Mercurial > repos > bgruening > bionano_scaffold

comparison bionano_scaffold.xml @ 6:5d7c5ae1b69b draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532"
author bgruening
date Thu, 21 Oct 2021 13:47:41 +0000
parents 96cacb31d571
children a7f16f24e9a1
comparison
equal deleted inserted replaced
5:96cacb31d571 6:5d7c5ae1b69b
1 <tool id="bionano_scaffold" name="Bionano Hybrid Scaffold" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01"> 1 <tool id="bionano_scaffold" name="Bionano Hybrid Scaffold" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>automates the scaffolding process</description> 2 <description>automates the scaffolding process</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/> 6 <expand macro="edam_ontology"/>
56 $zip_file 56 $zip_file
57 -o ./ 57 -o ./
58 #if $trim_cut_sites 58 #if $trim_cut_sites
59 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log' 59 && python '$__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' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log' 60 && python '$__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 $configuration_options.configuration == 'vgp'
66 <hybridScaffold> 66 <hybridScaffold>
435 <data name="report" format="txt" from_work_dir="hybrid_scaffolds/hybrid_scaffold_informatics_report.txt" label="${tool.name} on ${on_string}: hybrid scaffold report"/> 435 <data name="report" format="txt" from_work_dir="hybrid_scaffolds/hybrid_scaffold_informatics_report.txt" label="${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 ${on_string}: conflicts"/> 436 <data name="conflicts" format="txt" from_work_dir="hybrid_scaffolds/conflicts.txt" label="${tool.name} on ${on_string}: conflicts"/>
437 <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results"> 437 <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results">
438 <filter>zip_file</filter> 438 <filter>zip_file</filter>
439 </data> 439 </data>
440 <data name="ngs_contigs_scaffold_agp" format="agp" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.agp" label="${tool.name} on ${on_string}: AGP file"/>
440 </outputs> 441 </outputs>
441 <tests> 442 <tests>
442 <test expect_num_outputs="5"> 443 <test expect_num_outputs="6">
443 <param name="ngs_fasta" value="assembly.fasta.gz"/> 444 <param name="ngs_fasta" value="assembly.fasta.gz"/>
444 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 445 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
445 <param name="conflict_filter_genome" value="3"/> 446 <param name="conflict_filter_genome" value="3"/>
446 <param name="conflict_filter_sequence" value="3"/> 447 <param name="conflict_filter_sequence" value="3"/>
447 <conditional name="configuration_options"> 448 <conditional name="configuration_options">
461 <assert_contents> 462 <assert_contents>
462 <has_size value="0"/> 463 <has_size value="0"/>
463 </assert_contents> 464 </assert_contents>
464 </output> 465 </output>
465 <output name="report" file="test_01_report.txt" ftype="txt"/> 466 <output name="report" file="test_01_report.txt" ftype="txt"/>
467 <output name="ngs_contigs_scaffold_agp" file="test_01.agp" ftype="agp"/>
466 <output name="conflicts" ftype="txt"> 468 <output name="conflicts" ftype="txt">
467 <assert_contents> 469 <assert_contents>
468 <has_text text="alignmentOrientation" /> 470 <has_text text="alignmentOrientation" />
469 </assert_contents> 471 </assert_contents>
470 </output> 472 </output>
488 </assert_stdout> 490 </assert_stdout>
489 <assert_stdout> 491 <assert_stdout>
490 <has_text text="hybridScaffold"/> 492 <has_text text="hybridScaffold"/>
491 </assert_stdout> 493 </assert_stdout>
492 </test> 494 </test>
493 <test expect_num_outputs="4"> 495 <test expect_num_outputs="5">
494 <param name="ngs_fasta" value="assembly.fasta.gz"/> 496 <param name="ngs_fasta" value="assembly.fasta.gz"/>
495 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 497 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
496 <param name="conflict_filter_genome" value="2"/> 498 <param name="conflict_filter_genome" value="2"/>
497 <param name="conflict_filter_sequence" value="2"/> 499 <param name="conflict_filter_sequence" value="2"/>
498 <param name="trim_cut_sites" value="false"/> 500 <param name="trim_cut_sites" value="false"/>
511 <assert_contents> 513 <assert_contents>
512 <has_size value="0" /> 514 <has_size value="0" />
513 </assert_contents> 515 </assert_contents>
514 </output> 516 </output>
515 <output name="report" file="test_02_report.txt" ftype="txt"/> 517 <output name="report" file="test_02_report.txt" ftype="txt"/>
518 <output name="ngs_contigs_scaffold_agp" ftype="agp">
519 <assert_contents>
520 <has_size value="311" delta="20" />
521 <has_text text="##agp-version"/>
522 <has_n_lines n="9"/>
523 </assert_contents>
524 </output>
516 <output name="conflicts" ftype="txt"> 525 <output name="conflicts" ftype="txt">
517 <assert_contents> 526 <assert_contents>
518 <has_text text="alignmentOrientation" /> 527 <has_text text="alignmentOrientation" />
519 </assert_contents> 528 </assert_contents>
520 </output> <assert_stdout> 529 </output> <assert_stdout>
