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comparison bionano_scaffold.xml @ 9:faee8629b460 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
author bgruening
date Tue, 13 Dec 2022 09:26:04 +0000
parents 5258e18bbe23
children 22286dab5aa1
comparison
equal deleted inserted replaced
8:5258e18bbe23 9:faee8629b460
372 <param name="enzyme" type="text" value="CTTAAG" label="Restriction enzyme" help="Define single enzyme for in-silico FASTA to CMAP digestion. Avalible enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."> 372 <param name="enzyme" type="text" value="CTTAAG" label="Restriction enzyme" help="Define single enzyme for in-silico FASTA to CMAP digestion. Avalible enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1.">
373 <expand macro="sanitize_string" /> 373 <expand macro="sanitize_string" />
374 </param> 374 </param>
375 </when> 375 </when>
376 <when value="file"> 376 <when value="file">
377 <param name="configuration_file" type="data" format="xml" label="Configuration file" help="Depending on the complexity of the genome of interest, the values of certain parameters could be adjusted accordingly."/> 377 <param name="configuration_file" type="data" format="xml,txt" label="Configuration file" help="Depending on the complexity of the genome of interest, the values of certain parameters could be adjusted accordingly."/>
378 </when> 378 </when>
379 </conditional> 379 </conditional>
380 <param name="conflict_resolution" argument="-M" type="data" format="txt" optional="True" label="Conflict resolution file" help="Input a conflict resolution file indicating which NGS and BioNano conflicting contigs to be cut [optional]"/> 380 <param name="conflict_resolution" argument="-M" type="data" format="txt" optional="True" label="Conflict resolution file" help="Input a conflict resolution file indicating which NGS and BioNano conflicting contigs to be cut [optional]"/>
381 <param name="conflict_filter_genome" argument="-B" type="select" label="Genome maps conflict filter" help="Conflict filter level genome maps [required if not using -M option]"> 381 <param name="conflict_filter_genome" argument="-B" type="select" label="Genome maps conflict filter" help="Conflict filter level genome maps [required if not using -M option]">
382 <option value="1">No filter</option> 382 <option value="1">No filter</option>
386 <param name="conflict_filter_sequence" argument="-N" type="select" label="Sequences conflict filter" help="Conflict filter level for sequences [required if not using -M option]"> 386 <param name="conflict_filter_sequence" argument="-N" type="select" label="Sequences conflict filter" help="Conflict filter level for sequences [required if not using -M option]">
387 <option value="1">No filter</option> 387 <option value="1">No filter</option>
388 <option value="2">Cut contig at conflict</option> 388 <option value="2">Cut contig at conflict</option>
389 <option value="3">Exclude conflicting contig</option> 389 <option value="3">Exclude conflicting contig</option>
390 </param> 390 </param>
391 <param name="all_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Provide all files" help="Generate a collection with the files contained in the hybrid_scaffolds folder" />
391 <param name="zip_file" argument="-z" type="boolean" truevalue="-z results.zip" falsevalue="" checked="false" label="Generate an output package in ZIP format" help="The hybrid scaffold output package (.zip) can be imported into Access for visualization" /> 392 <param name="zip_file" argument="-z" type="boolean" truevalue="-z results.zip" falsevalue="" checked="false" label="Generate an output package in ZIP format" help="The hybrid scaffold output package (.zip) can be imported into Access for visualization" />
392 <param name="trim_cut_sites" type="boolean" checked="true" label="Remove BioNano cut sites" help="This option removes the spurious BioNano cut sites that are inserted into gaps in some assemblies, replacing them with Ns." /> 393 <param name="trim_cut_sites" type="boolean" checked="true" label="Remove BioNano cut sites" help="This option removes the spurious BioNano cut sites that are inserted into gaps in some assemblies, replacing them with Ns." />
393 <!-- 394 <!--
394 395
395 Those options have been disabled because the Docker container doesn't include the required packages 396 Those options have been disabled because the Docker container doesn't include the required packages
