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comparison semibin.xml @ 3:b5a7583b8db0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
author iuc
date Tue, 25 Mar 2025 15:55:28 +0000
parents 99ff9221182c
children fdb13ee4be38
comparison
equal deleted inserted replaced
2:99ff9221182c 3:b5a7583b8db0
16 #if $mode.select == 'single' or $mode.select == 'co' 16 #if $mode.select == 'single' or $mode.select == 'co'
17 single_easy_bin 17 single_easy_bin
18 #if $mode.select == 'single' and str($mode.environment) != '' 18 #if $mode.select == 'single' and str($mode.environment) != ''
19 --environment '$mode.environment' 19 --environment '$mode.environment'
20 #end if 20 #end if
21 #if $mode.ref.select == "cached" 21 #if $mode.ref.select == "cached":
22 --reference-db-data-dir '$mode.ref.cached_db.fields.path' 22 --reference-db-data-dir '$mode.ref.cached_db.fields.path'
23 #else 23 #end if
24 #if $mode.ref.select == "taxonomy"
24 --taxonomy-annotation-table '$mode.ref.taxonomy_annotation_table' 25 --taxonomy-annotation-table '$mode.ref.taxonomy_annotation_table'
25 #end if 26 #end if
26 #else 27 #else
27 multi_easy_bin 28 multi_easy_bin
28 --separator '$separator' 29 --separator '$separator'
29 #if $mode.ref.select == "cached" 30 #if $mode.ref.select == "cached":
30 --reference-db-data-dir '$mode.ref.cached_db.fields.path' 31 --reference-db-data-dir '$mode.ref.cached_db.fields.path'
31 #else 32 #end if
33 #if $mode.ref.select == "taxonomy"
32 --taxonomy-annotation-table 34 --taxonomy-annotation-table
33 #for $e in $mode.ref.taxonomy_annotation_table 35 #for $e in $mode.ref.taxonomy_annotation_table
34 '$e' 36 '$e'
35 #end for 37 #end for
36 #end if 38 #end if
41 --cannot-name 'cannot' 43 --cannot-name 'cannot'
42 @MIN_LEN@ 44 @MIN_LEN@
43 --orf-finder '$orf_finder' 45 --orf-finder '$orf_finder'
44 --random-seed $random_seed 46 --random-seed $random_seed
45 47
46 #if str($annot.ml_threshold) != '' 48 #if $annot.ml_threshold:
47 --ml-threshold $annot.ml_threshold 49 --ml-threshold $annot.ml_threshold
48 #end if 50 #end if
49 --epoches $training.epoches 51 --epoches $training.epoches
50 --batch-size $training.batch_size 52 --batch-size $training.batch_size
51 --max-node $bin.max_node 53 --max-node $bin.max_node
52 --max-edges $bin.max_edges 54 --max-edges $bin.max_edges
53 --minfasta-kbs $bin.minfasta_kbs 55 --minfasta-kbs $bin.minfasta_kbs
54 #if ($mode.select == 'single' or $mode.select == 'co') and "pre_reclustering_bins" in $extra_output 56 #if ($mode.select == 'single' or $mode.select == 'co') and $extra_output and "pre_reclustering_bins" in $extra_output
55 --write-pre-reclustering-bins 57 --write-pre-reclustering-bins
56 #end if 58 #end if
57 --compression none 59 --compression none
58 --threads \${GALAXY_SLOTS:-1} 60 --threads \${GALAXY_SLOTS:-1}
59 --processes \${GALAXY_SLOTS:-1} 61 --processes \${GALAXY_SLOTS:-1}
151 <conditional name="min_len"> 153 <conditional name="min_len">
152 <param name="method" value="min-len"/> 154 <param name="method" value="min-len"/>
153 <param name="min_len" value="0" /> 155 <param name="min_len" value="0" />
154 </conditional> 156 </conditional>
155 <param name="orf_finder" value="prodigal"/> 157 <param name="orf_finder" value="prodigal"/>
156 <param name="random-seed" value="0"/> 158 <param name="random_seed" value="0"/>
157 <section name="annot">
158 <param name="ml_threshold" value=""/>
159 </section>
160 <section name="training"> 159 <section name="training">
161 <param name="epoches" value="20"/> 160 <param name="epoches" value="20"/>
162 <param name="batch_size" value="2048"/> 161 <param name="batch_size" value="2048"/>
163 </section> 162 </section>
164 <section name="bin"> 163 <section name="bin">
190 <assert_contents> 189 <assert_contents>
