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comparison bionano_scaffold.xml @ 5:96cacb31d571 draft

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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03"
author bgruening
date Sat, 29 May 2021 15:58:03 +0000
parents 8cc3862f8b8e
children 5d7c5ae1b69b
comparison
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4:8cc3862f8b8e 5:96cacb31d571
53 ## #end if 53 ## #end if
54 ###end if 54 ###end if
55 -f 55 -f
56 $zip_file 56 $zip_file
57 -o ./ 57 -o ./
58 && cat $output_file_NCBI $output_file_not_scaffolded > total_contigs_raw.fasta
59 #if $trim_cut_sites 58 #if $trim_cut_sites
60 && python '$__tool_directory__/remove_fake_cut_sites.py' 'total_contigs_raw.fasta' 'total_contigs_trimmed.fasta' 'output.log' 59 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log'
60 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log'
61 #end if 61 #end if
62 ]]> </command> 62 ]]> </command>
63 <configfiles> 63 <configfiles>
64 <configfile name="vgp_mode"><![CDATA[ 64 <configfile name="vgp_mode"><![CDATA[
65 #if $configuration_options.configuration == 'vgp' 65 #if $configuration_options.configuration == 'vgp'
418 </when> 418 </when>
419 </conditional> 419 </conditional>
420 --> 420 -->
421 </inputs> 421 </inputs>
422 <outputs> 422 <outputs>
423 <data name="ngs_contigs" format="fasta" from_work_dir="total_contigs_raw.fasta" label="${tool.name} on ${on_string}: NGScontigs"> 423 <data name="ngs_contigs_scaffold" format="fasta" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta" label="${tool.name} on ${on_string}: NGScontigs scaffold NCBI">
424 <filter>trim_cut_sites == False</filter> 424 <filter>trim_cut_sites == False</filter>
425 </data> 425 </data>
426 <data name="ngs_contigs_trimmed" format="fasta" from_work_dir="total_contigs_trimmed.fasta" label="${tool.name} on ${on_string}: NGScontigs trimmed"> 426 <data name="ngs_contigs_not_scaffolded" format="fasta" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta" label="${tool.name} on ${on_string}: NGScontigs not scaffolded">
427 <filter>trim_cut_sites == False</filter>
428 </data>
429 <data name="ngs_contigs_scaffold_trimmed" format="fasta" from_work_dir="SCAFFOLD_NCBI_trimmed.fasta" label="${tool.name} on ${on_string}: NGScontigs scaffold NCBI trimmed">
427 <filter>trim_cut_sites</filter> 430 <filter>trim_cut_sites</filter>
428 </data> 431 </data>
429 <data name="ngs_contigs_trimmed_report" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: NGScontigs trimmed log"> 432 <data name="ngs_contigs_not_scaffolded_trimmed" format="fasta" from_work_dir="NOT_SCAFFOLDED_trimmed.fasta" label="${tool.name} on ${on_string}: NGScontigs not scaffolded trimmed">
430 <filter>trim_cut_sites</filter> 433 <filter>trim_cut_sites</filter>
431 </data> 434 </data>
432 <data name="report" format="txt" from_work_dir="hybrid_scaffolds/hybrid_scaffold_informatics_report.txt" label="${tool.name} on ${on_string}: hybrid scaffold report"/> 435 <data name="report" format="txt" from_work_dir="hybrid_scaffolds/hybrid_scaffold_informatics_report.txt" label="${tool.name} on ${on_string}: hybrid scaffold report"/>
436 <data name="conflicts" format="txt" from_work_dir="hybrid_scaffolds/conflicts.txt" label="${tool.name} on ${on_string}: conflicts"/>
433 <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results"> 437 <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results">
434 <filter>zip_file</filter> 438 <filter>zip_file</filter>
435 </data> 439 </data>
436 </outputs> 440 </outputs>
437 <tests> 441 <tests>
438 <test expect_num_outputs="3"> 442 <test expect_num_outputs="5">
439 <param name="ngs_fasta" value="assembly.fasta.gz"/> 443 <param name="ngs_fasta" value="assembly.fasta.gz"/>
440 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 444 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
