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comparison meryl.xml @ 9:eadfd71dde37 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b036dca639d7d67b55929be5575cab71473f53e4"
author iuc
date Tue, 05 Oct 2021 15:58:14 +0000
parents 5ae3496f9ca3
children 9cd178127b19
comparison
equal deleted inserted replaced
8:5ae3496f9ca3 9:eadfd71dde37
280 <param name="input_kmer_size" value="7" /> 280 <param name="input_kmer_size" value="7" />
281 </conditional> 281 </conditional>
282 </conditional> 282 </conditional>
283 <output name="read_db" ftype="meryldb"> 283 <output name="read_db" ftype="meryldb">
284 <assert_contents> 284 <assert_contents>
285 <has_size value="22152" delta="300" /> 285 <has_size value="22152" delta="1000" />
286 </assert_contents> 286 </assert_contents>
287 </output> 287 </output>
288 <assert_stdout> 288 <assert_stdout>
289 <has_line line="K-mer size: 7" /> 289 <has_line line="K-mer size: 7" />
290 </assert_stdout> 290 </assert_stdout>
298 <param name="N" value="100" /> 298 <param name="N" value="100" />
299 </conditional> 299 </conditional>
300 </conditional> 300 </conditional>
301 <output name="read_db" ftype="meryldb"> 301 <output name="read_db" ftype="meryldb">
302 <assert_contents> 302 <assert_contents>
303 <has_size value="32077" delta="300" /> 303 <has_size value="32077" delta="1000" />
304 </assert_contents> 304 </assert_contents>
305 </output> 305 </output>
306 </test> 306 </test>
307 <test expect_num_outputs="1"> 307 <test expect_num_outputs="1">
308 <conditional name="operation_type"> 308 <conditional name="operation_type">
313 <param name="N" value="80" /> 313 <param name="N" value="80" />
314 </conditional> 314 </conditional>
315 </conditional> 315 </conditional>
316 <output name="read_db" ftype="meryldb"> 316 <output name="read_db" ftype="meryldb">
317 <assert_contents> 317 <assert_contents>
318 <has_size value="49643" delta="300" /> 318 <has_size value="49643" delta="1000" />
319 </assert_contents> 319 </assert_contents>
320 </output> 320 </output>
321 </test> 321 </test>
322 <test expect_num_outputs="1"> 322 <test expect_num_outputs="1">
323 <conditional name="operation_type"> 323 <conditional name="operation_type">
328 <param name="distinct" value="0.9998" /> 328 <param name="distinct" value="0.9998" />
329 </conditional> 329 </conditional>
330 </conditional> 330 </conditional>
331 <output name="read_db" ftype="meryldb"> 331 <output name="read_db" ftype="meryldb">
332 <assert_contents> 332 <assert_contents>
333 <has_size value="1634" delta="300" /> 333 <has_size value="1634" delta="1000" />
334 </assert_contents> 334 </assert_contents>
335 </output> 335 </output>
336 </test> 336 </test>
337 <test expect_num_outputs="1"> 337 <test expect_num_outputs="1">
338 <conditional name="operation_type"> 338 <conditional name="operation_type">
343 <param name="N" value="100" /> 343 <param name="N" value="100" />
344 </conditional> 344 </conditional>
345 </conditional> 345 </conditional>
346 <output name="read_db" ftype="meryldb"> 346 <output name="read_db" ftype="meryldb">
347 <assert_contents> 347 <assert_contents>
348 <has_size value="2621" delta="300" /> 348 <has_size value="2621" delta="1000" />
349 </assert_contents> 349 </assert_contents>
350 </output> 350 </output>
351 </test> 351 </test>
352 <test expect_num_outputs="1"> 352 <test expect_num_outputs="1">
353 <conditional name="operation_type"> 353 <conditional name="operation_type">
358 <param name="N" value="100" /> 358 <param name="N" value="100" />
359 </conditional> 359 </conditional>
360 </conditional> 360 </conditional>
361 <output name="read_db" ftype="meryldb"> 361 <output name="read_db" ftype="meryldb">
362 <assert_contents> 362 <assert_contents>
363 <has_size value="59100" delta="300" /> 363 <has_size value="59100" delta="1000" />
364 </assert_contents> 364 </assert_contents>
365 </output> 365 </output>
366 </test> 366 </test>
367 <test expect_num_outputs="1"> 367 <test expect_num_outputs="1">
368 <conditional name="operation_type"> 368 <conditional name="operation_type">
371 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> 371 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
372 <param name="X" value="100000" /> 372 <param name="X" value="100000" />
