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comparison busco.xml @ 21:2babe6d5c561 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a
author iuc
date Fri, 30 Aug 2024 15:19:56 +0000
parents ea8146ee148f
children
comparison
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20:ea8146ee148f 21:2babe6d5c561
12 <requirement type="package" version="1">fonts-conda-ecosystem</requirement> 12 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
13 </requirements> 13 </requirements>
14 <version_command>busco --version</version_command> 14 <version_command>busco --version</version_command>
15 <command><![CDATA[ 15 <command><![CDATA[
16 16
17 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes': 17 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'augustus':
18 18
19 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi && 19 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
20 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && 20 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
21 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && 21 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
22 22
38 --contig_break ${adv.contig_break} 38 --contig_break ${adv.contig_break}
39 39
40 #if $lineage_conditional.selector == 'cached': 40 #if $lineage_conditional.selector == 'cached':
41 --offline 41 --offline
42 --download_path $lineage_conditional.cached_db.fields.path 42 --download_path $lineage_conditional.cached_db.fields.path
43 #else
44 --update-data
45 #end if 43 #end if
46 44
47 #if $lineage.lineage_mode == "auto_detect": 45 #if $lineage.lineage_mode == "auto_detect":
48 $lineage.auto_lineage 46 $lineage.auto_lineage
49 #else if $lineage.lineage_mode == "select_lineage": 47 #else if $lineage.lineage_mode == "select_lineage":
50 --lineage_dataset '${lineage.lineage_dataset}' 48 --lineage_dataset '${lineage.lineage_dataset}'
51 #end if 49 #end if
52 50
53 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes': 51 #if $busco_mode.mode == 'geno':
54 52 #if $busco_mode.use_augustus.use_augustus_selector == 'miniprot':
55 ${busco_mode.use_augustus.long}
56 --augustus
57
58 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
59 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
60 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
61 --augustus_species local
62 #end if
63 #end if
64
65 #if str( $busco_mode.mode ) == "geno":
66 #if $busco_mode.miniprot:
67 --miniprot 53 --miniprot
54 #elif $busco_mode.use_augustus.use_augustus_selector == 'augustus':
55 ${busco_mode.use_augustus.long}
56 --augustus
57
58 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
59 --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
60 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
61 --augustus_species local
62 #end if
63 #else:
64 --metaeuk
68 #end if 65 #end if
69 #end if 66 #end if
70 67
71 #if $outputs and 'image' in $outputs: 68 #if $outputs and 'image' in $outputs:
72 && 69 &&
109 <option value="geno">Genome assemblies (DNA)</option> 106 <option value="geno">Genome assemblies (DNA)</option>
110 <option value="tran">Transcriptome assemblies (DNA)</option> 107 <option value="tran">Transcriptome assemblies (DNA)</option>
111 <option value="prot">annotated gene sets (protein)</option> 108 <option value="prot">annotated gene sets (protein)</option>
112 </param> 109 </param>
113 <when value="geno"> 110 <when value="geno">
114 <param name="miniprot" type="boolean" checked="false" label="Generate miniprot output"/> 111 <conditional name="use_augustus">
115 <conditional name="use_augustus"> 112 <param name="use_augustus_selector" type="select" label="Select a gene predictor" help="In the case of a prokaryotic genome, Prodigal is the default gene predictor">
116 <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk"> 113 <option value="augustus">Augustus</option>
117 <option value="yes">Yes, use Augustus</option> 114 <option value="metaeuk">Metaeuk</option>
118 <option value="no" selected="true">Use Metaeuk</option> 115 <option value="miniprot" selected="true">Miniprot</option>
116
119 </param> 117 </param>
120 <when value="no" /> 118 <when value="metaeuk"/>
121 <when value="yes"> 119 <when value="miniprot"/>
120 <when value="augustus">
122 <conditional name="aug_prediction"> 121 <conditional name="aug_prediction">
123 <param name="augustus_mode" type="select" label="Augustus species model"> 122 <param name="augustus_mode" type="select" label="Augustus species model">
124 <option value="no" selected="true">Use the default species for selected lineage</option> 123 <option value="no" selected="true">Use the default species for selected lineage</option>
125 <option value="builtin">Use another predefined species model</option> 124 <option value="builtin">Use another predefined species model</option>
126 <option value="history">Use a custom species model</option> 125 <option value="history">Use a custom species model</option>
187 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png"> 186 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
