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comparison samtools_view.xml @ 8:bf328cec6a42 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
author iuc
date Wed, 02 Sep 2020 15:29:22 -0400
parents b01db2684fa5
children b72793637686
comparison
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7:b01db2684fa5 8:bf328cec6a42
1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy2">
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
18 <param name="collapsecigar" type="boolean" argument="-B" truevalue="-B" falsevalue="" checked="false" label="Collapse backward CIGAR operation" help="Collapse the backward CIGAR operation." /> 18 <param name="collapsecigar" type="boolean" argument="-B" truevalue="-B" falsevalue="" checked="false" label="Collapse backward CIGAR operation" help="Collapse the backward CIGAR operation." />
19 </section> 19 </section>
20 </xml> 20 </xml>
21 <xml name="output_format_selector"> 21 <xml name="output_format_selector">
22 <conditional name="output_format"> 22 <conditional name="output_format">
23 <param name="oformat" type="select" label="Output format"> 23 <param name="oformat" type="select" label="Output format"
24 help="Note on BAM output format: The tool will generate coordinate-sorted BAM, i.e., may change the order of reads compared to the input. For BAM input, select 'Same as input' to produce BAM output with the read order retained.">
25 <option value="input">Same as input</option>
24 <option value="sam">SAM</option> 26 <option value="sam">SAM</option>
25 <option value="bam" selected="True">BAM (-b)</option> 27 <option value="bam" selected="True">BAM (-b)</option>
26 <option value="cram">CRAM (-C)</option> 28 <option value="cram">CRAM (-C)</option>
27 </param> 29 </param>
30 <when value="input" />
28 <when value="sam"> 31 <when value="sam">
29 <yield /> 32 <yield />
30 <param name="fmtopt" type="hidden" value="" />
31 </when> 33 </when>
32 <when value="bam"> 34 <when value="bam" />
33 <param name="fmtopt" type="hidden" value="-b" /> 35 <when value="cram" />
34 </when>
35 <when value="cram">
36 <param name="fmtopt" type="hidden" value="-C" />
37 </when>
38 </conditional> 36 </conditional>
39 </xml> 37 </xml>
40 </macros> 38 </macros>
41 <expand macro="requirements"> 39 <expand macro="requirements">
42 <requirement type="package">gawk</requirement> 40 <requirement type="package">gawk</requirement>
47 @ADDTHREADS@ 45 @ADDTHREADS@
48 ## prepare reference data 46 ## prepare reference data
49 @PREPARE_FASTA_IDX@ 47 @PREPARE_FASTA_IDX@
50 @PREPARE_IDX@ 48 @PREPARE_IDX@
51 49
50 ## determine the output format flag to pass to samtools view
51 ## -c for count mode
52 ## -b to produce BAM-formatted output
53 ## -C to produce CRAM-formatted output
54 ## SAM is the default ouput format
55 #set $fmtopt = ''
56 #if str($mode.output_options.reads_report_type) == 'count':
57 #set $fmtopt = '-c'
58 #else:
59 #if str($mode.output_options.output_format.oformat) == 'bam':
60 #set $fmtopt = '-b'
61 #elif str($mode.output_options.output_format.oformat) == 'cram':
62 #set $fmtopt = '-C'
63 #elif str($mode.output_options.output_format.oformat) == 'input':
64 #if $input.is_of_type('bam'):
65 #set $fmtopt = '-b'
66 #elif $input.is_of_type('cram'):
67 #set $fmtopt = '-C'
68 #else:
69 ## input in SAM format, make sure to keep header if present
70 #set $fmtopt = '-h'
71 #end if
72 #end if
73 #end if
74
52 #if str($mode.outtype) == 'header': 75 #if str($mode.outtype) == 'header':
53 ## call samtools view and be done 76 ## call samtools view and be done
54 samtools view 77 samtools view
55 -H ${mode.output_options.output_format.fmtopt} -o outfile 78 -H $fmtopt -o outfile
56 @REF_DATA@ 79 @REF_DATA@
57 infile 80 infile
58 #else: 81 #else:
59 ## are filtering and/or subsampling in effect? 82 ## are filtering and/or subsampling in effect?