437 <data name="conflicts" format="txt" from_work_dir="hybrid_scaffolds/conflicts.txt" label="${tool.name} on ${on_string}: conflicts"/> 438 <data name="conflicts" format="txt" from_work_dir="hybrid_scaffolds/conflicts.txt" label="${tool.name} on ${on_string}: conflicts"/>
438 <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results"> 439 <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results">
439 <filter>zip_file</filter> 440 <filter>zip_file</filter>
440 </data> 441 </data>
441 <data name="ngs_contigs_scaffold_agp" format="agp" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.agp" label="${tool.name} on ${on_string}: AGP file"/> 442 <data name="ngs_contigs_scaffold_agp" format="agp" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.agp" label="${tool.name} on ${on_string}: AGP file"/>
443 <collection name="allfiles" type="list" label="${tool.name} on ${on_string}: hybrid scaffolds files">
444 <discover_datasets pattern="__name_and_ext__" directory="hybrid_scaffolds" />
445 <filter>all_files</filter>
446 </collection>
442 </outputs> 447 </outputs>
443 <tests> 448 <tests>
444 <test expect_num_outputs="6"> 449 <test expect_num_outputs="6">
445 <param name="ngs_fasta" value="assembly.fasta.gz"/> 450 <param name="ngs_fasta" value="assembly.fasta.gz"/>
446 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 451 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
457 <has_size value="4753369" delta="100" /> 462 <has_size value="4753369" delta="100" />
458 <has_n_lines n="2"/> 463 <has_n_lines n="2"/>
459 <has_line line=">Super-Scaffold_1"/> 464 <has_line line=">Super-Scaffold_1"/>
460 </assert_contents> 465 </assert_contents>
461 </output> 466 </output>
462 <output name="ngs_contigs_not_scaffolded" ftype="fasta">
463 <assert_contents>
464 <has_size value="0"/>
465 </assert_contents>
466 </output>
467 <output name="report" file="test_01_report.txt" ftype="txt"/> 467 <output name="report" file="test_01_report.txt" ftype="txt"/>
468 <output name="ngs_contigs_scaffold_agp" file="test_01.agp" ftype="agp"/> 468 <output name="ngs_contigs_scaffold_agp" file="test_01.agp" ftype="agp"/>
469 <output name="conflicts" ftype="txt"> 469 <output name="conflicts" ftype="txt">
470 <assert_contents> 470 <assert_contents>
471 <has_text text="alignmentOrientation" /> 471 <has_text text="alignmentOrientation" />
476 <has_archive_member path=".*/status.txt"/> 476 <has_archive_member path=".*/status.txt"/>
477 </assert_contents> 477 </assert_contents>
478 </output> 478 </output>
479 <assert_stdout> 479 <assert_stdout>
480 <has_text_matching expression='attr="maxmem" val0="\d+"'/> 480 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
481 </assert_stdout>
482 <assert_stdout>
483 <has_text_matching expression='attr="maxthreads" val0="\d+"'/> 481 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
484 </assert_stdout>
485 <assert_stdout>
486 <has_text_matching expression='attr="insertThreads" val0="\d+"'/> 482 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
487 </assert_stdout>
488 <assert_stdout>
489 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> 483 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
490 </assert_stdout>
491 <assert_stdout>
492 <has_text text="hybridScaffold"/> 484 <has_text text="hybridScaffold"/>
493 </assert_stdout> 485 </assert_stdout>
494 </test> 486 </test>
495 <test expect_num_outputs="5"> 487 <test expect_num_outputs="5">
496 <param name="ngs_fasta" value="assembly.fasta.gz"/> 488 <param name="ngs_fasta" value="assembly.fasta.gz"/>
507 <has_size value="4753369" delta="100" /> 499 <has_size value="4753369" delta="100" />
508 <has_n_lines n="2"/> 500 <has_n_lines n="2"/>
509 <has_line line=">Super-Scaffold_1"/> 501 <has_line line=">Super-Scaffold_1"/>
510 </assert_contents> 502 </assert_contents>
511 </output> 503 </output>
512 <output name="ngs_contigs_not_scaffolded" ftype="fasta">
513 <assert_contents>
514 <has_size value="0" />
515 </assert_contents>
516 </output>
517 <output name="report" file="test_02_report.txt" ftype="txt"/> 504 <output name="report" file="test_02_report.txt" ftype="txt"/>
518 <output name="ngs_contigs_scaffold_agp" ftype="agp"> 505 <output name="ngs_contigs_scaffold_agp" ftype="agp">
519 <assert_contents> 506 <assert_contents>
520 <has_size value="311" delta="20" /> 507 <has_size value="311" delta="20" />
521 <has_text text="##agp-version"/> 508 <has_text text="##agp-version"/>
524 </output> 511 </output>
525 <output name="conflicts" ftype="txt"> 512 <output name="conflicts" ftype="txt">