373 </conditional> 373 </conditional>
374 <output name="read_db" ftype="meryldb"> 374 <output name="read_db" ftype="meryldb">
375 <assert_contents> 375 <assert_contents>
376 <has_size value="59500" delta="300" /> 376 <has_size value="59500" delta="1000" />
377 </assert_contents> 377 </assert_contents>
378 </output> 378 </output>
379 </test> 379 </test>
380 <test expect_num_outputs="1"> 380 <test expect_num_outputs="1">
381 <conditional name="operation_type"> 381 <conditional name="operation_type">
384 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> 384 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
385 <param name="X" value="100" /> 385 <param name="X" value="100" />
386 </conditional> 386 </conditional>
387 <output name="read_db" ftype="meryldb"> 387 <output name="read_db" ftype="meryldb">
388 <assert_contents> 388 <assert_contents>
389 <has_size value="42313" delta="300" /> 389 <has_size value="42313" delta="1000" />
390 </assert_contents> 390 </assert_contents>
391 </output> 391 </output>
392 </test> 392 </test>
393 <test expect_num_outputs="1"> 393 <test expect_num_outputs="1">
394 <conditional name="operation_type"> 394 <conditional name="operation_type">
397 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> 397 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
398 <param name="X" value="3" /> 398 <param name="X" value="3" />
399 </conditional> 399 </conditional>
400 <output name="read_db" ftype="meryldb"> 400 <output name="read_db" ftype="meryldb">
401 <assert_contents> 401 <assert_contents>
402 <has_size value="60530" delta="300" /> 402 <has_size value="60530" delta="1000" />
403 </assert_contents> 403 </assert_contents>
404 </output> 404 </output>
405 </test> 405 </test>
406 <test expect_num_outputs="1"> 406 <test expect_num_outputs="1">
407 <conditional name="operation_type"> 407 <conditional name="operation_type">
410 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> 410 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
411 <param name="X" value="2" /> 411 <param name="X" value="2" />
412 </conditional> 412 </conditional>
413 <output name="read_db" ftype="meryldb"> 413 <output name="read_db" ftype="meryldb">
414 <assert_contents> 414 <assert_contents>
415 <has_size value="56200" delta="300" /> 415 <has_size value="56200" delta="1000" />
416 </assert_contents> 416 </assert_contents>
417 </output> 417 </output>
418 </test> 418 </test>
419 <test expect_num_outputs="1"> 419 <test expect_num_outputs="1">
420 <conditional name="operation_type"> 420 <conditional name="operation_type">
423 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> 423 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
424 <param name="X" value="2" /> 424 <param name="X" value="2" />
425 </conditional> 425 </conditional>
426 <output name="read_db" ftype="meryldb"> 426 <output name="read_db" ftype="meryldb">
427 <assert_contents> 427 <assert_contents>
428 <has_size value="56100" delta="300" /> 428 <has_size value="56100" delta="1000" />
429 </assert_contents> 429 </assert_contents>
430 </output> 430 </output>
431 </test> 431 </test>
432 <!-- test 12 --> 432 <!-- test 12 -->
433 <test expect_num_outputs="1"> 433 <test expect_num_outputs="1">
437 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> 437 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
438 <param name="X" value="3" /> 438 <param name="X" value="3" />
439 </conditional> 439 </conditional>
440 <output name="read_db" ftype="meryldb"> 440 <output name="read_db" ftype="meryldb">
441 <assert_contents> 441 <assert_contents>
442 <has_size value="37501" delta="300" /> 442 <has_size value="37501" delta="1000" />
443 </assert_contents> 443 </assert_contents>
444 </output> 444 </output>
445 </test> 445 </test>
446 <test expect_num_outputs="1"> 446 <test expect_num_outputs="1">
447 <conditional name="operation_type"> 447 <conditional name="operation_type">
450 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> 450 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
451 <param name="input_meryldb_03" value="" ftype="meryldb" /> 451 <param name="input_meryldb_03" value="" ftype="meryldb" />
452 </conditional> 452 </conditional>