60 #set $with_filtering = False 83 #set $with_filtering = False
128 #if $input.is_of_type('sam') or $std_filters or $reg_filters: 151 #if $input.is_of_type('sam') or $std_filters or $reg_filters:
129 ## There is no index or we cannot use it because we are 152 ## There is no index or we cannot use it because we are
130 ## not dealing with all of the reads in the indexed 153 ## not dealing with all of the reads in the indexed
131 ## file. We have to do an extra pass over the input to 154 ## file. We have to do an extra pass over the input to
132 ## count the reads to subsample. 155 ## count the reads to subsample.
133 sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=${mode.subsample_config.subsampling_mode.target}/s; print(frac < 1 ? $seed+frac : ".0")}'` && 156 sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; print(frac > 1 ? $seed+1/frac : ".0")}'` &&
134 #else: 157 #else:
135 ## We can get the count of reads to subsample using 158 ## We can get the count of reads to subsample using
136 ## an inexpensive call to idxstats. 159 ## an inexpensive call to idxstats.
137 sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=${mode.subsample_config.subsampling_mode.target}/s; print(frac < 1 ? $seed+frac : ".0")}'` && 160 sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; print(frac > 1 ? $seed+1/frac : ".0")}'` &&
138 #end if 161 #end if
139 #end if 162 #end if
140 #end if 163 #end if
141 164
142 ## call samtools view 165 ## call samtools view
143 samtools view 166 samtools view
144 -@ \$addthreads 167 -@ \$addthreads
145 168 $fmtopt
146 #if str($mode.output_options.reads_report_type) == 'count':
147 -c
148 #else:
149 ${mode.output_options.output_format.fmtopt}
150 #end if
151 169
152 ## filter options (except regions filter, which is the last parameter) 170 ## filter options (except regions filter, which is the last parameter)
153 $std_filters 171 $std_filters
154 172
155 #if $with_subsampling: 173 #if $with_subsampling:
302 <when value="fraction"> 320 <when value="fraction">
303 <param name="factor" type="float" optional="False" value="1" min="1" label="Downsampling factor" help="The factor by which to downsample the input reads. A fraction of approx. 1/factor of the reads will be kept (default: 1 = no downsampling)." /> 321 <param name="factor" type="float" optional="False" value="1" min="1" label="Downsampling factor" help="The factor by which to downsample the input reads. A fraction of approx. 1/factor of the reads will be kept (default: 1 = no downsampling)." />
304 <expand macro="seed_input" /> 322 <expand macro="seed_input" />
305 </when> 323 </when>
306 <when value="target"> 324 <when value="target">
307 <param name="target" type="integer" optional="False" min="0" value="" label="Target # of reads" help="Sets the approx. target number of reads to subsample." /> 325 <param name="target" type="integer" optional="False" min="1" value="" label="Target # of reads" help="Sets the approx. target number of reads to subsample." />
308 <expand macro="seed_input" /> 326 <expand macro="seed_input" />
309 </when> 327 </when>
310 </conditional> 328 </conditional>
311 </section> 329 </section>
312 <conditional name="output_options"> 330 <conditional name="output_options">
388 <when input="mode.output_options.output_format.oformat" value="sam" format="sam" /> 406 <when input="mode.output_options.output_format.oformat" value="sam" format="sam" />
389 <when input="mode.output_options.output_format.oformat" value="bam" format="bam" /> 407 <when input="mode.output_options.output_format.oformat" value="bam" format="bam" />
390 <when input="mode.output_options.output_format.oformat" value="cram" format="cram" /> 408 <when input="mode.output_options.output_format.oformat" value="cram" format="cram" />
391 </change_format> 409 </change_format>
392 </data> 410 </data>
393 <data name="outputcnt" format="txt" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts"> 411 <data name="outputcnt" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts">
394 <filter>mode['outtype'] != 'header' and mode['output_options']['reads_report_type'] == 'count'</filter> 412 <filter>mode['outtype'] != 'header' and mode['output_options']['reads_report_type'] == 'count'</filter>
395 </data> 413 </data>
396 </outputs> 414 </outputs>
397 <tests> 415 <tests>
398 <!-- sam to bam (copied from the sam_to_bam tool) --> 416 <!-- sam to bam (copied from the sam_to_bam tool) -->
414 <param name="addref_select" value="history" /> 432 <param name="addref_select" value="history" />
