Mercurial > repos > bgruening > bionano_scaffold
comparison bionano_scaffold.xml @ 9:faee8629b460 draft
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 |
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| 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[ |