441 <param name="conflict_filter_genome" value="3"/> 445 <param name="conflict_filter_genome" value="3"/>
442 <param name="conflict_filter_sequence" value="3"/> 446 <param name="conflict_filter_sequence" value="3"/>
443 <conditional name="configuration_options"> 447 <conditional name="configuration_options">
444 <param name="configuration" value="file"/> 448 <param name="configuration" value="file"/>
445 <param name="configuration_file" value="configuration.xml"/> 449 <param name="configuration_file" value="configuration.xml"/>
446 </conditional> 450 </conditional>
447 <param name="zip_file" value="true"/> 451 <param name="zip_file" value="true"/>
448 <param name="trim_cut_sites" value="false"/> 452 <param name="trim_cut_sites" value="false"/>
449 <output name="ngs_contigs" ftype="fasta"> 453 <output name="ngs_contigs_scaffold" ftype="fasta">
450 <assert_contents> 454 <assert_contents>
451 <has_size value="4753369" delta="300" /> 455 <has_size value="4753369" delta="100" />
456 <has_n_lines n="2"/>
457 <has_line line=">Super-Scaffold_1"/>
458 </assert_contents>
459 </output>
460 <output name="ngs_contigs_not_scaffolded" ftype="fasta">
461 <assert_contents>
462 <has_size value="0"/>
452 </assert_contents> 463 </assert_contents>
453 </output> 464 </output>
454 <output name="report" file="test_01_report.txt" ftype="txt"/> 465 <output name="report" file="test_01_report.txt" ftype="txt"/>
466 <output name="conflicts" ftype="txt">
467 <assert_contents>
468 <has_text text="alignmentOrientation" />
469 </assert_contents>
470 </output>
455 <output name="results" ftype="zip"> 471 <output name="results" ftype="zip">
456 <assert_contents> 472 <assert_contents>
457 <!--<has_size value="4231746" delta="300" />--> 473 <!--<has_size value="4231746" delta="300" />-->
458 <has_archive_member path=".*/status.txt"/> 474 <has_archive_member path=".*/status.txt"/>
459 </assert_contents> 475 </assert_contents>
472 </assert_stdout> 488 </assert_stdout>
473 <assert_stdout> 489 <assert_stdout>
474 <has_text text="hybridScaffold"/> 490 <has_text text="hybridScaffold"/>
475 </assert_stdout> 491 </assert_stdout>
476 </test> 492 </test>
477 <test expect_num_outputs="2"> 493 <test expect_num_outputs="4">
478 <param name="ngs_fasta" value="assembly.fasta.gz"/> 494 <param name="ngs_fasta" value="assembly.fasta.gz"/>
479 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 495 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
480 <param name="conflict_filter_genome" value="2"/> 496 <param name="conflict_filter_genome" value="2"/>
481 <param name="conflict_filter_sequence" value="2"/> 497 <param name="conflict_filter_sequence" value="2"/>
482 <param name="trim_cut_sites" value="false"/> 498 <param name="trim_cut_sites" value="false"/>
483 <conditional name="configuration_options"> 499 <conditional name="configuration_options">
484 <param name="configuration" value="file"/> 500 <param name="configuration" value="file"/>
485 <param name="configuration_file" value="configuration.xml"/> 501 <param name="configuration_file" value="configuration.xml"/>
486 </conditional> 502 </conditional>
487 <output name="ngs_contigs" ftype="fasta"> 503 <output name="ngs_contigs_scaffold" ftype="fasta">
488 <assert_contents> 504 <assert_contents>
489 <has_size value="4753369" delta="100" /> 505 <has_size value="4753369" delta="100" />
490 <has_n_lines n="2"/> 506 <has_n_lines n="2"/>
491 <has_line line=">Super-Scaffold_1"/> 507 <has_line line=">Super-Scaffold_1"/>
492 </assert_contents> 508 </assert_contents>
493 </output> 509 </output>
510 <output name="ngs_contigs_not_scaffolded" ftype="fasta">
511 <assert_contents>
512 <has_size value="0" />
513 </assert_contents>
514 </output>
494 <output name="report" file="test_02_report.txt" ftype="txt"/> 515 <output name="report" file="test_02_report.txt" ftype="txt"/>
495 <assert_stdout> 516 <output name="conflicts" ftype="txt">
517 <assert_contents>