415 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> 433 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
416 </conditional> 434 </conditional>
417 <output name="outputsam" ftype="bam" file="sam_to_bam_out3.bam" /> 435 <output name="outputsam" ftype="bam" file="sam_to_bam_out3.bam" />
418 </test> 436 </test>
419 <!-- bam to cram + region filter (adapted from bam_to_cram tool)--> 437
438 <!-- bam to cram -->
439 <test>
440 <param name="input" value="test.cram" ftype="cram" />
441 <conditional name="addref_cond">
442 <param name="addref_select" value="history" />
443 <param name="ref" value="test.fa" />
444 </conditional>
445 <output name="outputsam" file="test.bam" ftype="bam" />
446 </test>
447
448 <!-- within bam operations expected to result in sorting or not -->
449 <test>
450 <!-- sorted bam should always result in unmodifed output -->
451 <param name="input" ftype="bam" value="1_sort.bam" />
452 <assert_command>
453 <not_has_text text="samtools sort" />
454 </assert_command>
455 <output name="outputsam" ftype="bam" file="1_sort.bam" />
456 </test>
457 <test>
458 <!-- sorted bam should always result in unmodifed output -->
459 <param name="input" ftype="bam" value="1_sort.bam" />
460 <conditional name="mode">
461 <conditional name="output_options">
462 <conditional name="output_format">
463 <param name="oformat" value="input" />
464 </conditional>
465 </conditional>
466 </conditional>
467 <assert_command>
468 <not_has_text text="samtools sort" />
469 </assert_command>
470 <output name="outputsam" ftype="bam" file="1_sort.bam" />
471 </test>
472 <test>
473 <!-- qname_sorted.bam should get sorted during "conversion" to bam ... -->
474 <param name="input" ftype="qname_sorted.bam" value="1_sort_read_names.bam" />
475 <assert_command>
476 <has_text text="samtools sort" />
477 </assert_command>
478 <output name="outputsam" ftype="bam" file="1_sort.bam" />
479 </test>
480 <test>
481 <!-- ... but should be emitted unmodifed when using input format -->
482 <param name="input" ftype="qname_sorted.bam" value="1_sort_read_names.bam" />
483 <conditional name="mode">
484 <conditional name="output_options">
485 <conditional name="output_format">
486 <param name="oformat" value="input" />
487 </conditional>
488 </conditional>
489 </conditional>
490 <assert_command>
491 <not_has_text text="samtools sort" />
492 </assert_command>
493 <output name="outputsam" ftype="qname_sorted.bam" file="1_sort_read_names.bam" />
494 </test>
495 <test>
496 <!-- unsorted.bam should get sorted during "conversion" to bam ... -->
497 <param name="input" ftype="unsorted.bam" value="1_sort_read_names.bam" />
498 <assert_command>
499 <has_text text="samtools sort" />
500 </assert_command>
501 <output name="outputsam" ftype="bam" file="1_sort.bam" />
502 </test>
503 <test>
504 <!-- ... ... but should be emitted unmodifed when using input format -->
505 <param name="input" ftype="unsorted.bam" value="1_sort_read_names.bam" />
506 <conditional name="mode">
507 <conditional name="output_options">
508 <conditional name="output_format">
509 <param name="oformat" value="input" />
510 </conditional>
511 </conditional>
512 </conditional>
513 <assert_command>
514 <not_has_text text="samtools sort" />
515 </assert_command>
516 <output name="outputsam" ftype="unsorted.bam" file="1_sort_read_names.bam" />
517 </test>
518
519 <!-- bam to sam + header options (adapted from bam_to_sam tool)-->
520 <test>
521 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
522 <conditional name="mode">
523 <conditional name="output_options">
524 <conditional name="output_format">
525 <param name="oformat" value="sam" />
526 <param name="with_header" value="true" />
527 </conditional>
528 </conditional>
529 </conditional>
530 <output file="bam_to_sam_out1.sam" ftype="sam" name="outputsam" />
531 </test>
532 <test>
533 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
534 <conditional name="mode">
535 <param name="outtype" value="header" />
536 <conditional name="output_options">
537 <conditional name="output_format">
538 <param name="oformat" value="sam" />
539 </conditional>
540 </conditional>
541 </conditional>
542 <output file="bam_to_sam_out2.sam" ftype="sam" name="outputsam" />
543 </test>
544 <test>
545 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
546 <conditional name="mode">
547 <conditional name="output_options">
548 <conditional name="output_format">
549 <param name="oformat" value="sam" />
550 <param name="with_header" value="false" />