532 <assert_stdout> 541 <assert_stdout>
533 <has_text text="hybridScaffold"/> 542 <has_text text="hybridScaffold"/>
534 <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/--> 543 <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/-->
535 </assert_stdout> 544 </assert_stdout>
536 </test> 545 </test>
537 <test expect_num_outputs="5"> 546 <test expect_num_outputs="6">
538 <param name="ngs_fasta" value="assembly.fasta.gz"/> 547 <param name="ngs_fasta" value="assembly.fasta.gz"/>
539 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 548 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
540 <param name="conflict_filter_genome" value="2"/> 549 <param name="conflict_filter_genome" value="2"/>
541 <param name="conflict_filter_sequence" value="3"/> 550 <param name="conflict_filter_sequence" value="3"/>
542 <conditional name="configuration_options"> 551 <conditional name="configuration_options">
556 <assert_contents> 565 <assert_contents>
557 <has_size value="0"/> 566 <has_size value="0"/>
558 </assert_contents> 567 </assert_contents>
559 </output> 568 </output>
560 <output name="report" file="test_03_report.txt" ftype="txt"/> 569 <output name="report" file="test_03_report.txt" ftype="txt"/>
570 <output name="ngs_contigs_scaffold_agp" ftype="agp">
571 <assert_contents>
572 <has_size value="311" delta="20" />
573 <has_text text="##agp-version"/>
574 <has_n_lines n="9"/>
575 </assert_contents>
576 </output>
561 <output name="conflicts" ftype="txt"> 577 <output name="conflicts" ftype="txt">
562 <assert_contents> 578 <assert_contents>
563 <has_text text="alignmentOrientation" /> 579 <has_text text="alignmentOrientation" />
564 </assert_contents> 580 </assert_contents>
565 </output> 581 </output>
583 </assert_stdout> 599 </assert_stdout>
584 <assert_stdout> 600 <assert_stdout>
585 <has_text text="hybridScaffold"/> 601 <has_text text="hybridScaffold"/>
586 </assert_stdout> 602 </assert_stdout>
587 </test> 603 </test>
588 <test expect_num_outputs="5"> 604 <test expect_num_outputs="6">
589 <param name="ngs_fasta" value="assembly.fasta.gz"/> 605 <param name="ngs_fasta" value="assembly.fasta.gz"/>
590 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 606 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
591 <param name="conflict_filter_genome" value="2"/> 607 <param name="conflict_filter_genome" value="2"/>
592 <param name="conflict_filter_sequence" value="3"/> 608 <param name="conflict_filter_sequence" value="3"/>
593 <conditional name="configuration_options"> 609 <conditional name="configuration_options">
607 <assert_contents> 623 <assert_contents>
608 <has_size value="0"/> 624 <has_size value="0"/>
609 </assert_contents> 625 </assert_contents>
610 </output> 626 </output>
611 <output name="report" file="test_04_report.txt" ftype="txt"/> 627 <output name="report" file="test_04_report.txt" ftype="txt"/>
628 <output name="ngs_contigs_scaffold_agp" ftype="agp">
629 <assert_contents>
630 <has_size value="311" delta="20" />
631 <has_text text="##agp-version"/>
632 <has_n_lines n="9"/>
633 </assert_contents>
634 </output>
612 <output name="conflicts" ftype="txt"> 635 <output name="conflicts" ftype="txt">
613 <assert_contents> 636 <assert_contents>
614 <has_text text="alignmentOrientation" /> 637 <has_text text="alignmentOrientation" />
615 </assert_contents> 638 </assert_contents>
616 </output> 639 </output>
633 </assert_stdout> 656 </assert_stdout>
634 <assert_stdout> 657 <assert_stdout>
635 <has_text text="hybridScaffold"/> 658 <has_text text="hybridScaffold"/>
636 </assert_stdout> 659 </assert_stdout>
637 </test> 660 </test>
638 <test expect_num_outputs="4"> 661 <test expect_num_outputs="5">
639 <param name="ngs_fasta" value="assembly.fasta.gz"/> 662 <param name="ngs_fasta" value="assembly.fasta.gz"/>
640 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 663 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
641 <param name="conflict_filter_genome" value="3"/> 664 <param name="conflict_filter_genome" value="3"/>
642 <param name="conflict_filter_sequence" value="3"/> 665 <param name="conflict_filter_sequence" value="3"/>
643 <conditional name="configuration_options"> 666 <conditional name="configuration_options">
661 <assert_contents> 684 <assert_contents>
662 <has_text text="alignmentOrientation" /> 685 <has_text text="alignmentOrientation" />
663 </assert_contents> 686 </assert_contents>
664 </output> 687 </output>
665 <output name="report" file="test_05_report.txt" ftype="txt"/> 688 <output name="report" file="test_05_report.txt" ftype="txt"/>
689 <output name="ngs_contigs_scaffold_agp" ftype="agp">
690 <assert_contents>
691 <has_size value="311" delta="20" />
692 <has_text text="##agp-version"/>
693 <has_n_lines n="9"/>
694 </assert_contents>
695 </output>
666 <assert_stdout> 696 <assert_stdout>
667 <has_text text='attr="maxmem" val0="8"'/> 697 <has_text text='attr="maxmem" val0="8"'/>
668 </assert_stdout> 698 </assert_stdout>
669 <assert_stdout> 699 <assert_stdout>
670 <has_text text='attr="maxthreads" val0="1"'/> 700 <has_text text='attr="maxthreads" val0="1"'/>