518 <has_text text="alignmentOrientation" />
519 </assert_contents>
520 </output> <assert_stdout>
496 <has_text text='attr="maxmem" val0="8"'/> 521 <has_text text='attr="maxmem" val0="8"'/>
497 </assert_stdout> 522 </assert_stdout>
498 <assert_stdout> 523 <assert_stdout>
499 <has_text text='attr="maxthreads" val0="1"'/> 524 <has_text text='attr="maxthreads" val0="1"'/>
500 </assert_stdout> 525 </assert_stdout>
507 <assert_stdout> 532 <assert_stdout>
508 <has_text text="hybridScaffold"/> 533 <has_text text="hybridScaffold"/>
509 <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/--> 534 <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/-->
510 </assert_stdout> 535 </assert_stdout>
511 </test> 536 </test>
512 <test expect_num_outputs="3"> 537 <test expect_num_outputs="5">
513 <param name="ngs_fasta" value="assembly.fasta.gz"/> 538 <param name="ngs_fasta" value="assembly.fasta.gz"/>
514 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 539 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
515 <param name="conflict_filter_genome" value="2"/> 540 <param name="conflict_filter_genome" value="2"/>
516 <param name="conflict_filter_sequence" value="3"/> 541 <param name="conflict_filter_sequence" value="3"/>
517 <conditional name="configuration_options"> 542 <conditional name="configuration_options">
518 <param name="configuration" value="file"/> 543 <param name="configuration" value="file"/>
519 <param name="configuration_file" value="configuration.xml"/> 544 <param name="configuration_file" value="configuration.xml"/>
520 </conditional> 545 </conditional>
521 <param name="zip_file" value="true"/> 546 <param name="zip_file" value="true"/>
522 <param name="trim_cut_sites" value="false"/> 547 <param name="trim_cut_sites" value="false"/>
523 <output name="ngs_contigs" ftype="fasta"> 548 <output name="ngs_contigs_scaffold" ftype="fasta">
524 <assert_contents> 549 <assert_contents>
525 <has_size value="4753369" delta="100" /> 550 <has_size value="4753369" delta="100" />
526 <has_n_lines n="2"/> 551 <has_n_lines n="2"/>
527 <has_line line=">Super-Scaffold_1"/> 552 <has_line line=">Super-Scaffold_1"/>
528 </assert_contents> 553 </assert_contents>
529 </output> 554 </output>
555 <output name="ngs_contigs_not_scaffolded" ftype="fasta">
556 <assert_contents>
557 <has_size value="0"/>
558 </assert_contents>
559 </output>
530 <output name="report" file="test_03_report.txt" ftype="txt"/> 560 <output name="report" file="test_03_report.txt" ftype="txt"/>
561 <output name="conflicts" ftype="txt">
562 <assert_contents>
563 <has_text text="alignmentOrientation" />
564 </assert_contents>
565 </output>
531 <output name="results" ftype="zip"> 566 <output name="results" ftype="zip">
532 <assert_contents> 567 <assert_contents>
533 <!--<has_size value="4231908" delta="300" />--> 568 <!--<has_size value="4231908" delta="300" />-->
534 <has_archive_member path=".*/status.txt"/> 569 <has_archive_member path=".*/status.txt"/>
535 </assert_contents> 570 </assert_contents>
548 </assert_stdout> 583 </assert_stdout>
549 <assert_stdout> 584 <assert_stdout>
550 <has_text text="hybridScaffold"/> 585 <has_text text="hybridScaffold"/>
551 </assert_stdout> 586 </assert_stdout>
552 </test> 587 </test>
553 <test expect_num_outputs="3"> 588 <test expect_num_outputs="5">
554 <param name="ngs_fasta" value="assembly.fasta.gz"/> 589 <param name="ngs_fasta" value="assembly.fasta.gz"/>
555 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 590 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
556 <param name="conflict_filter_genome" value="2"/> 591 <param name="conflict_filter_genome" value="2"/>
557 <param name="conflict_filter_sequence" value="3"/> 592 <param name="conflict_filter_sequence" value="3"/>
558 <conditional name="configuration_options"> 593 <conditional name="configuration_options">
