_text text="##bcftools_viewCommand" />
357 <has_text text="5464562" /> 388 <has_text text="5464562" />
358 </assert_contents> 389 </assert_contents>
359 </output> 390 </output>
360 </test> 391 </test>
361 <test> 392 <test>
362 <param name="input_file" ftype="vcf" value="view.vcf" /> 393 <param name="input_file" ftype="vcf" value="view.vcf" />
363 <param name="exclude_types" value="snps" /> 394 <section name="sec_filter">
364 <param name="drop_genotypes" value="true" /> 395 <param name="exclude_types" value="snps" />
396 </section>
397 <section name="sec_output">
398 <param name="drop_genotypes" value="true" />
399 </section>
365 <param name="output_type" value="v" /> 400 <param name="output_type" value="v" />
366 <output name="output_file"> 401 <output name="output_file">
367 <assert_contents> 402 <assert_contents>
368 <not_has_text text="##FORMAT=&lt;ID=GT" /> 403 <not_has_text text="##FORMAT=&lt;ID=GT" />
369 <not_has_text text="rs62584840" /> 404 <not_has_text text="rs62584840" />
371 </assert_contents> 406 </assert_contents>
372 </output> 407 </output>
373 </test> 408 </test>
374 <test> 409 <test>
375 <param name="input_file" ftype="vcf" value="view.vcf" /> 410 <param name="input_file" ftype="vcf" value="view.vcf" />
376 <param name="phased" value="--phased" /> 411 <section name="sec_filter">
377 <param name="output_type" value="v" /> 412 <param name="phased" value="--phased" />
378 <param name="select_genotype" value="^het" /> 413 <param name="select_genotype" value="^het" />
414 </section>
415 <param name="output_type" value="v" />
379 <output name="output_file"> 416 <output name="output_file">
380 <assert_contents> 417 <assert_contents>
381 <has_text text="--genotype ^het" /> 418 <has_text text="--genotype ^het" />
382 <has_text text="rs78249411" /> 419 <has_text text="rs78249411" />
383 <not_has_text text="3048719" /> 420 <not_has_text text="3048719" />
385 </output> 422 </output>
386 </test> 423 </test>
387 <!-- Test region overlap option --> 424 <!-- Test region overlap option -->
388 <test> 425 <test>
389 <param name="input_file" ftype="vcf" value="view.vcf" /> 426 <param name="input_file" ftype="vcf" value="view.vcf" />
390 <param name="min_ac" value="1" /> 427 <section name="sec_filter">
391 <param name="max_ac" value="1" /> 428 <param name="min_ac" value="1" />
392 <param name="samples" value="NA00002" /> 429 <param name="max_ac" value="1" />
393 <param name="types" value="snps" /> 430 <param name="types" value="snps" />
431 </section>
432 <section name="sec_subset">
433 <param name="samples" value="NA00002" />
434 </section>
394 <param name="output_type" value="v" /> 435 <param name="output_type" value="v" />
395 <section name="sec_restrict"> 436 <section name="sec_restrict">
396 <param name="regions_overlap" value="1"/> 437 <conditional name="regions">
438 <param name="regions_src" value="regions" />
439 <repeat name="region_specs">
440 <param name="chrom" value="20" />
441 </repeat>
442 </conditional>
397 </section> 443 </section>
398 <output name="output_file"> 444 <output name="output_file">
399 <assert_contents> 445 <assert_contents>
400 <has_text text="rs2298108" /> 446 <has_text text="rs2298108" />
401 <not_has_text text="rs6111385" /> 447 <not_has_text text="rs6111385" />
417 @TARGETS_HELP@ 463 @TARGETS_HELP@
418 @EXPRESSIONS_HELP@ 464 @EXPRESSIONS_HELP@
419 465
420 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 466 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
421 467
422 @BCFTOOLS_WIKI@ 468 @BCFTOOLS_HOWTOS@
423 ]]> 469 ]]>
424 </help> 470 </help>
425 <expand macro="citations" /> 471 <expand macro="citations" />
426 </tool> 472 </tool>