453 <output name="read_db" ftype="meryldb"> 453 <output name="read_db" ftype="meryldb">
454 <assert_contents> 454 <assert_contents>
455 <has_size value="36100" delta="300" /> 455 <has_size value="36100" delta="1000" />
456 </assert_contents> 456 </assert_contents>
457 </output> 457 </output>
458 </test> 458 </test>
459 <test expect_num_outputs="1"> 459 <test expect_num_outputs="1">
460 <conditional name="operation_type"> 460 <conditional name="operation_type">
462 <param name="groups_operations" value="union-min" /> 462 <param name="groups_operations" value="union-min" />
463 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> 463 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
464 </conditional> 464 </conditional>
465 <output name="read_db" ftype="meryldb"> 465 <output name="read_db" ftype="meryldb">
466 <assert_contents> 466 <assert_contents>
467 <has_size value="58925" delta="350" /> 467 <has_size value="58925" delta="1000" />
468 </assert_contents> 468 </assert_contents>
469 </output> 469 </output>
470 </test> 470 </test>
471 <test expect_num_outputs="1"> 471 <test expect_num_outputs="1">
472 <conditional name="operation_type"> 472 <conditional name="operation_type">
474 <param name="groups_operations" value="union-max" /> 474 <param name="groups_operations" value="union-max" />
475 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> 475 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
476 </conditional> 476 </conditional>
477 <output name="read_db" ftype="meryldb"> 477 <output name="read_db" ftype="meryldb">
478 <assert_contents> 478 <assert_contents>
479 <has_size value="58930" delta="300" /> 479 <has_size value="58930" delta="1000" />
480 </assert_contents> 480 </assert_contents>
481 </output> 481 </output>
482 </test> 482 </test>
483 <test expect_num_outputs="1"> 483 <test expect_num_outputs="1">
484 <conditional name="operation_type"> 484 <conditional name="operation_type">
486 <param name="groups_operations" value="union-sum" /> 486 <param name="groups_operations" value="union-sum" />
487 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> 487 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
488 </conditional> 488 </conditional>
489 <output name="read_db" ftype="meryldb"> 489 <output name="read_db" ftype="meryldb">
490 <assert_contents> 490 <assert_contents>
491 <has_size value="58600" delta="300" /> 491 <has_size value="58600" delta="1000" />
492 </assert_contents> 492 </assert_contents>
493 </output> 493 </output>
494 </test> 494 </test>
495 <test expect_num_outputs="1"> 495 <test expect_num_outputs="1">
496 <conditional name="operation_type"> 496 <conditional name="operation_type">
498 <param name="groups_operations" value="intersect" /> 498 <param name="groups_operations" value="intersect" />
499 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> 499 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
500 </conditional> 500 </conditional>
501 <output name="read_db" ftype="meryldb"> 501 <output name="read_db" ftype="meryldb">
502 <assert_contents> 502 <assert_contents>
503 <has_size value="14951" delta="300" /> 503 <has_size value="14951" delta="1000" />
504 </assert_contents> 504 </assert_contents>
505 </output> 505 </output>
506 </test> 506 </test>
507 <test expect_num_outputs="1"> 507 <test expect_num_outputs="1">
508 <conditional name="operation_type"> 508 <conditional name="operation_type">
510 <param name="groups_operations" value="intersect-min" /> 510 <param name="groups_operations" value="intersect-min" />
511 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> 511 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
512 </conditional> 512 </conditional>
513 <output name="read_db" ftype="meryldb"> 513 <output name="read_db" ftype="meryldb">
514 <assert_contents> 514 <assert_contents>
515 <has_size value="14957" delta="300" /> 515 <has_size value="14957" delta="1000" />
516 </assert_contents> 516 </assert_contents>
517 </output> 517 </output>
518 </test> 518 </test>
519 <test expect_num_outputs="1"> 519 <test expect_num_outputs="1">
520 <conditional name="operation_type"> 520 <conditional name="operation_type">
522 <param name="groups_operations" value="intersect-max" /> 522 <param name="groups_operations" value="intersect-max" />
