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comparison bionano_scaffold.xml @ 4:8cc3862f8b8e draft

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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
author bgruening
date Tue, 25 May 2021 20:12:52 +0000
parents 295c0e28f4ee
children 96cacb31d571
comparison
equal deleted inserted replaced
3:295c0e28f4ee 4:8cc3862f8b8e
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/> 6 <expand macro="edam_ontology"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #set RefAligner = '/usr/local/bin/RefAligner' 9 #set RefAligner = '/usr/local/bin/RefAligner'
10 #set output_file_NCBI = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta'
11 #set output_file_not_scaffolded = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta'
10 ## softlinks do not work 12 ## softlinks do not work
11 cp '${ngs_fasta}' ./ngs.fasta 13 cp '${ngs_fasta}' ./ngs.fasta
12 && cp '${bionano_cmap}' ./bionano.cmap 14 && cp '${bionano_cmap}' ./bionano.cmap
13 && export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) 15 && export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024))
14 ## return max out of GALAXY_SLOTS and 2 --> use a minimum 2 slots 16 ## return max out of GALAXY_SLOTS and 2 --> use a minimum 2 slots
31 -b ./bionano.cmap 33 -b ./bionano.cmap
32 -c ./config.xml 34 -c ./config.xml
33 -r $RefAligner 35 -r $RefAligner
34 #if $conflict_resolution 36 #if $conflict_resolution
35 -M '${conflict_resolution}' 37 -M '${conflict_resolution}'
36 #end if 38 #else
37 #if not $conflict_resolution
38 -B $conflict_filter_genome 39 -B $conflict_filter_genome
39 -N $conflict_filter_sequence 40 -N $conflict_filter_sequence
40 #end if 41 #end if
41 ##$align_molecules_options.align_molecules 42 ##$align_molecules_options.align_molecules
42 ###if $align_molecules_options.align_molecules 43 ###if $align_molecules_options.align_molecules
52 ## #end if 53 ## #end if
53 ###end if 54 ###end if
54 -f 55 -f
55 $zip_file 56 $zip_file
56 -o ./ 57 -o ./
57 58 && cat $output_file_NCBI $output_file_not_scaffolded > total_contigs_raw.fasta
59 #if $trim_cut_sites
60 && python '$__tool_directory__/remove_fake_cut_sites.py' 'total_contigs_raw.fasta' 'total_contigs_trimmed.fasta' 'output.log'
61 #end if
58 ]]> </command> 62 ]]> </command>
59 <configfiles> 63 <configfiles>
60 <configfile name="vgp_mode"><![CDATA[ 64 <configfile name="vgp_mode"><![CDATA[
61 #if $configuration_options.configuration == 'vgp' 65 #if $configuration_options.configuration == 'vgp'
62 <hybridScaffold> 66 <hybridScaffold>
68 <flag attr="maxthreads" val0="__CORES__" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/> 72 <flag attr="maxthreads" val0="__CORES__" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>
69 <flag attr="maxvirtmem" val0="__MEMORY__"/> 73 <flag attr="maxvirtmem" val0="__MEMORY__"/>
70 <flag attr="RAmem" val0="3" val1="1"/> 74 <flag attr="RAmem" val0="3" val1="1"/>
71 </global> 75 </global>
72 <fasta2cmap> 76 <fasta2cmap>
73 <flag attr="enzyme" val0="$configuration_options.enzyme" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for in-silico FASTA to CMAP digestion. Avalible enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."/> 77 <flag attr="enzyme" val0="$configuration_options.enzyme" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for in-silico FASTA to CMAP digestion. Available enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."/>
74 <flag attr="channelNum" val0="1" display="Channel number" group="FASTA to CMAP digestion" description="Specify the channel the enzyme was used."/> 78 <flag attr="channelNum" val0="1" display="Channel number" group="FASTA to CMAP digestion" description="Specify the channel the enzyme was used."/>
75 <flag attr="minLabels" val0="0" display="Minimum label sites" group="FASTA to CMAP digestion" description="Specify minimum number of label sites per digested contig."/> 79 <flag attr="minLabels" val0="0" display="Minimum label sites" group="FASTA to CMAP digestion" description="Specify minimum number of label sites per digested contig."/>
76 <flag attr="minLength" val0="0" display="Minimum length (Kb)" group="FASTA to CMAP digestion" description="Specify minimum length in Kb of each digested contig."/> 80 <flag attr="minLength" val0="0" display="Minimum length (Kb)" group="FASTA to CMAP digestion" description="Specify minimum length in Kb of each digested contig."/>
