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comparison meryl.xml @ 6:31fa26c0692b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3"
author iuc
date Tue, 08 Jun 2021 07:20:29 +0000
parents d63739222f68
children 51c2360aa807
comparison
equal deleted inserted replaced
5:d63739222f68 6:31fa26c0692b
47 $operation_type.X 47 $operation_type.X
48 tmp.meryl 48 tmp.meryl
49 output read-db.meryl && 49 output read-db.meryl &&
50 tar -zcf read-db.meryldb read-db.meryl 50 tar -zcf read-db.meryldb read-db.meryl
51 #elif $operation_type.command_type == 'groups-kmers' 51 #elif $operation_type.command_type == 'groups-kmers'
52 mkdir -p ./temp_db/ && 52 #for $i,$mdb in enumerate($operation_type.input_meryldb_02)
53 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && 53 mkdir -p ./tmp_folder_$i/ &&
54 mv ./temp_db/* tmp_01.meryl && 54 tar -zxf $mdb -C ./tmp_folder_$i &&
55 tar -zxf $operation_type.input_meryldb_03 -C ./temp_db/ && 55 mv ./tmp_folder_$i/* db_'${i}'.meryl &&
56 mv ./temp_db/* tmp_02.meryl && 56 #end for
57 meryl 57 meryl $operation_type.groups_operations output read-db.meryl db_* &&
58 $operation_type.groups_operations
59 tmp_01.meryl
60 tmp_02.meryl
61 output read-db.meryl &&
62 tar -zcf read-db.meryldb read-db.meryl 58 tar -zcf read-db.meryldb read-db.meryl
63 #elif $operation_type.command_type == 'histogram-kmers' 59 #elif $operation_type.command_type == 'histogram-kmers'
64 mkdir -p ./temp_db/ && 60 mkdir -p ./temp_db/ &&
65 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && 61 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&
66 mv ./temp_db/* tmp.meryl && 62 mv ./temp_db/* tmp.meryl &&
218 <option value="intersect-sum">Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts</option> 214 <option value="intersect-sum">Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts</option>
219 <option value="subtract">Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs</option> 215 <option value="subtract">Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs</option>
220 <option value="difference">Difference: return k-mers that occur in the first input, but none of the other inputs</option> 216 <option value="difference">Difference: return k-mers that occur in the first input, but none of the other inputs</option>
221 <option value="symmetric-difference">Symmetric-difference: return k-mers that occur in exactly one input</option> 217 <option value="symmetric-difference">Symmetric-difference: return k-mers that occur in exactly one input</option>
222 </param> 218 </param>
223 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" /> 219 <param name="input_meryldb_02" type="data" multiple="true" format="meryldb" label="Input meryldb" />
224 <param name="input_meryldb_03" type="data" format="meryldb" label="Input meryldb" />
225 </when> 220 </when>
226 <when value="histogram-kmers"> 221 <when value="histogram-kmers">
227 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" /> 222 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" />
228 </when> 223 </when>
229 <when value="print"> 224 <when value="print">
448 </test> 443 </test>
449 <test expect_num_outputs="1"> 444 <test expect_num_outputs="1">
450 <conditional name="operation_type"> 445 <conditional name="operation_type">
451 <param name="command_type" value="groups-kmers" /> 446 <param name="command_type" value="groups-kmers" />
452 <param name="groups_operations" value="union" /> 447 <param name="groups_operations" value="union" />
453 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> 448 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
454 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> 449 <param name="input_meryldb_03" value="" ftype="meryldb" />
455 </conditional> 450 </conditional>
456 <output name="read_db" ftype="meryldb"> 451 <output name="read_db" ftype="meryldb">
457 <assert_contents> 452 <assert_contents>
458 <has_size value="36100" delta="300" /> 453 <has_size value="36100" delta="300" />
459 </assert_contents> 454 </assert_contents>
461 </test> 456 </test>
462 <test expect_num_outputs="1"> 457 <test expect_num_outputs="1">
463 <conditional name="operation_type"> 458 <conditional name="operation_type">
464 <param name="command_type" value="groups-kmers" /> 459 <param name="command_type" value="groups-kmers" />