523 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> 523 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
524 </conditional> 524 </conditional>
525 <output name="read_db" ftype="meryldb"> 525 <output name="read_db" ftype="meryldb">
526 <assert_contents> 526 <assert_contents>
527 <has_size value="14956" delta="300" /> 527 <has_size value="14956" delta="1000" />
528 </assert_contents> 528 </assert_contents>
529 </output> 529 </output>
530 </test> 530 </test>
531 <test expect_num_outputs="1"> 531 <test expect_num_outputs="1">
532 <conditional name="operation_type"> 532 <conditional name="operation_type">
534 <param name="groups_operations" value="intersect-sum" /> 534 <param name="groups_operations" value="intersect-sum" />
535 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> 535 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
536 </conditional> 536 </conditional>
537 <output name="read_db" ftype="meryldb"> 537 <output name="read_db" ftype="meryldb">
538 <assert_contents> 538 <assert_contents>
539 <has_size value="14953" delta="300" /> 539 <has_size value="14953" delta="1000" />
540 </assert_contents> 540 </assert_contents>
541 </output> 541 </output>
542 </test> 542 </test>
543 <!-- test 20 --> 543 <!-- test 20 -->
544 <test expect_num_outputs="1"> 544 <test expect_num_outputs="1">
547 <param name="groups_operations" value="subtract" /> 547 <param name="groups_operations" value="subtract" />
548 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> 548 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
549 </conditional> 549 </conditional>
550 <output name="read_db" ftype="meryldb"> 550 <output name="read_db" ftype="meryldb">
551 <assert_contents> 551 <assert_contents>
552 <has_size value="23999" delta="300" /> 552 <has_size value="23999" delta="1000" />
553 </assert_contents> 553 </assert_contents>
554 </output> 554 </output>
555 </test> 555 </test>
556 <test expect_num_outputs="1"> 556 <test expect_num_outputs="1">
557 <conditional name="operation_type"> 557 <conditional name="operation_type">
559 <param name="groups_operations" value="difference" /> 559 <param name="groups_operations" value="difference" />
560 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> 560 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
561 </conditional> 561 </conditional>
562 <output name="read_db" ftype="meryldb"> 562 <output name="read_db" ftype="meryldb">
563 <assert_contents> 563 <assert_contents>
564 <has_size value="24016" delta="300" /> 564 <has_size value="24016" delta="1000" />
565 </assert_contents> 565 </assert_contents>
566 </output> 566 </output>
567 </test> 567 </test>
568 <test expect_num_outputs="1"> 568 <test expect_num_outputs="1">
569 <conditional name="operation_type"> 569 <conditional name="operation_type">
571 <param name="groups_operations" value="symmetric-difference" /> 571 <param name="groups_operations" value="symmetric-difference" />
572 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> 572 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
573 </conditional> 573 </conditional>
574 <output name="read_db" ftype="meryldb"> 574 <output name="read_db" ftype="meryldb">
575 <assert_contents> 575 <assert_contents>
576 <has_size value="57455" delta="300" /> 576 <has_size value="57455" delta="1000" />
577 </assert_contents> 577 </assert_contents>
578 </output> 578 </output>
579 </test> 579 </test>
580 <test expect_num_outputs="6"> 580 <test expect_num_outputs="6">
581 <conditional name="operation_type"> 581 <conditional name="operation_type">
632 <param name="input_kmer_size" value="7" /> 632 <param name="input_kmer_size" value="7" />
633 </conditional> 633 </conditional>
634 </conditional> 634 </conditional>
635 <output name="read_db" ftype="meryldb"> 635 <output name="read_db" ftype="meryldb">
636 <assert_contents> 636 <assert_contents>
637 <has_size value="22200" delta="300" /> 637 <has_size value="22200" delta="1000" />
638 </assert_contents> 638 </assert_contents>
639 </output> 639 </output>
640 <assert_stdout> 640 <assert_stdout>
641 <has_line line="K-mer size: 7" /> 641 <has_line line="K-mer size: 7" />
642 </assert_stdout> 642 </assert_stdout>