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comparison bcftools_annotate.xml @ 24:06eaadeffb7d 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 08:19:20 +0000
parents 8a2e296c07ef
children
comparison
equal deleted inserted replaced
23:2c372041ed8c 24:06eaadeffb7d
7 </macros> 7 </macros>
8 <expand macro="bio_tools" /> 8 <expand macro="bio_tools" />
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="version_command" /> 10 <expand macro="version_command" />
11 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
12 @PREPARE_ENV@
13 @PREPARE_INPUT_FILE@ 12 @PREPARE_INPUT_FILE@
14 #set $annotation_file = None 13 #set $annotation_file = None
15 #set $annotation_hdr = None 14 #set $annotation_hdr = None
16 #set $section = $sec_annofile 15 #set $section = $sec_annofile
17 #if $section.annofile.anno_fmt == 'vcf': 16 #if $section.annofile.anno_fmt == 'vcf':
173 </section> 172 </section>
174 <section name="sec_restrict" expanded="false" title="Restrict to"> 173 <section name="sec_restrict" expanded="false" title="Restrict to">
175 <expand macro="macro_include" /> 174 <expand macro="macro_include" />
176 <expand macro="macro_exclude" /> 175 <expand macro="macro_exclude" />
177 <expand macro="macro_collapse" /> 176 <expand macro="macro_collapse" />
178 <expand macro="macro_restrict" /> 177 <expand macro="macro_region_restrict" />
179 <expand macro="macro_samples" /> 178 <expand macro="macro_samples" />
180 </section> 179 </section>
181 <expand macro="macro_select_output_type" /> 180 <expand macro="macro_select_output_type" />
182 </inputs> 181 </inputs>
183 <outputs> 182 <outputs>
184 <expand macro="macro_vcf_output"/> 183 <expand macro="macro_vcf_output"/>
185 </outputs> 184 </outputs>
186 <tests> 185 <tests>
187 <test> 186 <test>
188 <param name="input_file" ftype="vcf" value="annotate.vcf" /> 187 <param name="input_file" ftype="vcf" value="annotate.vcf" />
189 <param name="anno_fmt" value="tab" /> 188 <section name="sec_annofile">
190 <param name="annotations" value="annotate.tab" /> 189 <conditional name="annofile">
191 <param name="header_file" value="annotate.hdr" /> 190 <param name="anno_fmt" value="tab" />
192 <param name="columns" value="CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL" /> 191 <param name="annotations" value="annotate.tab" />
192 <param name="header_file" value="annotate.hdr" />
193 </conditional>
194 <param name="columns" value="CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL" />
195 </section>
193 <param name="output_type" value="v" /> 196 <param name="output_type" value="v" />
194 <output name="output_file"> 197 <output name="output_file">
195 <assert_contents> 198 <assert_contents>
196 <has_text text="snp_3000150" /> 199 <has_text text="snp_3000150" />
197 </assert_contents> 200 </assert_contents>
216 </assert_contents> 219 </assert_contents>
217 </output> 220 </output>
218 </test> 221 </test>
219 <test> 222 <test>
220 <param name="input_file" ftype="vcf" value="annotate.vcf" /> 223 <param name="input_file" ftype="vcf" value="annotate.vcf" />
221 <param name="anno_fmt" value="vcf" /> 224 <section name="sec_annofile">
222 <param name="annotations" value="annots.vcf" /> 225 <conditional name="annofile">
223 <param name="columns" value="STR,ID,QUAL,FILTER" /> 226 <param name="anno_fmt" value="vcf" />
227 <param name="annotations" value="annots.vcf" />
228 </conditional>
229 <param name="columns" value="STR,ID,QUAL,FILTER" />
230 </section>
224 <param name="output_type" value="v" /> 231 <param name="output_type" value="v" />
225 <output name="output_file"> 232 <output name="output_file">
226 <assert_contents> 233 <assert_contents>
227 <has_text text="idIndel" /> 234 <has_text text="idIndel" />
228 <has_text text="STR=testSNP" /> 235 <has_text text="STR=testSNP" />
229 </assert_contents> 236 </assert_contents>
230 </output> 237 </output>
231 </test> 238 </test>
