Mercurial > repos > iuc > samtools_view
comparison samtools_view.xml @ 15:6be888be75f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
author | iuc |
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date | Mon, 20 Nov 2023 22:17:43 +0000 |
parents | 5826298f6a73 |
children | 2dce91e11ca7 |
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14:5826298f6a73 | 15:6be888be75f9 |
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1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> | 1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
2 <description>- reformat, filter, or subsample SAM, BAM or CRAM</description> | 2 <description>- reformat, filter, or subsample SAM, BAM or CRAM</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 <token name="@REF_DATA@"> | 5 <token name="@REF_DATA@"> |
6 ## additional reference data | 6 ## additional reference data |
152 #if $input.is_of_type('sam') or $std_filters or $reg_filters: | 152 #if $input.is_of_type('sam') or $std_filters or $reg_filters: |
153 ## There is no index or we cannot use it because we are | 153 ## There is no index or we cannot use it because we are |
154 ## not dealing with all of the reads in the indexed | 154 ## not dealing with all of the reads in the indexed |
155 ## file. We have to do an extra pass over the input to | 155 ## file. We have to do an extra pass over the input to |
156 ## count the reads to subsample. | 156 ## count the reads to subsample. |
157 sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` && | 157 sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", fac > 1 ? 1/fac : 1)}'` && |
158 #else: | 158 #else: |
159 ## We can get the count of reads to subsample using | 159 ## We can get the count of reads to subsample using |
160 ## an inexpensive call to idxstats. | 160 ## an inexpensive call to idxstats. |
161 sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` && | 161 sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", fac > 1 ? 1/fac : 1)}'` && |
162 #end if | 162 #end if |
163 #end if | 163 #end if |
164 #end if | 164 #end if |
165 | 165 |
166 ## call samtools view | 166 ## call samtools view |
170 | 170 |
171 ## filter options (except regions filter, which is the last parameter) | 171 ## filter options (except regions filter, which is the last parameter) |
172 $std_filters | 172 $std_filters |
173 | 173 |
174 #if $with_subsampling: | 174 #if $with_subsampling: |
175 --subsample-seed $seed | |
175 #if str($mode.subsample_config.subsampling_mode.select_subsample) == "target": | 176 #if str($mode.subsample_config.subsampling_mode.select_subsample) == "target": |
176 ##this is calculated at execution time before the main samtools command | 177 ##this is calculated at execution time before the main samtools command |
177 -s \${sample_fragment} | 178 --subsample \${sample_fragment} |
178 #else: | 179 #else: |
179 #set $fraction = $seed + 1 / float($mode.subsample_config.subsampling_mode.factor) | 180 #set $fraction = 1 / float($mode.subsample_config.subsampling_mode.factor) |
180 -s $fraction | 181 --subsample $fraction |
181 #end if | 182 #end if |
182 #end if | 183 #end if |
183 | 184 |
184 ## output options | 185 ## output options |
185 #if str($mode.output_options.reads_report_type) == 'count': | 186 #if str($mode.output_options.reads_report_type) == 'count': |
396 <data name="outputcnt" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts"> | 397 <data name="outputcnt" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts"> |
397 <filter>mode['outtype'] != 'header' and mode['output_options']['reads_report_type'] == 'count'</filter> | 398 <filter>mode['outtype'] != 'header' and mode['output_options']['reads_report_type'] == 'count'</filter> |