77 </fasta2cmap> 81 </fasta2cmap>
78 <align0> 82 <align0>
382 <option value="1">No filter</option> 386 <option value="1">No filter</option>
383 <option value="2">Cut contig at conflict</option> 387 <option value="2">Cut contig at conflict</option>
384 <option value="3">Exclude conflicting contig</option> 388 <option value="3">Exclude conflicting contig</option>
385 </param> 389 </param>
386 <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" /> 390 <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" />
391 <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." />
387 <!-- 392 <!--
388 393
389 Those options have been disabled because the Docker container doesn't include the required packages 394 Those options have been disabled because the Docker container doesn't include the required packages
390 395
391 <conditional name="align_molecules_options"> 396 <conditional name="align_molecules_options">
413 </when> 418 </when>
414 </conditional> 419 </conditional>
415 --> 420 -->
416 </inputs> 421 </inputs>
417 <outputs> 422 <outputs>
418 <data name="ngs_contigs_scaffold_fasta" format="fasta" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.fasta" label="${tool.name} on ${on_string}: NGScontigs hybrid scaffold (fasta)"/> 423 <data name="ngs_contigs" format="fasta" from_work_dir="total_contigs_raw.fasta" label="${tool.name} on ${on_string}: NGScontigs">
419 <data name="ngs_contigs_scaffold_agp" format="txt" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.agp" label="${tool.name} on ${on_string}: NGScontigs hybrid scaffold (agp)"/> 424 <filter>trim_cut_sites == False</filter>
420 <data name="ngs_contigs_scaffold_gap" format="txt" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.gap" label="${tool.name} on ${on_string}: NGScontigs hybrid scaffold (gap)"/> 425 </data>
426 <data name="ngs_contigs_trimmed" format="fasta" from_work_dir="total_contigs_trimmed.fasta" label="${tool.name} on ${on_string}: NGScontigs trimmed">
427 <filter>trim_cut_sites</filter>
428 </data>
429 <data name="ngs_contigs_trimmed_report" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: NGScontigs trimmed log">
430 <filter>trim_cut_sites</filter>
431 </data>
421 <data name="report" format="txt" from_work_dir="hybrid_scaffolds/hybrid_scaffold_informatics_report.txt" label="${tool.name} on ${on_string}: hybrid scaffold report"/> 432 <data name="report" format="txt" from_work_dir="hybrid_scaffolds/hybrid_scaffold_informatics_report.txt" label="${tool.name} on ${on_string}: hybrid scaffold report"/>
422 <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results"> 433 <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results">
423 <filter>zip_file</filter> 434 <filter>zip_file</filter>
424 </data> 435 </data>
425 </outputs> 436 </outputs>
426 <tests> 437 <tests>
427 <test expect_num_outputs="5"> 438 <test expect_num_outputs="3">
428 <param name="ngs_fasta" value="assembly.fasta.gz"/> 439 <param name="ngs_fasta" value="assembly.fasta.gz"/>
429 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 440 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
430 <param name="conflict_filter_genome" value="3"/> 441 <param name="conflict_filter_genome" value="3"/>
431 <param name="conflict_filter_sequence" value="3"/> 442 <param name="conflict_filter_sequence" value="3"/>
432 <conditional name="configuration_options"> 443 <conditional name="configuration_options">
433 <param name="configuration" value="file"/> 444 <param name="configuration" value="file"/>
434 <param name="configuration_file" value="configuration.xml"/> 445 <param name="configuration_file" value="configuration.xml"/>
435 </conditional> 446 </conditional>
436 <param name="zip_file" value="true"/> 447 <param name="zip_file" value="true"/>
437 <output name="ngs_contigs_scaffold_fasta" ftype="fasta"> 448 <param name="trim_cut_sites" value="false"/>
449 <output name="ngs_contigs" ftype="fasta">
438 <assert_contents> 450 <assert_contents>
439 <has_size value="4753369" delta="300" /> 451 <has_size value="4753369" delta="300" />
440 </assert_contents> 452 </assert_contents>
441 </output> 453 </output>
442 <output name="ngs_contigs_scaffold_agp" file="test_01.agp" ftype="txt"/>
443 <output name="ngs_contigs_scaffold_gap" file="test_01.gap" ftype="txt"/>