188 <filter>outputs and 'image' in outputs</filter> 187 <filter>outputs and 'image' in outputs</filter>
189 </data> 188 </data>
190 <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff"> 189 <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
191 <filter>outputs and 'gff' in outputs</filter> 190 <filter>outputs and 'gff' in outputs</filter>
192 </data> 191 </data>
193 <data name='busco_miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="busco_galaxy/run_*/miniprot_output/*.gff">
194 <filter>busco_mode['mode'] == 'geno' and busco_mode['miniprot']</filter>
195 </data>
196 </outputs> 192 </outputs>
197 193
198 <tests> 194 <tests>
199 <test expect_num_outputs="4"> 195 <test expect_num_outputs="4">
200 <param name="input" value="genome.fa" /> 196 <param name="input" value="genome.fa" />
203 <param name="lineage_dataset" value="arthropoda_odb10" /> 199 <param name="lineage_dataset" value="arthropoda_odb10" />
204 </conditional> 200 </conditional>
205 <conditional name="busco_mode"> 201 <conditional name="busco_mode">
206 <param name="mode" value="geno" /> 202 <param name="mode" value="geno" />
207 <conditional name="use_augustus"> 203 <conditional name="use_augustus">
208 <param name="use_augustus_selector" value="yes" /> 204 <param name="use_augustus_selector" value="augustus" />
209 </conditional> 205 </conditional>
210 </conditional> 206 </conditional>
211 <param name="outputs" value="short_summary,missing,gff" /> 207 <param name="outputs" value="short_summary,missing,gff" />
212 <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline" /> 208 <output name="busco_sum">
213 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> 209 <assert_contents>
210 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
211 <has_text text="Gene predictor used: augustus"/>
212 </assert_contents>
213 </output>
214 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
214 <output name="busco_gff"> 215 <output name="busco_gff">
215 <assert_contents> 216 <assert_contents>
216 <has_n_lines n="1"/> 217 <has_n_lines n="1"/>
217 <has_text text="##gff-version 3" /> 218 <has_text text="##gff-version 3" />
218 </assert_contents> 219 </assert_contents>
219 </output> 220 </output>
220 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"> 221 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
221 <assert_contents>
222 <has_text text="# BUSCO version is: @TOOL_VERSION@" />
223 </assert_contents>
224 </output>
225 </test> 222 </test>
226 <test expect_num_outputs="5"> 223 <test expect_num_outputs="5">
227 <param name="input" value="proteome.fa" /> 224 <param name="input" value="proteome.fa" />
228 <conditional name="lineage"> 225 <conditional name="lineage">
229 <param name="lineage_mode" value="select_lineage" /> 226 <param name="lineage_mode" value="select_lineage" />
231 </conditional> 228 </conditional>
232 <conditional name="busco_mode"> 229 <conditional name="busco_mode">
233 <param name="mode" value="prot" /> 230 <param name="mode" value="prot" />
234 </conditional> 231 </conditional>
235 <param name="outputs" value="short_summary,missing,image,gff" /> 232 <param name="outputs" value="short_summary,missing,image,gff" />
236 <output name="busco_sum" file="proteome_results/short_summary" compare="re_match_multiline" /> 233 <output name="busco_sum">
237 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" /> 234 <assert_contents>
238 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" /> 235 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
236 <has_text text="BUSCO was run in mode: proteins" />
237 </assert_contents>
238 </output>
239 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10" />
240 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10" />
239 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" /> 241 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
240 <output name="busco_gff"> 242 <output name="busco_gff">
241 <assert_contents> 243 <assert_contents>
242 <has_n_lines n="1"/> 244 <has_n_lines n="1"/>
243 <has_text text="##gff-version 3" /> 245 <has_text text="##gff-version 3" />
252 </conditional> 254 </conditional>
253 <conditional name="busco_mode"> 255 <conditional name="busco_mode">
254 <param name="mode" value="tran" /> 256 <param name="mode" value="tran" />
255 </conditional> 257 </conditional>
256 <param name="outputs" value="short_summary,missing,image,gff" /> 258 <param name="outputs" value="short_summary,missing,image,gff" />
257 <output name="busco_sum" file="transcriptome_results/short_summary" compare="re_match_multiline" /> 259 <output name="busco_sum">
260 <assert_contents>
261 <has_text text="BUSCO was run in mode: euk_tran" />
262 </assert_contents>
263 </output>
258 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" /> 264 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
259 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" /> 265 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
260 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" /> 266 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
261 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" /> 267 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" />