398 </data> | 399 </data> |
399 </outputs> | 400 </outputs> |
400 <tests> | 401 <tests> |
401 <!-- 1) sam to bam (copied from the sam_to_bam tool) --> | 402 <!-- 1) sam to bam (copied from the sam_to_bam tool) --> |
402 <test> | 403 <test expect_num_outputs="1"> |
403 <param name="input" ftype="sam" value="in_test_1.sam" /> | 404 <param name="input" ftype="sam" value="in_test_1.sam" /> |
404 <output name="outputsam" ftype="bam" file="test_1.bam" lines_diff="4" /> | 405 <output name="outputsam" ftype="bam" file="test_1.bam" lines_diff="4" /> |
405 </test> | 406 </test> |
406 <!-- 2) --> | 407 <!-- 2) --> |
407 <test> | 408 <test expect_num_outputs="1"> |
408 <param name="input" ftype="sam" dbkey="equCab2" value="in_test_1.sam" /> | 409 <param name="input" ftype="sam" dbkey="equCab2" value="in_test_1.sam" /> |
409 <conditional name="addref_cond"> | 410 <conditional name="addref_cond"> |
410 <param name="addref_select" value="cached" /> | 411 <param name="addref_select" value="cached" /> |
411 <param name="ref" value="equCab2chrM" /> | 412 <param name="ref" value="equCab2chrM" /> |
412 </conditional> | 413 </conditional> |
413 <output name="outputsam" ftype="bam" file="test_2.bam" lines_diff="4" /> | 414 <output name="outputsam" ftype="bam" file="test_2.bam" lines_diff="4" /> |
414 </test> | 415 </test> |
415 <!-- 3) --> | 416 <!-- 3) --> |
416 <test> | 417 <test expect_num_outputs="1"> |
417 <param name="input" ftype="sam" value="in_test_3.sam" /> | 418 <param name="input" ftype="sam" value="in_test_3.sam" /> |
418 <conditional name="addref_cond"> | 419 <conditional name="addref_cond"> |
419 <param name="addref_select" value="history" /> | 420 <param name="addref_select" value="history" /> |
420 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> | 421 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> |
421 </conditional> | 422 </conditional> |
422 <output name="outputsam" ftype="bam" file="test_3.bam" lines_diff="4" /> | 423 <output name="outputsam" ftype="bam" file="test_3.bam" lines_diff="4" /> |
423 </test> | 424 </test> |
424 <!-- 4) cram to bam --> | 425 <!-- 4) cram to bam --> |
425 <test> | 426 <test expect_num_outputs="1"> |
426 <param name="input" value="in_test_4.cram" ftype="cram" /> | 427 <param name="input" value="in_test_4.cram" ftype="cram" /> |
427 <conditional name="addref_cond"> | 428 <conditional name="addref_cond"> |
428 <param name="addref_select" value="history" /> | 429 <param name="addref_select" value="history" /> |
429 <param name="ref" value="test.fa" /> | 430 <param name="ref" value="test.fa" /> |
430 </conditional> | 431 </conditional> |
431 <output name="outputsam" file="test_4.bam" ftype="bam" lines_diff="4" /> | 432 <output name="outputsam" file="test_4.bam" ftype="bam" lines_diff="4" /> |
432 </test> | 433 </test> |
433 <!-- 5) within bam operations expected to result in sorting or not --> | 434 <!-- 5) within bam operations expected to result in sorting or not --> |
434 <test > | 435 <test expect_num_outputs="1"> |
435 <!-- sorted bam should always result in unmodifed output --> | 436 <!-- sorted bam should always result in unmodifed output --> |
436 <param name="input" ftype="bam" value="in_test_5.bam" /> | 437 <param name="input" ftype="bam" value="in_test_5.bam" /> |
437 <assert_command> | 438 <assert_command> |
438 <not_has_text text="samtools sort" /> | 439 <not_has_text text="samtools sort" /> |
439 </assert_command> | 440 </assert_command> |
440 <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/> | 441 <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/> |