526 <assert_contents> 513 <assert_contents>
527 <has_text text="alignmentOrientation" /> 514 <has_text text="alignmentOrientation" />
528 </assert_contents> 515 </assert_contents>
529 </output> <assert_stdout> 516 </output>
517 <assert_stdout>
530 <has_text_matching expression='attr="maxmem" val0="\d+"'/> 518 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
531 </assert_stdout>
532 <assert_stdout>
533 <has_text_matching expression='attr="maxthreads" val0="\d+"'/> 519 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
534 </assert_stdout>
535 <assert_stdout>
536 <has_text_matching expression='attr="insertThreads" val0="\d+"'/> 520 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
537 </assert_stdout>
538 <assert_stdout>
539 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> 521 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
540 </assert_stdout>
541 <assert_stdout>
542 <has_text text="hybridScaffold"/> 522 <has_text text="hybridScaffold"/>
543 </assert_stdout> 523 </assert_stdout>
544 </test> 524 </test>
545 <test expect_num_outputs="6"> 525 <test expect_num_outputs="6">
546 <param name="ngs_fasta" value="assembly.fasta.gz"/> 526 <param name="ngs_fasta" value="assembly.fasta.gz"/>
558 <has_size value="4753369" delta="100" /> 538 <has_size value="4753369" delta="100" />
559 <has_n_lines n="2"/> 539 <has_n_lines n="2"/>
560 <has_line line=">Super-Scaffold_1"/> 540 <has_line line=">Super-Scaffold_1"/>
561 </assert_contents> 541 </assert_contents>
562 </output> 542 </output>
563 <output name="ngs_contigs_not_scaffolded" ftype="fasta">
564 <assert_contents>
565 <has_size value="0"/>
566 </assert_contents>
567 </output>
568 <output name="report" file="test_03_report.txt" ftype="txt"/> 543 <output name="report" file="test_03_report.txt" ftype="txt"/>
569 <output name="ngs_contigs_scaffold_agp" ftype="agp"> 544 <output name="ngs_contigs_scaffold_agp" ftype="agp">
570 <assert_contents> 545 <assert_contents>
571 <has_size value="311" delta="20" /> 546 <has_size value="311" delta="20" />
572 <has_text text="##agp-version"/> 547 <has_text text="##agp-version"/>
583 <has_archive_member path=".*/status.txt"/> 558 <has_archive_member path=".*/status.txt"/>
584 </assert_contents> 559 </assert_contents>
585 </output> 560 </output>
586 <assert_stdout> 561 <assert_stdout>
587 <has_text_matching expression='attr="maxmem" val0="\d+"'/> 562 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
588 </assert_stdout>
589 <assert_stdout>
590 <has_text_matching expression='attr="maxthreads" val0="\d+"'/> 563 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
591 </assert_stdout>
592 <assert_stdout>
593 <has_text_matching expression='attr="insertThreads" val0="\d+"'/> 564 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
594 </assert_stdout>
595 <assert_stdout>
596 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> 565 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
597 </assert_stdout>
598 <assert_stdout>
599 <has_text text="hybridScaffold"/> 566 <has_text text="hybridScaffold"/>
600 </assert_stdout> 567 </assert_stdout>
601 </test> 568 </test>
602 <test expect_num_outputs="6"> 569 <test expect_num_outputs="6">
603 <param name="ngs_fasta" value="assembly.fasta.gz"/> 570 <param name="ngs_fasta" value="assembly.fasta.gz"/>
615 <has_size value="4753369" delta="100" /> 582 <has_size value="4753369" delta="100" />
616 <has_n_lines n="2"/> 583 <has_n_lines n="2"/>
617 <has_line line=">Super-Scaffold_1"/> 584 <has_line line=">Super-Scaffold_1"/>
618 </assert_contents> 585 </assert_contents>
619 </output> 586 </output>
620 <output name="ngs_contigs_not_scaffolded" ftype="fasta">
621 <assert_contents>
622 <has_size value="0"/>
623 </assert_contents>
624 </output>
625 <output name="report" file="test_04_report.txt" ftype="txt"/> 587 <output name="report" file="test_04_report.txt" ftype="txt"/>
626 <output name="ngs_contigs_scaffold_agp" ftype="agp"> 588 <output name="ngs_contigs_scaffold_agp" ftype="agp">
627 <assert_contents> 589 <assert_contents>
628 <has_size value="311" delta="20" /> 590 <has_size value="311" delta="20" />
629 <has_text text="##agp-version"/> 591 <has_text text="##agp-version"/>
640 <has_archive_member path=".*/status.txt"/> 602 <has_archive_member path=".*/status.txt"/>
641 </assert_contents> 603 </assert_contents>
642 </output> 604 </output>
643 <assert_stdout> 605 <assert_stdout>
644 <has_text_matching expression='attr="maxmem" val0="\d+"'/> 606 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