262 </test> 268 </test>
263 <test expect_num_outputs="4"> 269 <test expect_num_outputs="3">
264 <param name="input" value="genome.fa" /> 270 <param name="input" value="genome.fa" />
265 <conditional name="lineage"> 271 <conditional name="lineage">
266 <param name="lineage_mode" value="select_lineage" /> 272 <param name="lineage_mode" value="select_lineage" />
267 <param name="lineage_dataset" value="arthropoda_odb10" /> 273 <param name="lineage_dataset" value="arthropoda_odb10" />
268 </conditional> 274 </conditional>
269 <conditional name="busco_mode"> 275 <conditional name="busco_mode">
270 <param name="mode" value="geno" /> 276 <param name="mode" value="geno" />
271 <param name="miniprot" value="true"/> 277 <conditional name="use_augustus">
272 <conditional name="use_augustus"> 278 <param name="use_augustus_selector" value="augustus" />
273 <param name="use_augustus_selector" value="yes" />
274 <conditional name="aug_prediction"> 279 <conditional name="aug_prediction">
275 <param name="augustus_mode" value="builtin" /> 280 <param name="augustus_mode" value="builtin" />
276 <param name="augustus_species" value="human" /> 281 <param name="augustus_species" value="human" />
277 </conditional> 282 </conditional>
278 </conditional> 283 </conditional>
279 </conditional> 284 </conditional>
280 <param name="outputs" value="short_summary,gff" /> 285 <param name="outputs" value="short_summary,gff" />
281 <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline"/> 286 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
282 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> 287 <assert_contents>
288 <has_text text="# Gene predictor used: augustus"/>
289 </assert_contents>
290 </output>
291 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
283 <output name="busco_gff"> 292 <output name="busco_gff">
284 <assert_contents> 293 <assert_contents>
285 <has_n_lines n="1"/> 294 <has_n_lines n="1"/>
286 <has_text text="##gff-version 3" /> 295 <has_text text="##gff-version 3" />
287 </assert_contents> 296 </assert_contents>
288 </output> 297 </output>
289 <!-- The miniprot.gff file is too large. A file containing only the first 1000 lines is used for this test. -->
290 <output name="busco_miniprot" file="genome_results/miniprot_1000.gff" compare="contains" lines_diff="304463"/>
291 </test> 298 </test>
292 <test expect_num_outputs="3"> 299 <test expect_num_outputs="3">
293 <param name="input" value="genome.fa" /> 300 <param name="input" value="genome.fa" />
294 <conditional name="lineage"> 301 <conditional name="lineage">
295 <param name="lineage_mode" value="select_lineage" /> 302 <param name="lineage_mode" value="select_lineage" />
296 <param name="lineage_dataset" value="arthropoda_odb10" /> 303 <param name="lineage_dataset" value="arthropoda_odb10" />
297 </conditional> 304 </conditional>
298 <conditional name="busco_mode"> 305 <conditional name="busco_mode">
299 <param name="mode" value="geno" /> 306 <param name="mode" value="geno" />
300 <conditional name="use_augustus"> 307 <conditional name="use_augustus">
301 <param name="use_augustus_selector" value="yes" /> 308 <param name="use_augustus_selector" value="augustus" />
302 <conditional name="aug_prediction"> 309 <conditional name="aug_prediction">
303 <param name="augustus_mode" value="history" /> 310 <param name="augustus_mode" value="history" />
304 <param name="augustus_model" value="local.tar.gz" ftype="augustus" /> 311 <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
305 </conditional> 312 </conditional>
306 </conditional> 313 </conditional>
307 </conditional> 314 </conditional>
308 <param name="outputs" value="short_summary,missing" /> 315 <param name="outputs" value="short_summary,missing" />
309 <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline" /> 316 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
310 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> 317 <assert_contents>
311 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" /> 318 <has_text text="# Gene predictor used: augustus"/>
319 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
320 </assert_contents>
321 </output>
322 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
323 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10" />
312 </test> 324 </test>
313 <test expect_num_outputs="5"> 325 <test expect_num_outputs="5">
314 <param name="input" value="genome.fa" /> 326 <param name="input" value="genome.fa" />
315 <conditional name="lineage"> 327 <conditional name="lineage">
316 <param name="lineage_mode" value="select_lineage" /> 328 <param name="lineage_mode" value="select_lineage" />
317 <param name="lineage_dataset" value="arthropoda_odb10" /> 329 <param name="lineage_dataset" value="arthropoda_odb10" />
318 </conditional> 330 </conditional>
319 <conditional name="busco_mode"> 331 <conditional name="busco_mode">
320 <param name="mode" value="geno" /> 332 <param name="mode" value="geno" />
321 <conditional name="use_augustus"> 333 <conditional name="use_augustus">
322 <param name="use_augustus_selector" value="no" /> 334 <param name="use_augustus_selector" value="metaeuk" />