441 </test> | 442 </test> |
442 <!-- 6) --> | 443 <!-- 6) --> |
443 <test> | 444 <test expect_num_outputs="1"> |
444 <!-- sorted bam should always result in unmodifed output --> | 445 <!-- sorted bam should always result in unmodifed output --> |
445 <param name="input" ftype="bam" value="in_test_5.bam" /> | 446 <param name="input" ftype="bam" value="in_test_5.bam" /> |
446 <conditional name="mode"> | 447 <conditional name="mode"> |
447 <conditional name="output_options"> | 448 <conditional name="output_options"> |
448 <conditional name="output_format"> | 449 <conditional name="output_format"> |
454 <not_has_text text="samtools sort" /> | 455 <not_has_text text="samtools sort" /> |
455 </assert_command> | 456 </assert_command> |
456 <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/> | 457 <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/> |
457 </test> | 458 </test> |
458 <!-- 7) --> | 459 <!-- 7) --> |
459 <test> | 460 <test expect_num_outputs="1"> |
460 <!-- qname_sorted.bam should get sorted during "conversion" to bam ... --> | 461 <!-- qname_sorted.bam should get sorted during "conversion" to bam ... --> |
461 <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" /> | 462 <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" /> |
462 <assert_command> | 463 <assert_command> |
463 <has_text text="samtools sort" /> | 464 <has_text text="samtools sort" /> |
464 </assert_command> | 465 </assert_command> |
465 <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" /> | 466 <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" /> |
466 </test> | 467 </test> |
467 <!-- 8) --> | 468 <!-- 8) --> |
468 <test> | 469 <test expect_num_outputs="1"> |
469 <!-- ... but should be emitted unmodifed when using input format --> | 470 <!-- ... but should be emitted unmodifed when using input format --> |
470 <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" /> | 471 <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" /> |
471 <conditional name="mode"> | 472 <conditional name="mode"> |
472 <conditional name="output_options"> | 473 <conditional name="output_options"> |
473 <conditional name="output_format"> | 474 <conditional name="output_format"> |
479 <not_has_text text="samtools sort" /> | 480 <not_has_text text="samtools sort" /> |
480 </assert_command> | 481 </assert_command> |
481 <output name="outputsam" ftype="qname_sorted.bam" file="test_8.bam" lines_diff="2"/> | 482 <output name="outputsam" ftype="qname_sorted.bam" file="test_8.bam" lines_diff="2"/> |
482 </test> | 483 </test> |
483 <!-- 9) --> | 484 <!-- 9) --> |
484 <test> | 485 <test expect_num_outputs="1"> |
485 <!-- unsorted.bam should get sorted during "conversion" to bam ... --> | 486 <!-- unsorted.bam should get sorted during "conversion" to bam ... --> |
486 <param name="input" ftype="unsorted.bam" value="in_test_7.bam" /> | 487 <param name="input" ftype="unsorted.bam" value="in_test_7.bam" /> |
487 <assert_command> | 488 <assert_command> |
488 <has_text text="samtools sort" /> | 489 <has_text text="samtools sort" /> |
489 </assert_command> | 490 </assert_command> |
490 <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" /> | 491 <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" /> |
491 </test> | 492 </test> |
492 <!-- 10) --> | 493 <!-- 10) --> |
493 <test> | 494 <test expect_num_outputs="1"> |
494 <!-- ... ... but should be emitted unmodifed when using input format --> | 495 <!-- ... ... but should be emitted unmodifed when using input format --> |
495 <param name="input" ftype="unsorted.bam" value="in_test_7.bam" /> | 496 <param name="input" ftype="unsorted.bam" value="in_test_7.bam" /> |