444 <output name="report" file="test_01_report.txt" ftype="txt"/> 454 <output name="report" file="test_01_report.txt" ftype="txt"/>
445 <output name="results" ftype="zip"> 455 <output name="results" ftype="zip">
446 <assert_contents> 456 <assert_contents>
447 <!--<has_size value="4231746" delta="300" />--> 457 <!--<has_size value="4231746" delta="300" />-->
448 <has_archive_member path=".*/status.txt"/> 458 <has_archive_member path=".*/status.txt"/>
462 </assert_stdout> 472 </assert_stdout>
463 <assert_stdout> 473 <assert_stdout>
464 <has_text text="hybridScaffold"/> 474 <has_text text="hybridScaffold"/>
465 </assert_stdout> 475 </assert_stdout>
466 </test> 476 </test>
467 <test expect_num_outputs="4"> 477 <test expect_num_outputs="2">
468 <param name="ngs_fasta" value="assembly.fasta.gz"/> 478 <param name="ngs_fasta" value="assembly.fasta.gz"/>
469 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 479 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
470 <param name="conflict_filter_genome" value="2"/> 480 <param name="conflict_filter_genome" value="2"/>
471 <param name="conflict_filter_sequence" value="2"/> 481 <param name="conflict_filter_sequence" value="2"/>
482 <param name="trim_cut_sites" value="false"/>
472 <conditional name="configuration_options"> 483 <conditional name="configuration_options">
473 <param name="configuration" value="file"/> 484 <param name="configuration" value="file"/>
474 <param name="configuration_file" value="configuration.xml"/> 485 <param name="configuration_file" value="configuration.xml"/>
475 </conditional> 486 </conditional>
476 <output name="ngs_contigs_scaffold_fasta" ftype="fasta"> 487 <output name="ngs_contigs" ftype="fasta">
477 <assert_contents> 488 <assert_contents>
478 <has_size value="4753369" delta="100" /> 489 <has_size value="4753369" delta="100" />
479 <has_n_lines n="2"/> 490 <has_n_lines n="2"/>
480 <has_line line=">Super-Scaffold_1"/> 491 <has_line line=">Super-Scaffold_1"/>
481 </assert_contents> 492 </assert_contents>
482 </output> 493 </output>
483 <output name="ngs_contigs_scaffold_agp" file="test_02.agp" ftype="txt"/>
484 <output name="ngs_contigs_scaffold_gap" file="test_02.gap" ftype="txt"/>
485 <output name="report" file="test_02_report.txt" ftype="txt"/> 494 <output name="report" file="test_02_report.txt" ftype="txt"/>
486 <assert_stdout> 495 <assert_stdout>
487 <has_text text='attr="maxmem" val0="8"'/> 496 <has_text text='attr="maxmem" val0="8"'/>
488 </assert_stdout> 497 </assert_stdout>
489 <assert_stdout> 498 <assert_stdout>
498 <assert_stdout> 507 <assert_stdout>
499 <has_text text="hybridScaffold"/> 508 <has_text text="hybridScaffold"/>
500 <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/--> 509 <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/-->
501 </assert_stdout> 510 </assert_stdout>
502 </test> 511 </test>
503 <test expect_num_outputs="5"> 512 <test expect_num_outputs="3">
504 <param name="ngs_fasta" value="assembly.fasta.gz"/> 513 <param name="ngs_fasta" value="assembly.fasta.gz"/>
505 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 514 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
506 <param name="conflict_filter_genome" value="2"/> 515 <param name="conflict_filter_genome" value="2"/>
507 <param name="conflict_filter_sequence" value="3"/> 516 <param name="conflict_filter_sequence" value="3"/>
508 <conditional name="configuration_options"> 517 <conditional name="configuration_options">
509 <param name="configuration" value="file"/> 518 <param name="configuration" value="file"/>
510 <param name="configuration_file" value="configuration.xml"/> 519 <param name="configuration_file" value="configuration.xml"/>
511 </conditional> 520 </conditional>
512 <param name="zip_file" value="true"/> 521 <param name="zip_file" value="true"/>
513 <output name="ngs_contigs_scaffold_fasta" ftype="fasta"> 522 <param name="trim_cut_sites" value="false"/>
523 <output name="ngs_contigs" ftype="fasta">
514 <assert_contents> 524 <assert_contents>
515 <has_size value="4753369" delta="100" /> 525 <has_size value="4753369" delta="100" />
516 <has_n_lines n="2"/> 526 <has_n_lines n="2"/>
517 <has_line line=">Super-Scaffold_1"/> 527 <has_line line=">Super-Scaffold_1"/>
518 </assert_contents> 528 </assert_contents>
519 </output> 529 </output>
520 <output name="ngs_contigs_scaffold_agp" file="test_03.agp" ftype="txt"/>