191 <has_size value="1" delta="1"/> 190 <has_size value="1" delta="1"/>
192 </assert_contents> 191 </assert_contents>
193 </output> 192 </output>
194 </test> 193 </test>
194 <test expect_num_outputs="5">
195 <conditional name="mode">
196 <param name="select" value="single"/>
197 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
198 <param name="input_bam" ftype="bam" value="input_single.bam"/>
199 <conditional name="ref">
200 <param name="select" value="ml"/>
201 </conditional>
202 <param name="environment" value="human_gut"/>
203 </conditional>
204 <conditional name="min_len">
205 <param name="method" value="min-len"/>
206 <param name="min_len" value="0" />
207 </conditional>
208 <param name="orf_finder" value="prodigal"/>
209 <param name="random_seed" value="0"/>
210 <section name="training">
211 <param name="epoches" value="20"/>
212 <param name="batch_size" value="2048"/>
213 </section>
214 <section name="bin">
215 <param name="max_node" value="1"/>
216 <param name="max_edges" value="200"/>
217 <param name="minfasta_kbs" value="200"/>
218 </section>
219 <param name="extra_output" value="data,coverage,contigs"/>
220 <output_collection name="output_bins" count="0"/>
221 <output name="single_data" ftype="csv">
222 <assert_contents>
223 <has_text text="g1k_0"/>
224 <has_text text="g4k_7"/>
225 </assert_contents>
226 </output>
227 <output name="single_data_split" ftype="csv">
228 <assert_contents>
229 <has_text text="g1k_0_1"/>
230 <has_text text="g1k_6_2"/>
231 </assert_contents>
232 </output>
233 <output name="single_cov" ftype="csv">
234 <assert_contents>
235 <has_text text="g1k_0"/>
236 <has_text text="0.027"/>
237 </assert_contents>
238 </output>
239 <output name="single_split_cov" ftype="csv">
240 <assert_contents>
241 <has_size value="1" delta="1"/>
242 </assert_contents>
243 </output>
244 </test>
195 <test expect_num_outputs="3"> 245 <test expect_num_outputs="3">
196 <conditional name="mode"> 246 <conditional name="mode">
197 <param name="select" value="co"/> 247 <param name="select" value="co"/>
198 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> 248 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
199 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/> 249 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
200 <conditional name="ref"> 250 <conditional name="ref">
201 <param name="select" value="taxonomy"/> 251 <param name="select" value="ml"/>
202 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
203 </conditional> 252 </conditional>
204 </conditional> 253 </conditional>
205 <conditional name="min_len"> 254 <conditional name="min_len">
206 <param name="method" value="ratio"/> 255 <param name="method" value="ratio"/>
207 <param name="ratio" value="0.05"/> 256 <param name="ratio" value="0.05"/>
208 </conditional> 257 </conditional>
209 <param name="orf_finder" value="fast-naive"/> 258 <param name="orf_finder" value="fast-naive"/>
210 <param name="random-seed" value="0"/> 259 <param name="random_seed" value="0"/>
211 <section name="annot">
212 <param name="ml_threshold" value=""/>
213 </section>
214 <section name="training"> 260 <section name="training">
215 <param name="epoches" value="20"/> 261 <param name="epoches" value="20"/>
216 <param name="batch_size" value="2048"/> 262 <param name="batch_size" value="2048"/>
217 </section> 263 </section>
218 <section name="bin"> 264 <section name="bin">
275 </conditional> 321 </conditional>
276 <conditional name="min_len"> 322 <conditional name="min_len">
277 <param name="method" value="ratio"/> 323 <param name="method" value="ratio"/>
278 <param name="ratio" value="0.05"/> 324 <param name="ratio" value="0.05"/>
279 </conditional> 325 </conditional>