323 </conditional> 335 </conditional>
324 </conditional> 336 </conditional>
325 <param name="outputs" value="short_summary,missing,image,gff" /> 337 <param name="outputs" value="short_summary,missing,image,gff" />
326 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="re_match_multiline" /> 338 <output name="busco_sum">
327 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" /> 339 <assert_contents>
328 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" /> 340 <has_text text="# Gene predictor used: metaeuk"/>
329 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" /> 341 </assert_contents>
330 <output name="busco_gff" ftype="gff3"> 342 </output>
331 <assert_contents> 343 <output name="busco_table" file="genome_results_metaeuk/full_table">
332 <has_n_lines n="13"/> 344 <assert_contents>
333 </assert_contents> 345 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
334 </output> 346 <has_text text="9647at6656"/>
347 </assert_contents>
348 </output>
349 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list">
350 <assert_contents>
351 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
352 <has_text text="9647at6656"/>
353 </assert_contents>
354 </output>
355 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size"/>
356 <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6" />
335 </test> 357 </test>
336 <test expect_num_outputs="5"> 358 <test expect_num_outputs="5">
337 <param name="input" value="genome.fa" /> 359 <param name="input" value="genome.fa" />
338 <conditional name="lineage"> 360 <conditional name="lineage">
339 <param name="lineage_mode" value="auto_detect" /> 361 <param name="lineage_mode" value="auto_detect" />
340 <param name="auto_lineage" value="--auto-lineage" /> 362 <param name="auto_lineage" value="--auto-lineage" />
341 </conditional> 363 </conditional>
342 <conditional name="busco_mode"> 364 <conditional name="busco_mode">
343 <param name="mode" value="geno" /> 365 <param name="mode" value="geno" />
344 <conditional name="use_augustus"> 366 <conditional name="use_augustus">
345 <param name="use_augustus_selector" value="no" /> 367 <param name="use_augustus_selector" value="metaeuk" />
346 </conditional> 368 </conditional>
347 </conditional> 369 </conditional>
348 <param name="outputs" value="short_summary,missing,image,gff" /> 370 <param name="outputs" value="short_summary,missing,image,gff" />
349 <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" /> 371 <output name="busco_sum">
350 <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="6" /> 372 <assert_contents>
351 <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" /> 373 <has_text text="Gene predictor used: metaeuk"/>
374 </assert_contents>
375 </output>
376 <output name="busco_table">
377 <assert_contents>
378 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
379 <has_text text="The lineage dataset is: eukaryota_odb10"/>
380 </assert_contents>
381 </output>
382 <output name="busco_missing">
383 <assert_contents>
384 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
385 <has_text text="The lineage dataset is: eukaryota_odb10"/>
386 </assert_contents>
387 </output>
352 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" /> 388 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
353 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" /> 389 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />
354 </test> 390 </test>
355 <test expect_num_outputs="2"> 391 <test expect_num_outputs="3">
356 <param name="input" value="genome.fa" /> 392 <param name="input" value="genome.fa" />
357 <conditional name="lineage_conditional"> 393 <conditional name="lineage">
358 <param name="selector" value="cached"/> 394 <param name="lineage_mode" value="select_lineage" />
359 <param name="cached_db" value="busco-demo-db-20230328"/> 395 <param name="lineage_dataset" value="arthropoda_odb10" />
360 </conditional> 396 </conditional>
361 <conditional name="lineage"> 397 <param name="outputs" value="short_summary,gff" />
362 <param name="lineage_mode" value="select_lineage" /> 398 <output name="busco_sum">
363 <param name="lineage_dataset" value="archaea_odb10" /> 399 <assert_contents>
364 </conditional> 400 <has_text text="# Gene predictor used: miniprot"/>
365 <param name="outputs" value="short_summary" /> 401 </assert_contents>
366 <output name="busco_sum" file="genome_results/short_summary_cached" compare="diff" lines_diff="6" /> 402 </output>
367 <output name="busco_table" file="genome_results/full_table_cached" compare="diff" lines_diff="4" /> 403 <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff" />
368 <assert_stdout> 404 <output name="busco_table" file="genome_results_miniprot/full_table">
369 <has_text text="Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)"/> 405 <assert_contents>
370 </assert_stdout> 406 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
407 <has_text text="9647at6656"/>
408 </assert_contents>
409 </output>
371 </test> 410 </test>
372 </tests> 411 </tests>
373 <help><![CDATA[ 412 <help><![CDATA[
374 413
375 414