521 <output name="ngs_contigs_scaffold_gap" file="test_03.gap" ftype="txt"/>
522 <output name="report" file="test_03_report.txt" ftype="txt"/> 530 <output name="report" file="test_03_report.txt" ftype="txt"/>
523 <output name="results" ftype="zip"> 531 <output name="results" ftype="zip">
524 <assert_contents> 532 <assert_contents>
525 <!--<has_size value="4231908" delta="300" />--> 533 <!--<has_size value="4231908" delta="300" />-->
526 <has_archive_member path=".*/status.txt"/> 534 <has_archive_member path=".*/status.txt"/>
540 </assert_stdout> 548 </assert_stdout>
541 <assert_stdout> 549 <assert_stdout>
542 <has_text text="hybridScaffold"/> 550 <has_text text="hybridScaffold"/>
543 </assert_stdout> 551 </assert_stdout>
544 </test> 552 </test>
545 <test expect_num_outputs="5"> 553 <test expect_num_outputs="3">
546 <param name="ngs_fasta" value="assembly.fasta.gz"/> 554 <param name="ngs_fasta" value="assembly.fasta.gz"/>
547 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 555 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
548 <param name="conflict_filter_genome" value="2"/> 556 <param name="conflict_filter_genome" value="2"/>
549 <param name="conflict_filter_sequence" value="3"/> 557 <param name="conflict_filter_sequence" value="3"/>
550 <conditional name="configuration_options"> 558 <conditional name="configuration_options">
551 <param name="configuration" value="vgp"/> 559 <param name="configuration" value="vgp"/>
552 <param name="enzyme" value="BspQI"/> 560 <param name="enzyme" value="BspQI"/>
553 </conditional> 561 </conditional>
554 <param name="zip_file" value="true"/> 562 <param name="zip_file" value="true"/>
555 <output name="ngs_contigs_scaffold_fasta" ftype="fasta"> 563 <param name="trim_cut_sites" value="false"/>
564 <output name="ngs_contigs" ftype="fasta">
556 <assert_contents> 565 <assert_contents>
557 <has_size value="4753369" delta="100" /> 566 <has_size value="4753369" delta="100" />
558 <has_n_lines n="2"/> 567 <has_n_lines n="2"/>
559 <has_line line=">Super-Scaffold_1"/> 568 <has_line line=">Super-Scaffold_1"/>
560 </assert_contents> 569 </assert_contents>
561 </output> 570 </output>
562 <output name="ngs_contigs_scaffold_agp" file="test_04.agp" ftype="txt"/>
563 <output name="ngs_contigs_scaffold_gap" file="test_04.gap" ftype="txt"/>
564 <output name="report" file="test_04_report.txt" ftype="txt"/> 571 <output name="report" file="test_04_report.txt" ftype="txt"/>
565 <output name="results" ftype="zip"> 572 <output name="results" ftype="zip">
566 <assert_contents> 573 <assert_contents>
567 <has_archive_member path=".*/status.txt"/> 574 <has_archive_member path=".*/status.txt"/>
568 </assert_contents> 575 </assert_contents>
569 </output> 576 </output>
577 <assert_stdout>
578 <has_text text='attr="maxmem" val0="8"'/>
579 </assert_stdout>
580 <assert_stdout>
581 <has_text text='attr="maxthreads" val0="1"'/>
582 </assert_stdout>
583 <assert_stdout>
584 <has_text text='attr="insertThreads" val0="1"'/>
585 </assert_stdout>
586 <assert_stdout>
587 <has_text text='attr="maxvirtmem" val0="8"'/>
588 </assert_stdout>
589 <assert_stdout>
590 <has_text text="hybridScaffold"/>
591 </assert_stdout>
592 </test>
593 <test expect_num_outputs="3">
594 <param name="ngs_fasta" value="assembly.fasta.gz"/>
595 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
596 <param name="conflict_filter_genome" value="3"/>
597 <param name="conflict_filter_sequence" value="3"/>
598 <conditional name="configuration_options">
599 <param name="configuration" value="file"/>
600 <param name="configuration_file" value="configuration.xml"/>
601 </conditional>
602 <param name="trim_cut_sites" value="true"/>
603 <output name="ngs_contigs_trimmed" ftype="fasta">
604 <assert_contents>
605 <has_size value="4832591" delta="300" />
606 </assert_contents>
607 </output>
608 <output name="ngs_contigs_trimmed_report" ftype="txt">
609 <assert_contents>
610 <has_size value="0" />
611 </assert_contents>
612 </output>
613 <output name="report" file="test_05_report.txt" ftype="txt"/>
570 <assert_stdout> 614 <assert_stdout>
571 <has_text text='attr="maxmem" val0="8"'/> 615 <has_text text='attr="maxmem" val0="8"'/>
572 </assert_stdout> 616 </assert_stdout>
573 <assert_stdout> 617 <assert_stdout>
574 <has_text text='attr="maxthreads" val0="1"'/> 618 <has_text text='attr="maxthreads" val0="1"'/>