Mercurial > repos > iuc > hisat2
comparison hisat2.xml @ 16:21e8ea8e1adb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
author | iuc |
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date | Sat, 30 Sep 2017 04:43:26 -0400 |
parents | d5fe9aead222 |
children | 40e1083a4430 |
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15:d5fe9aead222 | 16:21e8ea8e1adb |
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288 | 288 |
289 #if str($sum.summary_file) == "true": | 289 #if str($sum.summary_file) == "true": |
290 --summary-file summary.txt | 290 --summary-file summary.txt |
291 #end if | 291 #end if |
292 | 292 |
293 | |
294 ## Convert SAM output to sorted BAM | 293 ## Convert SAM output to sorted BAM |
295 | 294 |
296 | samtools sort - -@ \${GALAXY_SLOTS:-1} -l 6 -o '${output_alignments}' | 295 | samtools sort - -@ \${GALAXY_SLOTS:-1} -l 6 -o '${output_alignments}' |
297 | |
298 | 296 |
299 ## Rename any output fastq files | 297 ## Rename any output fastq files |
300 | 298 |
301 #if $output_unaligned_reads_l and $output_unaligned_reads_r: | 299 #if $output_unaligned_reads_l and $output_unaligned_reads_r: |
302 #from os.path import splitext | 300 #from os.path import splitext |
538 <!-- BAM --> | 536 <!-- BAM --> |
539 <data name="output_alignments" format="bam" label="${tool.name} on ${on_string}: aligned reads (BAM) " /> | 537 <data name="output_alignments" format="bam" label="${tool.name} on ${on_string}: aligned reads (BAM) " /> |
540 | 538 |
541 <!-- Unaligned fastq (L) --> | 539 <!-- Unaligned fastq (L) --> |
542 <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (L)"> | 540 <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (L)"> |
543 <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True)</filter> | 541 <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True</filter> |
544 </data> | 542 </data> |
545 | 543 |
546 <!-- Aligned fastq (L) --> | 544 <!-- Aligned fastq (L) --> |
547 <data name="output_aligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (L)"> | 545 <data name="output_aligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (L)"> |
548 <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True)</filter> | 546 <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True</filter> |
549 </data> | 547 </data> |
550 | 548 |
551 <!-- Unaligned fastq (R) --> | 549 <!-- Unaligned fastq (R) --> |
552 <data name="output_unaligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (R)"> | 550 <data name="output_unaligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (R)"> |
553 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection') and (adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True) </filter> | 551 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection') and (adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True) </filter> |
566 </outputs> | 564 </outputs> |
567 | 565 |
568 <!-- Define tests --> | 566 <!-- Define tests --> |
569 | 567 |
570 <tests> | 568 <tests> |
571 <test><!-- Ensure bam output works --> | 569 <!-- Ensure bam output works --> |
570 <test expect_num_outputs="1" > | |
572 <param name="type" value="paired" /> | 571 <param name="type" value="paired" /> |
573 <param name="source" value="history" /> | 572 <param name="source" value="history" /> |
574 <param name="history_item" ftype="fasta" value="phiX.fa" /> | 573 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
575 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" /> | 574 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" /> |
576 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" /> | 575 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" /> |
577 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> | 576 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> |
578 </test> | 577 </test> |
579 <test><!-- Ensure built-in reference works --> | 578 <!-- Ensure built-in reference works --> |
579 <test expect_num_outputs="1"> | |
580 <param name="type" value="paired" /> | 580 <param name="type" value="paired" /> |
581 <param name="source" value="indexed" /> | 581 <param name="source" value="indexed" /> |
582 <param name="input_1" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_forward.fastq" /> | 582 <param name="input_1" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_forward.fastq" /> |
583 <param name="input_2" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_reverse.fastq" /> | 583 <param name="input_2" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_reverse.fastq" /> |
584 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> | 584 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> |
585 </test> | 585 </test> |
586 <test><!-- Ensure trimming works --> | 586 <!-- Ensure trimming works --> |
587 <test expect_num_outputs="1"> | |
587 <param name="type" value="paired" /> | 588 <param name="type" value="paired" /> |
588 <param name="source" value="history" /> | 589 <param name="source" value="history" /> |
589 <param name="history_item" ftype="fasta" value="phiX.fa" /> | 590 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
590 <param name="input_options_selector" value="advanced" /> | 591 <param name="input_options_selector" value="advanced" /> |
591 <param name="trim3" value="15" /> | 592 <param name="trim3" value="15" /> |
592 <param name="trim5" value="15" /> | 593 <param name="trim5" value="15" /> |
593 <param name="input_1" ftype="fastqsanger" value="hisat_input_2_forward.fastq" /> | 594 <param name="input_1" ftype="fastqsanger" value="hisat_input_2_forward.fastq" /> |
594 <param name="input_2" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" /> | 595 <param name="input_2" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" /> |
595 <output name="output_alignments" file="hisat_output_2.bam" ftype="bam" lines_diff="2" /> | 596 <output name="output_alignments" file="hisat_output_2.bam" ftype="bam" lines_diff="2" /> |
596 </test> | 597 </test> |
597 <test><!-- Ensure paired options works --> | 598 <!-- Ensure paired options works --> |
599 <test expect_num_outputs="1"> | |
598 <param name="type" value="paired" /> | 600 <param name="type" value="paired" /> |
599 <param name="source" value="history" /> | 601 <param name="source" value="history" /> |
600 <param name="history_item" ftype="fasta" value="phiX.fa" /> | 602 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
601 <param name="input_options_selector" value="advanced" /> | 603 <param name="input_options_selector" value="advanced" /> |
602 <param name="trim3" value="15" /> | 604 <param name="trim3" value="15" /> |
606 <param name="paired_options_selector" value="advanced" /> | 608 <param name="paired_options_selector" value="advanced" /> |