496 <conditional name="mode"> | 497 <conditional name="mode"> |
497 <conditional name="output_options"> | 498 <conditional name="output_options"> |
498 <conditional name="output_format"> | 499 <conditional name="output_format"> |
504 <not_has_text text="samtools sort" /> | 505 <not_has_text text="samtools sort" /> |
505 </assert_command> | 506 </assert_command> |
506 <output name="outputsam" ftype="unsorted.bam" file="test_8.bam" lines_diff="2" /> | 507 <output name="outputsam" ftype="unsorted.bam" file="test_8.bam" lines_diff="2" /> |
507 </test> | 508 </test> |
508 <!-- 11) bam to sam + header options (adapted from bam_to_sam tool)--> | 509 <!-- 11) bam to sam + header options (adapted from bam_to_sam tool)--> |
509 <test> | 510 <test expect_num_outputs="1"> |
510 <param ftype="bam" name="input" value="in_test_11.bam" /> | 511 <param ftype="bam" name="input" value="in_test_11.bam" /> |
511 <conditional name="mode"> | 512 <conditional name="mode"> |
512 <conditional name="output_options"> | 513 <conditional name="output_options"> |
513 <conditional name="output_format"> | 514 <conditional name="output_format"> |
514 <param name="oformat" value="sam" /> | 515 <param name="oformat" value="sam" /> |
517 </conditional> | 518 </conditional> |
518 </conditional> | 519 </conditional> |
519 <output file="test_11.sam" ftype="sam" name="outputsam" lines_diff="2" /> | 520 <output file="test_11.sam" ftype="sam" name="outputsam" lines_diff="2" /> |
520 </test> | 521 </test> |
521 <!-- 12) --> | 522 <!-- 12) --> |
522 <test> | 523 <test expect_num_outputs="1"> |
523 <param ftype="bam" name="input" value="in_test_11.bam" /> | 524 <param ftype="bam" name="input" value="in_test_11.bam" /> |
524 <conditional name="mode"> | 525 <conditional name="mode"> |
525 <param name="outtype" value="header" /> | 526 <param name="outtype" value="header" /> |
526 <conditional name="output_options"> | 527 <conditional name="output_options"> |
527 <conditional name="output_format"> | 528 <conditional name="output_format"> |
530 </conditional> | 531 </conditional> |
531 </conditional> | 532 </conditional> |
532 <output file="test_12.sam" ftype="sam" name="outputsam" lines_diff="2" /> | 533 <output file="test_12.sam" ftype="sam" name="outputsam" lines_diff="2" /> |
533 </test> | 534 </test> |
534 <!-- 13) --> | 535 <!-- 13) --> |
535 <test> | 536 <test expect_num_outputs="1"> |
536 <param ftype="bam" name="input" value="in_test_11.bam" /> | 537 <param ftype="bam" name="input" value="in_test_11.bam" /> |
537 <conditional name="mode"> | 538 <conditional name="mode"> |
538 <conditional name="output_options"> | 539 <conditional name="output_options"> |
539 <conditional name="output_format"> | 540 <conditional name="output_format"> |
540 <param name="oformat" value="sam" /> | 541 <param name="oformat" value="sam" /> |
543 </conditional> | 544 </conditional> |
544 </conditional> | 545 </conditional> |
545 <output file="test_13.sam" ftype="sam" name="outputsam" lines_diff="2" /> | 546 <output file="test_13.sam" ftype="sam" name="outputsam" lines_diff="2" /> |
546 </test> | 547 </test> |
547 <!-- 14) count alignments --> | 548 <!-- 14) count alignments --> |
548 <test> | 549 <test expect_num_outputs="1"> |
549 <param name="input" value="in_test_14.bam" ftype="bam" /> | 550 <param name="input" value="in_test_14.bam" ftype="bam" /> |
550 <conditional name="mode"> | 551 <conditional name="mode"> |
551 <param name="outtype" value="all_reads" /> | 552 <param name="outtype" value="all_reads" /> |
552 <conditional name="output_options"> | 553 <conditional name="output_options"> |