280 <param name="orf_finder" value="fraggenescan"/> 326 <param name="orf_finder" value="fast-naive"/>
281 <param name="random-seed" value="0"/> 327 <param name="random_seed" value="0"/>
282 <section name="annot">
283 <param name="ml_threshold" value=""/>
284 </section>
285 <section name="training"> 328 <section name="training">
286 <param name="epoches" value="20"/> 329 <param name="epoches" value="20"/>
287 <param name="batch_size" value="2048"/> 330 <param name="batch_size" value="2048"/>
288 </section> 331 </section>
289 <section name="bin"> 332 <section name="bin">
332 <has_text text="g2k_7_2"/> 375 <has_text text="g2k_7_2"/>
333 </assert_contents> 376 </assert_contents>
334 </element> 377 </element>
335 </output_collection> 378 </output_collection>
336 </test> 379 </test>
380 <test expect_num_outputs="3">
381 <conditional name="mode">
382 <param name="select" value="co"/>
383 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
384 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
385 <conditional name="ref">
386 <param name="select" value="taxonomy"/>
387 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
388 </conditional>
389 </conditional>
390 <conditional name="min_len">
391 <param name="method" value="ratio"/>
392 <param name="ratio" value="0.05"/>
393 </conditional>
394 <param name="orf_finder" value="fraggenescan"/>
395 <param name="random_seed" value="0"/>
396 <section name="training">
397 <param name="epoches" value="20"/>
398 <param name="batch_size" value="2048"/>
399 </section>
400 <section name="bin">
401 <param name="max_node" value="1"/>
402 <param name="max_edges" value="200"/>
403 <param name="minfasta_kbs" value="200"/>
404 </section>
405 <param name="extra_output" value="coverage"/>
406 <output_collection name="output_bins" count="0"/>
407 <output_collection name="co_cov" count="5">
408 <element name="0" ftype="csv">
409 <assert_contents>
410 <has_text text="g1k_0"/>
411 <has_text text="g2k_7"/>
412 </assert_contents>
413 </element>
414 <element name="1" ftype="csv">
415 <assert_contents>
416 <has_text text="g1k_0"/>
417 <has_text text="g2k_7"/>
418 </assert_contents>
419 </element>
420 <element name="4" ftype="csv">
421 <assert_contents>
422 <has_text text="g1k_0"/>
423 <has_text text="g2k_7"/>
424 </assert_contents>
425 </element>
426 </output_collection>
427 <output_collection name="co_split_cov" count="5">
428 <element name="0" ftype="csv">
429 <assert_contents>
430 <has_text text="g1k_0_1"/>
431 <has_text text="g2k_7_2"/>
432 </assert_contents>
433 </element>
434 <element name="1" ftype="csv">
435 <assert_contents>
436 <has_text text="g1k_0_1"/>
437 <has_text text="g2k_7_2"/>
438 </assert_contents>
439 </element>
440 <element name="2" ftype="csv">
441 <assert_contents>
442 <has_text text="g1k_0_1"/>
443 <has_text text="g2k_7_2"/>
444 </assert_contents>
445 </element>
446 </output_collection>
447 </test>
337 <test expect_num_outputs="1"> 448 <test expect_num_outputs="1">
338 <conditional name="mode"> 449 <conditional name="mode">
339 <param name="select" value="single"/> 450 <param name="select" value="single"/>
340 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> 451 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
341 <param name="input_bam" ftype="bam" value="input_single.bam"/> 452 <param name="input_bam" ftype="bam" value="input_single.bam"/>
342 <conditional name="ref"> 453 <conditional name="ref">
343 <param name="db_selector" value="cached"/> 454 <param name="select" value="cached"/>
344 <param name="cached_db" value="test-db"/> 455 <param name="cached_db" value="test-db"/>
345 </conditional> 456 </conditional>
346 </conditional> 457 </conditional>
347 <conditional name="min_len"> 458 <conditional name="min_len">