607 <param name="no_mixed" value="True" /> | 609 <param name="no_mixed" value="True" /> |
608 <param name="no_discordant" value="True" /> | 610 <param name="no_discordant" value="True" /> |
609 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> | 611 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> |
610 </test> | 612 </test> |
611 <test><!-- Ensure unaligned output works --> | 613 <!-- Ensure single unaligned output works --> |
614 <test expect_num_outputs="2"> | |
612 <param name="type" value="single" /> | 615 <param name="type" value="single" /> |
613 <param name="source" value="history" /> | 616 <param name="source" value="history" /> |
614 <param name="history_item" ftype="fasta" value="phiX.fa" /> | 617 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
615 <param name="output_options_selector" value="advanced" /> | 618 <param name="output_options_selector" value="advanced" /> |
616 <param name="unaligned_file" value="true" /> | 619 <param name="unaligned_file" value="true" /> |
617 <param name="aligned_file" value="true" /> | |
618 <param name="history_item" ftype="fasta" value="phiX.fa" /> | 620 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
619 <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" /> | 621 <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" /> |
620 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> | 622 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> |
621 </test> | 623 </test> |
622 <test><!-- Ensure paired unaligned output works --> | 624 <!-- Ensure paired unaligned/aligned output works --> |
625 <test expect_num_outputs="5"> | |
623 <param name="type" value="paired" /> | 626 <param name="type" value="paired" /> |
624 <param name="source" value="history" /> | 627 <param name="source" value="history" /> |
625 <param name="output_options_selector" value="advanced" /> | 628 <param name="output_options_selector" value="advanced" /> |
626 <param name="unaligned_file" value="true" /> | 629 <param name="unaligned_file" value="true" /> |
627 <param name="aligned_file" value="true" /> | 630 <param name="aligned_file" value="true" /> |
629 <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" /> | 632 <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" /> |
630 <param name="input_2" ftype="fasta" value="test_unaligned_reads.fasta" /> | 633 <param name="input_2" ftype="fasta" value="test_unaligned_reads.fasta" /> |
631 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> | 634 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> |
632 <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" /> | 635 <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" /> |
633 </test> | 636 </test> |
634 <test><!-- Ensure fastqsanger.gz works --> | 637 <!-- Ensure fastqsanger.gz works --> |
638 <test expect_num_outputs="1"> | |
635 <param name="type" value="paired" /> | 639 <param name="type" value="paired" /> |
636 <param name="source" value="history" /> | 640 <param name="source" value="history" /> |
637 <param name="history_item" ftype="fasta" value="phiX.fa" /> | 641 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
638 <param name="input_options_selector" value="advanced" /> | 642 <param name="input_options_selector" value="advanced" /> |
639 <param name="trim3" value="15" /> | 643 <param name="trim3" value="15" /> |
643 <param name="paired_options_selector" value="advanced" /> | 647 <param name="paired_options_selector" value="advanced" /> |
644 <param name="no_mixed" value="True" /> | 648 <param name="no_mixed" value="True" /> |
645 <param name="no_discordant" value="True" /> | 649 <param name="no_discordant" value="True" /> |
646 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> | 650 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> |
647 </test> | 651 </test> |
648 <test><!-- Ensure fastqsanger.bz2 works --> | 652 <!-- Ensure fastqsanger.bz2 works --> |
653 <test expect_num_outputs="1"> | |
649 <param name="type" value="paired" /> | 654 <param name="type" value="paired" /> |
650 <param name="source" value="history" /> | 655 <param name="source" value="history" /> |
651 <param name="history_item" ftype="fasta" value="phiX.fa" /> | 656 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
652 <param name="input_options_selector" value="advanced" /> | 657 <param name="input_options_selector" value="advanced" /> |
653 <param name="trim3" value="15" /> | 658 <param name="trim3" value="15" /> |
657 <param name="paired_options_selector" value="advanced" /> | 662 <param name="paired_options_selector" value="advanced" /> |
658 <param name="no_mixed" value="True" /> | 663 <param name="no_mixed" value="True" /> |
659 <param name="no_discordant" value="True" /> | 664 <param name="no_discordant" value="True" /> |
660 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> | 665 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> |
661 </test> | 666 </test> |
662 <test><!-- Ensure paired strandness works --> | 667 <!-- Ensure paired strandness works --> |
668 <test expect_num_outputs="1"> | |
663 <param name="type" value="paired" /> | 669 <param name="type" value="paired" /> |
664 <param name="source" value="history" /> | 670 <param name="source" value="history" /> |
665 <param name="history_item" ftype="fasta" value="phiX.fa" /> | 671 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
666 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" /> | 672 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" /> |
667 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" /> | 673 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" /> |
668 <param name="rna_strandness" value="FR" /> | 674 <param name="rna_strandness" value="FR" /> |
669 <output name="output_alignments" file="hisat_output_4.bam" ftype="bam" lines_diff="2" /> | 675 <output name="output_alignments" file="hisat_output_4.bam" ftype="bam" lines_diff="2" /> |
670 </test> | 676 </test> |
671 <test><!-- Ensure summary file output works --> | 677 <!-- Ensure summary file output works --> |
678 <test expect_num_outputs="2"> | |
672 <param name="type" value="single" /> | 679 <param name="type" value="single" /> |
673 <param name="source" value="history" /> | 680 <param name="source" value="history" /> |
674 <param name="history_item" ftype="fasta" value="phiX.fa" /> | 681 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
675 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" /> | 682 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" /> |
676 <param name="rna_strandness" value="R" /> | 683 <param name="rna_strandness" value="R" /> |