Mercurial > repos > iuc > hisat2

comparison hisat2.xml @ 16:21e8ea8e1adb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
author iuc
date Sat, 30 Sep 2017 04:43:26 -0400
parents d5fe9aead222
children 40e1083a4430
comparison
equal deleted inserted replaced
15:d5fe9aead222 16:21e8ea8e1adb
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" />