559 <param name="configuration" value="vgp"/> 594 <param name="configuration" value="vgp"/>
560 <param name="enzyme" value="BspQI"/> 595 <param name="enzyme" value="BspQI"/>
561 </conditional> 596 </conditional>
562 <param name="zip_file" value="true"/> 597 <param name="zip_file" value="true"/>
563 <param name="trim_cut_sites" value="false"/> 598 <param name="trim_cut_sites" value="false"/>
564 <output name="ngs_contigs" ftype="fasta"> 599 <output name="ngs_contigs_scaffold" ftype="fasta">
565 <assert_contents> 600 <assert_contents>
566 <has_size value="4753369" delta="100" /> 601 <has_size value="4753369" delta="100" />
567 <has_n_lines n="2"/> 602 <has_n_lines n="2"/>
568 <has_line line=">Super-Scaffold_1"/> 603 <has_line line=">Super-Scaffold_1"/>
569 </assert_contents> 604 </assert_contents>
570 </output> 605 </output>
606 <output name="ngs_contigs_not_scaffolded" ftype="fasta">
607 <assert_contents>
608 <has_size value="0"/>
609 </assert_contents>
610 </output>
571 <output name="report" file="test_04_report.txt" ftype="txt"/> 611 <output name="report" file="test_04_report.txt" ftype="txt"/>
612 <output name="conflicts" ftype="txt">
613 <assert_contents>
614 <has_text text="alignmentOrientation" />
615 </assert_contents>
616 </output>
572 <output name="results" ftype="zip"> 617 <output name="results" ftype="zip">
573 <assert_contents> 618 <assert_contents>
574 <has_archive_member path=".*/status.txt"/> 619 <has_archive_member path=".*/status.txt"/>
575 </assert_contents> 620 </assert_contents>
576 </output> 621 </output>
588 </assert_stdout> 633 </assert_stdout>
589 <assert_stdout> 634 <assert_stdout>
590 <has_text text="hybridScaffold"/> 635 <has_text text="hybridScaffold"/>
591 </assert_stdout> 636 </assert_stdout>
592 </test> 637 </test>
593 <test expect_num_outputs="3"> 638 <test expect_num_outputs="4">
594 <param name="ngs_fasta" value="assembly.fasta.gz"/> 639 <param name="ngs_fasta" value="assembly.fasta.gz"/>
595 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 640 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
596 <param name="conflict_filter_genome" value="3"/> 641 <param name="conflict_filter_genome" value="3"/>
597 <param name="conflict_filter_sequence" value="3"/> 642 <param name="conflict_filter_sequence" value="3"/>
598 <conditional name="configuration_options"> 643 <conditional name="configuration_options">
599 <param name="configuration" value="file"/> 644 <param name="configuration" value="file"/>
600 <param name="configuration_file" value="configuration.xml"/> 645 <param name="configuration_file" value="configuration.xml"/>
601 </conditional> 646 </conditional>
602 <param name="trim_cut_sites" value="true"/> 647 <param name="trim_cut_sites" value="true"/>
603 <output name="ngs_contigs_trimmed" ftype="fasta"> 648 <output name="ngs_contigs_scaffold_trimmed" ftype="fasta">
604 <assert_contents> 649 <assert_contents>
605 <has_size value="4832591" delta="300" /> 650 <has_size value="4832591" delta="100" />
606 </assert_contents> 651 <has_n_lines n="79224"/>
607 </output> 652 <has_line line=">Super-Scaffold_1"/>
608 <output name="ngs_contigs_trimmed_report" ftype="txt"> 653 </assert_contents>
654 </output>
655 <output name="ngs_contigs_not_scaffolded_trimmed" ftype="fasta">
609 <assert_contents> 656 <assert_contents>
610 <has_size value="0" /> 657 <has_size value="0" />
611 </assert_contents> 658 </assert_contents>
612 </output> 659 </output>
660 <output name="conflicts" ftype="txt">
661 <assert_contents>
662 <has_text text="alignmentOrientation" />
663 </assert_contents>
664 </output>
613 <output name="report" file="test_05_report.txt" ftype="txt"/> 665 <output name="report" file="test_05_report.txt" ftype="txt"/>
614 <assert_stdout> 666 <assert_stdout>
615 <has_text text='attr="maxmem" val0="8"'/> 667 <has_text text='attr="maxmem" val0="8"'/>
616 </assert_stdout> 668 </assert_stdout>
617 <assert_stdout> 669 <assert_stdout>