551 </conditional>
552 </conditional>
553 </conditional>
554 <output file="bam_to_sam_out3.sam" ftype="sam" name="outputsam" />
555 </test>
556
557 <!-- count alignments -->
420 <test> 558 <test>
421 <param name="input" value="test.bam" ftype="bam" /> 559 <param name="input" value="test.bam" ftype="bam" />
560 <conditional name="mode">
561 <param name="outtype" value="all_reads" />
562 <conditional name="output_options">
563 <param name="reads_report_type" value="count" />
564 </conditional>
565 </conditional>
566 <output name="outputcnt" file="test_counts.tab" ftype="tabular" />
567 </test>
568
569 <!-- region filters -->
570 <test>
571 <param name="input" value="test.sam" ftype="sam" />
422 <conditional name="mode"> 572 <conditional name="mode">
423 <param name="outtype" value="selected_reads" /> 573 <param name="outtype" value="selected_reads" />
424 <section name="filter_config"> 574 <section name="filter_config">
425 <conditional name="cond_region"> 575 <conditional name="cond_region">
426 <param name="select_region" value="no"/> 576 <param name="select_region" value="no"/>
436 <param name="addref_select" value="history" /> 586 <param name="addref_select" value="history" />
437 <param name="ref" value="test.fa" /> 587 <param name="ref" value="test.fa" />
438 </conditional> 588 </conditional>
439 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" /> 589 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
440 </test> 590 </test>
441 <!-- count alignments --> 591 <test>
442 <test>
443 <param name="input" value="test.bam" ftype="bam" /> 592 <param name="input" value="test.bam" ftype="bam" />
444 <conditional name="mode">
445 <param name="outtype" value="all_reads" />
446 <conditional name="output_options">
447 <param name="reads_report_type" value="count" />
448 </conditional>
449 </conditional>
450 <output name="outputcnt" file="test_counts.tab" ftype="txt" />
451 </test>
452 <test>
453 <param name="input" value="test.sam" ftype="sam" />
454 <conditional name="mode"> 593 <conditional name="mode">
455 <param name="outtype" value="selected_reads" /> 594 <param name="outtype" value="selected_reads" />
456 <section name="filter_config"> 595 <section name="filter_config">
457 <conditional name="cond_region"> 596 <conditional name="cond_region">
458 <param name="select_region" value="no"/> 597 <param name="select_region" value="no"/>
467 <conditional name="addref_cond"> 606 <conditional name="addref_cond">
468 <param name="addref_select" value="history" /> 607 <param name="addref_select" value="history" />
469 <param name="ref" value="test.fa" /> 608 <param name="ref" value="test.fa" />
470 </conditional> 609 </conditional>
471 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" /> 610 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
611 </test>
612 <test>
613 <param name="input" value="test2.cram" dbkey="equCab2" ftype="cram" />
614 <conditional name="mode">
615 <param name="outtype" value="selected_reads" />
616 <section name="filter_config">
617 <conditional name="cond_region">
618 <param name="select_region" value="no"/>
619 </conditional>
620 </section>
621 <conditional name="output_options">
622 <conditional name="output_format">
623 <param name="oformat" value="bam" />
624 </conditional>
625 </conditional>
626 </conditional>
627 <conditional name="addref_cond">
628 <param name="addref_select" value="cached" />
629 <param name="ref" value="equCab2chrM" />
630 </conditional>
631 <output name="outputsam" file="sam_to_bam_out2.bam" ftype="bam" />
472 </test> 632 </test>
473 <test> 633 <test>
474 <param name="input" value="test.bam" ftype="bam" /> 634 <param name="input" value="test.bam" ftype="bam" />
475 <conditional name="mode"> 635 <conditional name="mode">
476 <param name="outtype" value="selected_reads" /> 636 <param name="outtype" value="selected_reads" />
490 <param name="addref_select" value="history" /> 650 <param name="addref_select" value="history" />
491 <param name="ref" value="test.fa" /> 651 <param name="ref" value="test.fa" />
492 </conditional> 652 </conditional>
493 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" /> 653 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
494 </test> 654 </test>
495 <!-- bam to sam + header options (adapted from bam_to_sam tool)-->
496 <test>
497 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
498 <conditional name="mode">
499 <conditional name="output_options">
500 <conditional name="output_format">
501 <param name="oformat" value="sam" />