465 <param name="groups_operations" value="union-min" /> 460 <param name="groups_operations" value="union-min" />
466 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> 461 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
467 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
468 </conditional> 462 </conditional>
469 <output name="read_db" ftype="meryldb"> 463 <output name="read_db" ftype="meryldb">
470 <assert_contents> 464 <assert_contents>
471 <has_size value="58925" delta="350" /> 465 <has_size value="58925" delta="350" />
472 </assert_contents> 466 </assert_contents>
474 </test> 468 </test>
475 <test expect_num_outputs="1"> 469 <test expect_num_outputs="1">
476 <conditional name="operation_type"> 470 <conditional name="operation_type">
477 <param name="command_type" value="groups-kmers" /> 471 <param name="command_type" value="groups-kmers" />
478 <param name="groups_operations" value="union-max" /> 472 <param name="groups_operations" value="union-max" />
479 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> 473 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
480 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
481 </conditional> 474 </conditional>
482 <output name="read_db" ftype="meryldb"> 475 <output name="read_db" ftype="meryldb">
483 <assert_contents> 476 <assert_contents>
484 <has_size value="58930" delta="300" /> 477 <has_size value="58930" delta="300" />
485 </assert_contents> 478 </assert_contents>
487 </test> 480 </test>
488 <test expect_num_outputs="1"> 481 <test expect_num_outputs="1">
489 <conditional name="operation_type"> 482 <conditional name="operation_type">
490 <param name="command_type" value="groups-kmers" /> 483 <param name="command_type" value="groups-kmers" />
491 <param name="groups_operations" value="union-sum" /> 484 <param name="groups_operations" value="union-sum" />
492 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> 485 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
493 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
494 </conditional> 486 </conditional>
495 <output name="read_db" ftype="meryldb"> 487 <output name="read_db" ftype="meryldb">
496 <assert_contents> 488 <assert_contents>
497 <has_size value="58600" delta="300" /> 489 <has_size value="58600" delta="300" />
498 </assert_contents> 490 </assert_contents>
500 </test> 492 </test>
501 <test expect_num_outputs="1"> 493 <test expect_num_outputs="1">
502 <conditional name="operation_type"> 494 <conditional name="operation_type">
503 <param name="command_type" value="groups-kmers" /> 495 <param name="command_type" value="groups-kmers" />
504 <param name="groups_operations" value="intersect" /> 496 <param name="groups_operations" value="intersect" />
505 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> 497 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
506 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
507 </conditional> 498 </conditional>
508 <output name="read_db" ftype="meryldb"> 499 <output name="read_db" ftype="meryldb">
509 <assert_contents> 500 <assert_contents>
510 <has_size value="14951" delta="300" /> 501 <has_size value="14951" delta="300" />
511 </assert_contents> 502 </assert_contents>
513 </test> 504 </test>
514 <test expect_num_outputs="1"> 505 <test expect_num_outputs="1">
515 <conditional name="operation_type"> 506 <conditional name="operation_type">
516 <param name="command_type" value="groups-kmers" /> 507 <param name="command_type" value="groups-kmers" />
517 <param name="groups_operations" value="intersect-min" /> 508 <param name="groups_operations" value="intersect-min" />
518 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> 509 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
519 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
520 </conditional> 510 </conditional>
521 <output name="read_db" ftype="meryldb"> 511 <output name="read_db" ftype="meryldb">
522 <assert_contents> 512 <assert_contents>
523 <has_size value="14957" delta="300" /> 513 <has_size value="14957" delta="300" />
524 </assert_contents> 514 </assert_contents>
526 </test> 516 </test>
527 <test expect_num_outputs="1"> 517 <test expect_num_outputs="1">
528 <conditional name="operation_type"> 518 <conditional name="operation_type">