232 <test> 239 <test>
233 <param name="input_file" ftype="vcf" value="annotate.vcf" /> 240 <param name="input_file" ftype="vcf" value="annotate.vcf" />
234 <param name="anno_fmt" value="vcf" /> 241 <section name="sec_annofile">
235 <param name="annotations" value="annots.bcf" /> 242 <conditional name="annofile">
236 <param name="columns" value="STR,ID,QUAL,FILTER" /> 243 <param name="anno_fmt" value="vcf" />
244 <param name="annotations" value="annots.bcf" />
245 </conditional>
246 <param name="columns" value="STR,ID,QUAL,FILTER" />
247 </section>
237 <param name="output_type" value="v" /> 248 <param name="output_type" value="v" />
238 <output name="output_file"> 249 <output name="output_file">
239 <assert_contents> 250 <assert_contents>
240 <has_text text="idIndel" /> 251 <has_text text="idIndel" />
241 <has_text text="STR=testSNP" /> 252 <has_text text="STR=testSNP" />
242 </assert_contents> 253 </assert_contents>
243 </output> 254 </output>
244 </test> 255 </test>
245 <test> 256 <test>
246 <param name="input_file" ftype="vcf" value="annotate2.vcf" /> 257 <param name="input_file" ftype="vcf" value="annotate2.vcf" />
247 <param name="anno_fmt" value="vcf" /> 258 <section name="sec_annofile">
248 <param name="annotations" value="annots2.vcf" /> 259 <conditional name="annofile">
249 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" /> 260 <param name="anno_fmt" value="vcf" />
261 <param name="annotations" value="annots2.vcf" />
262 </conditional>
263 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" />
264 </section>
250 <param name="output_type" value="v" /> 265 <param name="output_type" value="v" />
251 <output name="output_file"> 266 <output name="output_file">
252 <assert_contents> 267 <assert_contents>
253 <has_text text="q99" /> 268 <has_text text="q99" />
254 <has_text text="FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999" /> 269 <has_text text="FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999" />
255 </assert_contents> 270 </assert_contents>
256 </output> 271 </output>
257 </test> 272 </test>
258 <test> 273 <test>
259 <param name="input_file" ftype="vcf" value="annotate2.vcf" /> 274 <param name="input_file" ftype="vcf" value="annotate2.vcf" />
260 <param name="anno_fmt" value="vcf" /> 275 <section name="sec_annofile">
261 <param name="annotations" value="annots2.vcf" /> 276 <conditional name="annofile">
262 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" /> 277 <param name="anno_fmt" value="vcf" />
263 <param name="samples" value="A" /> 278 <param name="annotations" value="annots2.vcf" />
279 </conditional>
280 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" />
281 </section>
282 <section name="sec_restrict">
283 <param name="samples" value="A" />
284 </section>
264 <param name="output_type" value="v" /> 285 <param name="output_type" value="v" />
265 <output name="output_file"> 286 <output name="output_file">
266 <assert_contents> 287 <assert_contents>
267 <has_text text="q11" /> 288 <has_text text="q11" />
268 <has_text text="FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999" /> 289 <has_text text="FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999" />
269 </assert_contents> 290 </assert_contents>
270 </output> 291 </output>
271 </test> 292 </test>
272 <test> 293 <test>
273 <param name="input_file" ftype="vcf" value="annotate3.vcf" /> 294 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
274 <param name="anno_fmt" value="none" /> 295 <section name="sec_annofile">
275 <param name="remove" value="ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL" /> 296 <conditional name="annofile">
297 <param name="anno_fmt" value="none" />
298 </conditional>
299 </section>
300 <section name="sec_annotate">
301 <param name="remove" value="ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL" />
302 </section>