553 <param name="reads_report_type" value="count" /> | 554 <param name="reads_report_type" value="count" /> |
554 </conditional> | 555 </conditional> |
555 </conditional> | 556 </conditional> |
556 <output name="outputcnt" file="test_14.tab" ftype="tabular" lines_diff="2" /> | 557 <output name="outputcnt" file="test_14.tab" ftype="tabular" lines_diff="2" /> |
557 </test> | 558 </test> |
558 <!-- 15) region filters --> | 559 <!-- 15) region filters --> |
559 <test> | 560 <test expect_num_outputs="1"> |
560 <param name="input" value="in_test_15.sam" ftype="sam" /> | 561 <param name="input" value="in_test_15.sam" ftype="sam" /> |
561 <conditional name="mode"> | 562 <conditional name="mode"> |
562 <param name="outtype" value="selected_reads" /> | 563 <param name="outtype" value="selected_reads" /> |
563 <section name="filter_config"> | 564 <section name="filter_config"> |
564 <conditional name="cond_region"> | 565 <conditional name="cond_region"> |
576 <param name="ref" value="test.fa" /> | 577 <param name="ref" value="test.fa" /> |
577 </conditional> | 578 </conditional> |
578 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" /> | 579 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" /> |
579 </test> | 580 </test> |
580 <!-- 16) --> | 581 <!-- 16) --> |
581 <test> | 582 <test expect_num_outputs="1"> |
582 <param name="input" value="in_test_14.bam" ftype="bam" /> | 583 <param name="input" value="in_test_14.bam" ftype="bam" /> |
583 <conditional name="mode"> | 584 <conditional name="mode"> |
584 <param name="outtype" value="selected_reads" /> | 585 <param name="outtype" value="selected_reads" /> |
585 <section name="filter_config"> | 586 <section name="filter_config"> |
586 <conditional name="cond_region"> | 587 <conditional name="cond_region"> |
598 <param name="ref" value="test.fa" /> | 599 <param name="ref" value="test.fa" /> |
599 </conditional> | 600 </conditional> |
600 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" /> | 601 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" /> |
601 </test> | 602 </test> |
602 <!-- 17) --> | 603 <!-- 17) --> |
603 <test> | 604 <test expect_num_outputs="1"> |
604 <param name="input" value="in_test_17.cram" dbkey="equCab2" ftype="cram" /> | 605 <param name="input" value="in_test_17.cram" dbkey="equCab2" ftype="cram" /> |
605 <conditional name="mode"> | 606 <conditional name="mode"> |
606 <param name="outtype" value="selected_reads" /> | 607 <param name="outtype" value="selected_reads" /> |
607 <section name="filter_config"> | 608 <section name="filter_config"> |
608 <conditional name="cond_region"> | 609 <conditional name="cond_region"> |
620 <param name="ref" value="equCab2chrM" /> | 621 <param name="ref" value="equCab2chrM" /> |
621 </conditional> | 622 </conditional> |
622 <output name="outputsam" file="test_17.bam" ftype="bam" lines_diff="4" /> | 623 <output name="outputsam" file="test_17.bam" ftype="bam" lines_diff="4" /> |
623 </test> | 624 </test> |
624 <!-- 18) --> | 625 <!-- 18) --> |
625 <test> | 626 <test expect_num_outputs="1"> |
626 <param name="input" value="in_test_14.bam" ftype="bam" /> | 627 <param name="input" value="in_test_14.bam" ftype="bam" /> |
627 <conditional name="mode"> | 628 <conditional name="mode"> |
628 <param name="outtype" value="selected_reads" /> | 629 <param name="outtype" value="selected_reads" /> |
629 <section name="filter_config"> | 630 <section name="filter_config"> |
630 <conditional name="cond_region"> | 631 <conditional name="cond_region"> |
643 <param name="ref" value="test.fa" /> | 644 <param name="ref" value="test.fa" /> |
644 </conditional> | 645 </conditional> |