502 <param name="with_header" value="true" />
503 </conditional>
504 </conditional>
505 </conditional>
506 <output file="bam_to_sam_out1.sam" ftype="sam" name="outputsam" />
507 </test>
508 <test>
509 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
510 <conditional name="mode">
511 <param name="outtype" value="header" />
512 <conditional name="output_options">
513 <conditional name="output_format">
514 <param name="oformat" value="sam" />
515 </conditional>
516 </conditional>
517 </conditional>
518 <output file="bam_to_sam_out2.sam" ftype="sam" name="outputsam" />
519 </test>
520 <test>
521 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
522 <conditional name="mode">
523 <conditional name="output_options">
524 <conditional name="output_format">
525 <param name="oformat" value="sam" />
526 <param name="with_header" value="false" />
527 </conditional>
528 </conditional>
529 </conditional>
530 <output file="bam_to_sam_out3.sam" ftype="sam" name="outputsam" />
531 </test>
532 <!-- cram to bam + region (adapted from cram_to_bam tool)-->
533 <test>
534 <param name="input" value="test.cram" ftype="cram" />
535 <conditional name="addref_cond">
536 <param name="addref_select" value="history" />
537 <param name="ref" value="test.fa" />
538 </conditional>
539 <output name="outputsam" file="test.bam" ftype="bam" />
540 </test>
541 <test> 655 <test>
542 <param name="input" value="test.cram" ftype="cram" /> 656 <param name="input" value="test.cram" ftype="cram" />
543 <conditional name="mode"> 657 <conditional name="mode">
544 <param name="outtype" value="selected_reads" /> 658 <param name="outtype" value="selected_reads" />
545 <section name="filter_config"> 659 <section name="filter_config">
580 <param name="addref_select" value="history" /> 694 <param name="addref_select" value="history" />
581 <param name="ref" value="test.fa" /> 695 <param name="ref" value="test.fa" />
582 </conditional> 696 </conditional>
583 <output name="outputsam" file="test.bam" ftype="bam" /> 697 <output name="outputsam" file="test.bam" ftype="bam" />
584 </test> 698 </test>
585 <test> 699
586 <param name="input" value="test2.cram" dbkey="equCab2" ftype="cram" />
587 <conditional name="mode">
588 <param name="outtype" value="selected_reads" />
589 <section name="filter_config">
590 <conditional name="cond_region">
591 <param name="select_region" value="no"/>
592 </conditional>
593 </section>
594 <conditional name="output_options">
595 <conditional name="output_format">
596 <param name="oformat" value="bam" />
597 </conditional>
598 </conditional>
599 </conditional>
600 <conditional name="addref_cond">
601 <param name="addref_select" value="cached" />
602 <param name="ref" value="equCab2chrM" />
603 </conditional>
604 <output name="outputsam" file="sam_to_bam_out2.bam" ftype="bam" />
605 </test>
606 <!-- sampling options--> 700 <!-- sampling options-->
607 <test> 701 <test>
608 <param name="input" value="test.sam" ftype="sam" /> 702 <param name="input" value="test.sam" ftype="sam" />
609 <conditional name="mode"> 703 <conditional name="mode">
610 <param name="outtype" value="selected_reads" /> 704 <param name="outtype" value="selected_reads" />
614 <param name="target" value="2" /> 708 <param name="target" value="2" />
615 </conditional> 709 </conditional>
616 </section> 710 </section>
617 <conditional name="output_options"> 711 <conditional name="output_options">
618 <conditional name="output_format"> 712 <conditional name="output_format">
619 <param name="oformat" value="sam" /> 713 <param name="oformat" value="input" />
620 </conditional> 714 </conditional>
621 </conditional> 715 </conditional>
622 </conditional> 716 </conditional>
623 <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" /> 717 <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" />
624 </test> 718 </test>
632 <param name="target" value="20" /> 726 <param name="target" value="20" />
633 </conditional> 727 </conditional>
634 </section> 728 </section>
635 <conditional name="output_options"> 729 <conditional name="output_options">
636 <conditional name="output_format"> 730 <conditional name="output_format">
637 <param name="oformat" value="sam" /> 731 <param name="oformat" value="input" />
638 </conditional> 732 </conditional>
639 </conditional> 733 </conditional>
640 </conditional> 734 </conditional>
641 <output name="outputsam" file="test.sam" ftype="sam" /> 735 <output name="outputsam" file="test.sam" ftype="sam" />
736 </test>
737 <test>
738 <!-- subsampling SAM input without reads -->