529 <param name="command_type" value="groups-kmers" /> 519 <param name="command_type" value="groups-kmers" />
530 <param name="groups_operations" value="intersect-max" /> 520 <param name="groups_operations" value="intersect-max" />
531 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> 521 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
532 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
533 </conditional> 522 </conditional>
534 <output name="read_db" ftype="meryldb"> 523 <output name="read_db" ftype="meryldb">
535 <assert_contents> 524 <assert_contents>
536 <has_size value="14956" delta="300" /> 525 <has_size value="14956" delta="300" />
537 </assert_contents> 526 </assert_contents>
539 </test> 528 </test>
540 <test expect_num_outputs="1"> 529 <test expect_num_outputs="1">
541 <conditional name="operation_type"> 530 <conditional name="operation_type">
542 <param name="command_type" value="groups-kmers" /> 531 <param name="command_type" value="groups-kmers" />
543 <param name="groups_operations" value="intersect-sum" /> 532 <param name="groups_operations" value="intersect-sum" />
544 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> 533 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
545 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
546 </conditional> 534 </conditional>
547 <output name="read_db" ftype="meryldb"> 535 <output name="read_db" ftype="meryldb">
548 <assert_contents> 536 <assert_contents>
549 <has_size value="14953" delta="300" /> 537 <has_size value="14953" delta="300" />
550 </assert_contents> 538 </assert_contents>
553 <!-- test 20 --> 541 <!-- test 20 -->
554 <test expect_num_outputs="1"> 542 <test expect_num_outputs="1">
555 <conditional name="operation_type"> 543 <conditional name="operation_type">
556 <param name="command_type" value="groups-kmers" /> 544 <param name="command_type" value="groups-kmers" />
557 <param name="groups_operations" value="subtract" /> 545 <param name="groups_operations" value="subtract" />
558 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> 546 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
559 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
560 </conditional> 547 </conditional>
561 <output name="read_db" ftype="meryldb"> 548 <output name="read_db" ftype="meryldb">
562 <assert_contents> 549 <assert_contents>
563 <has_size value="23999" delta="300" /> 550 <has_size value="23999" delta="300" />
564 </assert_contents> 551 </assert_contents>
566 </test> 553 </test>
567 <test expect_num_outputs="1"> 554 <test expect_num_outputs="1">
568 <conditional name="operation_type"> 555 <conditional name="operation_type">
569 <param name="command_type" value="groups-kmers" /> 556 <param name="command_type" value="groups-kmers" />
570 <param name="groups_operations" value="difference" /> 557 <param name="groups_operations" value="difference" />
571 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> 558 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
572 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
573 </conditional> 559 </conditional>
574 <output name="read_db" ftype="meryldb"> 560 <output name="read_db" ftype="meryldb">
575 <assert_contents> 561 <assert_contents>
576 <has_size value="24016" delta="300" /> 562 <has_size value="24016" delta="300" />
577 </assert_contents> 563 </assert_contents>
579 </test> 565 </test>
580 <test expect_num_outputs="1"> 566 <test expect_num_outputs="1">
581 <conditional name="operation_type"> 567 <conditional name="operation_type">
582 <param name="command_type" value="groups-kmers" /> 568 <param name="command_type" value="groups-kmers" />
583 <param name="groups_operations" value="symmetric-difference" /> 569 <param name="groups_operations" value="symmetric-difference" />
584 <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> 570 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
585 <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
586 </conditional> 571 </conditional>
587 <output name="read_db" ftype="meryldb"> 572 <output name="read_db" ftype="meryldb">
588 <assert_contents> 573 <assert_contents>
589 <has_size value="57455" delta="300" /> 574 <has_size value="57455" delta="300" />
590 </assert_contents> 575 </assert_contents>