276 <param name="output_type" value="v" /> 303 <param name="output_type" value="v" />
277 <output name="output_file"> 304 <output name="output_file">
278 <assert_contents> 305 <assert_contents>
279 <not_has_text text="fltY" /> 306 <not_has_text text="fltY" />
280 </assert_contents> 307 </assert_contents>
281 </output> 308 </output>
282 </test> 309 </test>
283 <test> 310 <test>
284 <param name="input_file" ftype="vcf" value="annotate3.vcf" /> 311 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
285 <param name="anno_fmt" value="none" /> 312 <section name="sec_annofile">
286 <param name="remove" value="FORMAT" /> 313 <conditional name="annofile">
314 <param name="anno_fmt" value="none" />
315 </conditional>
316 </section>
317 <section name="sec_annotate">
318 <param name="remove" value="FORMAT" />
319 </section>
287 <param name="output_type" value="v" /> 320 <param name="output_type" value="v" />
288 <output name="output_file"> 321 <output name="output_file">
289 <assert_contents> 322 <assert_contents>
290 <not_has_text text="GT:X:PL:Y:AA" /> 323 <not_has_text text="GT:X:PL:Y:AA" />
291 </assert_contents> 324 </assert_contents>
292 </output> 325 </output>
293 </test> 326 </test>
294 <!-- Test region overlap option --> 327 <!-- Test region overlap option -->
295 <test> 328 <test>
296 <param name="input_file" ftype="vcf" value="annotate3.vcf" /> 329 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
297 <param name="anno_fmt" value="none" /> 330 <section name="sec_annofile">
298 <param name="remove" value="FORMAT" /> 331 <conditional name="annofile">
332 <param name="anno_fmt" value="none" />
333 </conditional>
334 </section>
335 <section name="sec_annotate">
336 <param name="remove" value="FORMAT" />
337 </section>
299 <param name="output_type" value="v" /> 338 <param name="output_type" value="v" />
300 <section name="sec_restrict"> 339 <section name="sec_restrict">
301 <param name="regions_overlap" value="1"/> 340 <conditional name="regions">
341 <param name="regions_src" value="regions" />
342 <repeat name="region_specs">
343 <param name="chrom" value="1" />
344 </repeat>
345 </conditional>
302 </section> 346 </section>
303 <output name="output_file"> 347 <output name="output_file">
304 <assert_contents> 348 <assert_contents>
305 <not_has_text text="GT:X:PL:Y:AA" /> 349 <not_has_text text="GT:X:PL:Y:AA" />
306 </assert_contents> 350 </assert_contents>
310 </assert_command> 354 </assert_command>
311 </test> 355 </test>
312 <!-- Test min overlap option --> 356 <!-- Test min overlap option -->
313 <test> 357 <test>
314 <param name="input_file" ftype="vcf" value="annotate3.vcf" /> 358 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
315 <param name="anno_fmt" value="none" /> 359 <section name="sec_annofile">
316 <param name="remove" value="FORMAT" /> 360 <conditional name="annofile">
317 <param name="output_type" value="v" /> 361 <param name="anno_fmt" value="none" />
318 <section name="sec_annofile"> 362 </conditional>
319 <param name="min_overlap" value="0.5"/> 363 <param name="min_overlap" value="0.5"/>
320 </section> 364 </section>
365 <section name="sec_annotate">
366 <param name="remove" value="FORMAT" />
367 </section>
368 <param name="output_type" value="v" />
321 <output name="output_file"> 369 <output name="output_file">
322 <assert_contents> 370 <assert_contents>
323 <not_has_text text="GT:X:PL:Y:AA" /> 371 <not_has_text text="GT:X:PL:Y:AA" />
324 </assert_contents> 372 </assert_contents>
325 </output> 373 </output>
364 @REGIONS_HELP@ 412 @REGIONS_HELP@
365 @EXPRESSIONS_HELP@ 413 @EXPRESSIONS_HELP@
366 414
367 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 415 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
368 416
369 @BCFTOOLS_WIKI@ 417 @BCFTOOLS_HOWTOS@
370 ]]> 418 ]]>
371 </help> 419 </help>
372 <expand macro="citations" /> 420 <expand macro="citations" />
373 </tool> 421 </tool>