645 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" /> | 646 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" /> |
646 </test> | 647 </test> |
647 <!-- 19) --> | 648 <!-- 19) --> |
648 <test> | 649 <test expect_num_outputs="1"> |
649 <param name="input" value="test_15.cram" ftype="cram" /> | 650 <param name="input" value="test_15.cram" ftype="cram" /> |
650 <conditional name="mode"> | 651 <conditional name="mode"> |
651 <param name="outtype" value="selected_reads" /> | 652 <param name="outtype" value="selected_reads" /> |
652 <section name="filter_config"> | 653 <section name="filter_config"> |
653 <conditional name="cond_region"> | 654 <conditional name="cond_region"> |
666 <param name="ref" value="test.fa" /> | 667 <param name="ref" value="test.fa" /> |
667 </conditional> | 668 </conditional> |
668 <output name="outputsam" file="test_19.bam" ftype="bam" lines_diff="4"/> | 669 <output name="outputsam" file="test_19.bam" ftype="bam" lines_diff="4"/> |
669 </test> | 670 </test> |
670 <!-- 20) --> | 671 <!-- 20) --> |
671 <test> | 672 <test expect_num_outputs="1"> |
672 <param name="input" value="test_15.cram" ftype="cram" /> | 673 <param name="input" value="test_15.cram" ftype="cram" /> |
673 <conditional name="mode"> | 674 <conditional name="mode"> |
674 <param name="outtype" value="selected_reads" /> | 675 <param name="outtype" value="selected_reads" /> |
675 <section name="filter_config"> | 676 <section name="filter_config"> |
676 <conditional name="cond_region"> | 677 <conditional name="cond_region"> |
689 <param name="ref" value="test.fa" /> | 690 <param name="ref" value="test.fa" /> |
690 </conditional> | 691 </conditional> |
691 <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" /> | 692 <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" /> |
692 </test> | 693 </test> |
693 <!-- 21) sampling options target < total reads --> | 694 <!-- 21) sampling options target < total reads --> |
694 <test> | 695 <test expect_num_outputs="1"> |
695 <param name="input" value="in_test_15.sam" ftype="sam" /> | 696 <param name="input" value="in_test_15.sam" ftype="sam" /> |
696 <conditional name="mode"> | 697 <conditional name="mode"> |
697 <param name="outtype" value="selected_reads" /> | 698 <param name="outtype" value="selected_reads" /> |
698 <section name="subsample_config"> | 699 <section name="subsample_config"> |
699 <conditional name="subsampling_mode"> | 700 <conditional name="subsampling_mode"> |
708 </conditional> | 709 </conditional> |
709 </conditional> | 710 </conditional> |
710 <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="10" /> | 711 <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="10" /> |
711 </test> | 712 </test> |
712 <!-- 22) target > total reads --> | 713 <!-- 22) target > total reads --> |
713 <test> | 714 <test expect_num_outputs="1"> |
714 <param name="input" value="in_test_15.sam" ftype="sam" /> | 715 <param name="input" value="in_test_15.sam" ftype="sam" /> |
715 <conditional name="mode"> | 716 <conditional name="mode"> |
716 <param name="outtype" value="selected_reads" /> | 717 <param name="outtype" value="selected_reads" /> |
717 <section name="subsample_config"> | 718 <section name="subsample_config"> |
718 <conditional name="subsampling_mode"> | 719 <conditional name="subsampling_mode"> |
727 </conditional> | 728 </conditional> |
728 </conditional> | 729 </conditional> |
729 <output name="outputsam" file="test_22.sam" ftype="sam" lines_diff="2"/> | 730 <output name="outputsam" file="test_22.sam" ftype="sam" lines_diff="2"/> |
730 </test> | 731 </test> |
731 <!-- 23) --> | 732 <!-- 23) --> |