645 </assert_stdout>
646 <assert_stdout>
647 <has_text_matching expression='attr="maxthreads" val0="\d+"'/> 607 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
648 </assert_stdout>
649 <assert_stdout>
650 <has_text_matching expression='attr="insertThreads" val0="\d+"'/> 608 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
651 </assert_stdout>
652 <assert_stdout>
653 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> 609 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
654 </assert_stdout>
655 <assert_stdout>
656 <has_text text="hybridScaffold"/> 610 <has_text text="hybridScaffold"/>
657 </assert_stdout> 611 </assert_stdout>
658 </test> 612 </test>
659 <test expect_num_outputs="5"> 613 <test expect_num_outputs="5">
660 <param name="ngs_fasta" value="assembly.fasta.gz"/> 614 <param name="ngs_fasta" value="assembly.fasta.gz"/>
671 <has_size value="4832591" delta="100" /> 625 <has_size value="4832591" delta="100" />
672 <has_n_lines n="79224"/> 626 <has_n_lines n="79224"/>
673 <has_line line=">Super-Scaffold_1"/> 627 <has_line line=">Super-Scaffold_1"/>
674 </assert_contents> 628 </assert_contents>
675 </output> 629 </output>
676 <output name="ngs_contigs_not_scaffolded_trimmed" ftype="fasta">
677 <assert_contents>
678 <has_size value="0" />
679 </assert_contents>
680 </output>
681 <output name="conflicts" ftype="txt"> 630 <output name="conflicts" ftype="txt">
682 <assert_contents> 631 <assert_contents>
683 <has_text text="alignmentOrientation" /> 632 <has_text text="alignmentOrientation" />
684 </assert_contents> 633 </assert_contents>
685 </output> 634 </output>
691 <has_n_lines n="9"/> 640 <has_n_lines n="9"/>
692 </assert_contents> 641 </assert_contents>
693 </output> 642 </output>
694 <assert_stdout> 643 <assert_stdout>
695 <has_text_matching expression='attr="maxmem" val0="\d+"'/> 644 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
645 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
646 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
647 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
648 <has_text text="hybridScaffold"/>
696 </assert_stdout> 649 </assert_stdout>
650 </test>
651 <test expect_num_outputs="6">
652 <param name="ngs_fasta" value="assembly.fasta.gz"/>
653 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
654 <param name="conflict_filter_genome" value="3"/>
655 <param name="conflict_filter_sequence" value="3"/>
656 <param name="all_files" value="true"/>
657 <conditional name="configuration_options">
658 <param name="configuration" value="file"/>
659 <param name="configuration_file" value="configuration.xml"/>
660 </conditional>
661 <param name="trim_cut_sites" value="true"/>
662 <output name="ngs_contigs_scaffold_trimmed" ftype="fasta">
663 <assert_contents>
664 <has_size value="4832591" delta="100" />
665 <has_n_lines n="79224"/>
666 <has_line line=">Super-Scaffold_1"/>
667 </assert_contents>
668 </output>
669 <output name="conflicts" ftype="txt">
670 <assert_contents>
671 <has_text text="alignmentOrientation" />
672 </assert_contents>
673 </output>
674 <output name="report" file="test_05_report.txt" ftype="txt"/>
675 <output name="ngs_contigs_scaffold_agp" ftype="agp">
676 <assert_contents>
677 <has_size value="311" delta="20" />
678 <has_text text="##agp-version"/>
679 <has_n_lines n="9"/>
680 </assert_contents>
681 </output>
682 <output_collection name="allfiles" type="list" count="21">
683 <element name="BSPQI_bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_NGScontigs_q">
684 <assert_contents>
685 <has_text text="Number of Consensus Maps"/>
686 <has_n_lines n="534" delta="50"/>
687 </assert_contents>
688 </element>
689 </output_collection>
697 <assert_stdout> 690 <assert_stdout>
691 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
698 <has_text_matching expression='attr="maxthreads" val0="\d+"'/> 692 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
699 </assert_stdout>
700 <assert_stdout>
701 <has_text_matching expression='attr="insertThreads" val0="\d+"'/> 693 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
702 </assert_stdout>
703 <assert_stdout>
704 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> 694 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
705 </assert_stdout>
706 <assert_stdout>
707 <has_text text="hybridScaffold"/> 695 <has_text text="hybridScaffold"/>
708 </assert_stdout> 696 </assert_stdout>
709 </test> 697 </test>
710 </tests> 698 </tests>
711 <help><![CDATA[ 699 <help><![CDATA[