348 <param name="method" value="ratio"/> 459 <param name="method" value="ratio"/>
349 <param name="ratio" value="0.05"/> 460 <param name="ratio" value="0.05"/>
350 </conditional> 461 </conditional>
351 <param name="orf_finder" value="fraggenescan"/> 462 <param name="orf_finder" value="fraggenescan"/>
352 <param name="random-seed" value="0"/> 463 <param name="random_seed" value="0"/>
353 <section name="annot"> 464 <section name="training">
354 <param name="ml_threshold" value=""/> 465 <param name="epoches" value="20"/>
355 </section> 466 <param name="batch_size" value="2048"/>
356 <section name="training"> 467 </section>
357 <param name="epoches" value="20"/> 468 <section name="bin">
358 <param name="batch_size" value="2048"/> 469 <param name="max_node" value="1"/>
359 </section> 470 <param name="max_edges" value="200"/>
360 <section name="bin"> 471 <param name="minfasta_kbs" value="200"/>
361 <param name="max_node" value="1"/> 472 </section>
362 <param name="max_edges" value="200"/>
363 <param name="minfasta_kbs" value="200"/>
364 </section>
365 <param name="extra_output" value=""/>
366 <output_collection name="output_bins" count="1"> 473 <output_collection name="output_bins" count="1">
367 <element name="SemiBin_30" ftype="fasta"> 474 <element name="SemiBin_30" ftype="fasta">
368 <assert_contents> 475 <assert_contents>
369 <has_text text=">g3k_0"/> 476 <has_text text=">g3k_0"/>
370 </assert_contents> 477 </assert_contents>
375 <conditional name="mode"> 482 <conditional name="mode">
376 <param name="select" value="single"/> 483 <param name="select" value="single"/>
377 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> 484 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
378 <param name="input_bam" ftype="bam" value="input_single.bam"/> 485 <param name="input_bam" ftype="bam" value="input_single.bam"/>
379 <conditional name="ref"> 486 <conditional name="ref">
380 <param name="db_selector" value="cached"/> 487 <param name="select" value="cached"/>
381 <param name="cached_db" value="test-db"/> 488 <param name="cached_db" value="test-db"/>
382 </conditional> 489 </conditional>
383 </conditional> 490 </conditional>
384 <conditional name="min_len"> 491 <conditional name="min_len">
385 <param name="method" value="ratio"/> 492 <param name="method" value="ratio"/>
386 <param name="ratio" value="0.05"/> 493 <param name="ratio" value="0.05"/>
387 </conditional> 494 </conditional>
388 <param name="orf_finder" value="fraggenescan"/> 495 <param name="orf_finder" value="fraggenescan"/>
389 <param name="random-seed" value="0"/> 496 <param name="random_seed" value="0"/>
390 <section name="annot">
391 <param name="ml_threshold" value=""/>
392 </section>
393 <section name="training"> 497 <section name="training">
394 <param name="epoches" value="20"/> 498 <param name="epoches" value="20"/>
395 <param name="batch_size" value="2048"/> 499 <param name="batch_size" value="2048"/>
396 </section> 500 </section>
397 <section name="bin"> 501 <section name="bin">
442 <param name="method" value="ratio"/> 546 <param name="method" value="ratio"/>
443 <param name="ratio" value="0.05"/> 547 <param name="ratio" value="0.05"/>
444 </conditional> 548 </conditional>
445 <param name="orf_finder" value="fraggenescan"/> 549 <param name="orf_finder" value="fraggenescan"/>
446 <param name="random_seed" value="0"/> 550 <param name="random_seed" value="0"/>
447 <section name="annot">
448 <param name="ml_threshold" value=""/>
449 </section>
450 <section name="training"> 551 <section name="training">
451 <param name="epoches" value="20"/> 552 <param name="epoches" value="20"/>
452 <param name="batch_size" value="2048"/> 553 <param name="batch_size" value="2048"/>
453 </section> 554 </section>
454 <section name="bin"> 555 <section name="bin">