732 <test> | 733 <test expect_num_outputs="1"> |
733 <!-- subsampling SAM input without reads --> | 734 <!-- subsampling SAM input without reads --> |
734 <param name="input" value="in_test_23.sam" ftype="sam" /> | 735 <param name="input" value="in_test_23.sam" ftype="sam" /> |
735 <conditional name="mode"> | 736 <conditional name="mode"> |
736 <param name="outtype" value="selected_reads" /> | 737 <param name="outtype" value="selected_reads" /> |
737 <section name="subsample_config"> | 738 <section name="subsample_config"> |
747 </conditional> | 748 </conditional> |
748 </conditional> | 749 </conditional> |
749 <output name="outputsam" file="test_23.sam" ftype="sam" lines_diff="2"/> | 750 <output name="outputsam" file="test_23.sam" ftype="sam" lines_diff="2"/> |
750 </test> | 751 </test> |
751 <!-- 24) --> | 752 <!-- 24) --> |
752 <test> | 753 <test expect_num_outputs="1"> |
753 <!-- subsampling BAM input without reads --> | 754 <!-- subsampling BAM input without reads --> |
754 <param name="input" value="in_test_24.bam" ftype="bam" /> | 755 <param name="input" value="in_test_24.bam" ftype="bam" /> |
755 <conditional name="mode"> | 756 <conditional name="mode"> |
756 <param name="outtype" value="selected_reads" /> | 757 <param name="outtype" value="selected_reads" /> |
757 <section name="subsample_config"> | 758 <section name="subsample_config"> |
767 </conditional> | 768 </conditional> |
768 </conditional> | 769 </conditional> |
769 <output name="outputsam" file="test_24.bam" ftype="bam" lines_diff="2" /> | 770 <output name="outputsam" file="test_24.bam" ftype="bam" lines_diff="2" /> |
770 </test> | 771 </test> |
771 <!-- 25) --> | 772 <!-- 25) --> |
772 <test> | 773 <test expect_num_outputs="1"> |
773 <param name="input" value="in_test_15.sam" ftype="sam" /> | 774 <param name="input" value="in_test_15.sam" ftype="sam" /> |
774 <conditional name="mode"> | 775 <conditional name="mode"> |
775 <param name="outtype" value="selected_reads" /> | 776 <param name="outtype" value="selected_reads" /> |
776 <section name="subsample_config"> | 777 <section name="subsample_config"> |
777 <conditional name="subsampling_mode"> | 778 <conditional name="subsampling_mode"> |
787 </conditional> | 788 </conditional> |
788 </conditional> | 789 </conditional> |
789 <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="2" /> | 790 <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="2" /> |
790 </test> | 791 </test> |
791 <!-- 26) --> | 792 <!-- 26) --> |
792 <test> | 793 <test expect_num_outputs="1"> |
793 <param name="input" value="in_test_14.bam" ftype="bam" /> | 794 <param name="input" value="in_test_14.bam" ftype="bam" /> |
794 <conditional name="mode"> | 795 <conditional name="mode"> |
795 <param name="outtype" value="selected_reads" /> | 796 <param name="outtype" value="selected_reads" /> |
796 <section name="subsample_config"> | 797 <section name="subsample_config"> |
797 <conditional name="subsampling_mode"> | 798 <conditional name="subsampling_mode"> |
807 </conditional> | 808 </conditional> |
808 </conditional> | 809 </conditional> |
809 <output name="outputsam" file="test_26.bam" ftype="bam" lines_diff="2" /> | 810 <output name="outputsam" file="test_26.bam" ftype="bam" lines_diff="2" /> |
810 </test> | 811 </test> |
811 <!-- 27) --> | 812 <!-- 27) --> |
812 <test> | 813 <test expect_num_outputs="1"> |
813 <param name="input" value="in_test_14.bam" ftype="bam" /> | 814 <param name="input" value="in_test_14.bam" ftype="bam" /> |
814 <conditional name="mode"> | 815 <conditional name="mode"> |
815 <param name="outtype" value="selected_reads" /> | 816 <param name="outtype" value="selected_reads" /> |
816 <section name="subsample_config"> | 817 <section name="subsample_config"> |
817 <conditional name="subsampling_mode"> | 818 <conditional name="subsampling_mode"> |
827 </conditional> | 828 </conditional> |
828 </conditional> | 829 </conditional> |
829 <output name="outputsam" file="test_27.bam" ftype="bam" lines_diff="2"/> | 830 <output name="outputsam" file="test_27.bam" ftype="bam" lines_diff="2"/> |
830 </test> | 831 </test> |
831 <!-- 28) --> | 832 <!-- 28) --> |
832 <test> | 833 <test expect_num_outputs="1"> |
833 <param name="input" value="in_test_14.bam" ftype="bam" /> | 834 <param name="input" value="in_test_14.bam" ftype="bam" /> |
834 <conditional name="mode"> | 835 <conditional name="mode"> |
835 <param name="outtype" value="selected_reads" /> | 836 <param name="outtype" value="selected_reads" /> |
836 <section name="subsample_config"> | 837 <section name="subsample_config"> |
837 <conditional name="subsampling_mode"> | 838 <conditional name="subsampling_mode"> |
847 </conditional> | 848 </conditional> |
848 </conditional> | 849 </conditional> |
849 <output name="outputsam" file="test_28.bam" ftype="bam" lines_diff="2" /> | 850 <output name="outputsam" file="test_28.bam" ftype="bam" lines_diff="2" /> |
850 </test> | 851 </test> |
851 <!-- 29) --> | 852 <!-- 29) --> |
852 <test> | 853 <test expect_num_outputs="1"> |
853 <param name="input" value="in_test_14.bam" ftype="bam" /> | 854 <param name="input" value="in_test_14.bam" ftype="bam" /> |
854 <conditional name="mode"> | 855 <conditional name="mode"> |
855 <param name="outtype" value="selected_reads" /> | 856 <param name="outtype" value="selected_reads" /> |
856 <section name="subsample_config"> | 857 <section name="subsample_config"> |
857 <conditional name="subsampling_mode"> | 858 <conditional name="subsampling_mode"> |
868 </conditional> | 869 </conditional> |
869 </conditional> | 870 </conditional> |
870 <output name="outputsam" file="test_29.bam" ftype="bam" lines_diff="2"/> | 871 <output name="outputsam" file="test_29.bam" ftype="bam" lines_diff="2"/> |
871 </test> | 872 </test> |
872 <!-- 30) testing tag filtering --> | 873 <!-- 30) testing tag filtering --> |
873 <test> | 874 <test expect_num_outputs="1"> |
874 <param name="input" value="in_test_30.bam" ftype="bam" /> | 875 <param name="input" value="in_test_30.bam" ftype="bam" /> |
875 <conditional name="mode"> | 876 <conditional name="mode"> |
876 <param name="outtype" value="selected_reads" /> | 877 <param name="outtype" value="selected_reads" /> |
877 <section name="filter_config"> | 878 <section name="filter_config"> |
878 <param name="tag" value="XS:-18" /> | 879 <param name="tag" value="XS:-18" /> |
887 <has_text text="--tag 'XS:-18'"/> | 888 <has_text text="--tag 'XS:-18'"/> |
888 </assert_command> | 889 </assert_command> |
889 <output name="outputsam" file="test_30.bam" ftype="bam" lines_diff="2" /> | 890 <output name="outputsam" file="test_30.bam" ftype="bam" lines_diff="2" /> |
890 </test> | 891 </test> |
891 <!-- 31) testing readname filtering --> | 892 <!-- 31) testing readname filtering --> |
892 <test> | 893 <test expect_num_outputs="1"> |
893 <param name="input" value="in_test_30.bam" ftype="bam" /> | 894 <param name="input" value="in_test_30.bam" ftype="bam" /> |
894 <conditional name="mode"> | 895 <conditional name="mode"> |
895 <param name="outtype" value="selected_reads" /> | 896 <param name="outtype" value="selected_reads" /> |
896 <section name="filter_config"> | 897 <section name="filter_config"> |
897 <param name="qname_file" value="readnames.txt" /> | 898 <param name="qname_file" value="readnames.txt" /> |