739 <param name="input" value="no_reads.sam" ftype="sam" />
740 <conditional name="mode">
741 <param name="outtype" value="selected_reads" />
742 <section name="subsample_config">
743 <conditional name="subsampling_mode">
744 <param name="select_subsample" value="target" />
745 <param name="target" value="20" />
746 </conditional>
747 </section>
748 <conditional name="output_options">
749 <conditional name="output_format">
750 <param name="oformat" value="input" />
751 </conditional>
752 </conditional>
753 </conditional>
754 <output name="outputsam" file="no_reads.sam" ftype="sam" />
755 </test>
756 <test>
757 <!-- subsampling BAM input without reads -->
758 <param name="input" value="no_reads.bam" ftype="bam" />
759 <conditional name="mode">
760 <param name="outtype" value="selected_reads" />
761 <section name="subsample_config">
762 <conditional name="subsampling_mode">
763 <param name="select_subsample" value="target" />
764 <param name="target" value="20" />
765 </conditional>
766 </section>
767 <conditional name="output_options">
768 <conditional name="output_format">
769 <param name="oformat" value="input" />
770 </conditional>
771 </conditional>
772 </conditional>
773 <output name="outputsam" file="no_reads.bam" ftype="bam" />
642 </test> 774 </test>
643 <test> 775 <test>
644 <param name="input" value="test.sam" ftype="sam" /> 776 <param name="input" value="test.sam" ftype="sam" />
645 <conditional name="mode"> 777 <conditional name="mode">
646 <param name="outtype" value="selected_reads" /> 778 <param name="outtype" value="selected_reads" />
651 <param name="target" value="2" /> 783 <param name="target" value="2" />
652 </conditional> 784 </conditional>
653 </section> 785 </section>
654 <conditional name="output_options"> 786 <conditional name="output_options">
655 <conditional name="output_format"> 787 <conditional name="output_format">
656 <param name="oformat" value="sam" /> 788 <param name="oformat" value="input" />
657 </conditional> 789 </conditional>
658 </conditional> 790 </conditional>
659 </conditional> 791 </conditional>
660 <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" /> 792 <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" />
661 </test> 793 </test>
670 <param name="target" value="2" /> 802 <param name="target" value="2" />
671 </conditional> 803 </conditional>
672 </section> 804 </section>
673 <conditional name="output_options"> 805 <conditional name="output_options">
674 <conditional name="output_format"> 806 <conditional name="output_format">
675 <param name="oformat" value="bam" /> 807 <param name="oformat" value="input" />
676 </conditional> 808 </conditional>
677 </conditional> 809 </conditional>
678 </conditional> 810 </conditional>
679 <output name="outputsam" file="test_ds.bam" ftype="bam" /> 811 <output name="outputsam" file="test_ds.bam" ftype="bam" />
680 </test> 812 </test>
689 <param name="target" value="20" /> 821 <param name="target" value="20" />
690 </conditional> 822 </conditional>
691 </section> 823 </section>
692 <conditional name="output_options"> 824 <conditional name="output_options">
693 <conditional name="output_format"> 825 <conditional name="output_format">
694 <param name="oformat" value="bam" /> 826 <param name="oformat" value="input" />
695 </conditional> 827 </conditional>
696 </conditional> 828 </conditional>
697 </conditional> 829 </conditional>
698 <output name="outputsam" file="test.bam" ftype="bam" /> 830 <output name="outputsam" file="test.bam" ftype="bam" />
699 </test> 831 </test>
708 <param name="factor" value="5" /> 840 <param name="factor" value="5" />
709 </conditional> 841 </conditional>
710 </section> 842 </section>
711 <conditional name="output_options"> 843 <conditional name="output_options">
712 <conditional name="output_format"> 844 <conditional name="output_format">
713 <param name="oformat" value="bam" /> 845 <param name="oformat" value="input" />
714 </conditional> 846 </conditional>
715 </conditional> 847 </conditional>
716 </conditional> 848 </conditional>
717 <output name="outputsam" file="test_ds.bam" ftype="bam" /> 849 <output name="outputsam" file="test_ds.bam" ftype="bam" />
718 </test> 850 </test>
728 </conditional> 860 </conditional>
729 </section> 861 </section>
730 <conditional name="output_options"> 862 <conditional name="output_options">
731 <param name="reads_report_type" value="dropped" /> 863 <param name="reads_report_type" value="dropped" />
732 <conditional name="output_format"> 864 <conditional name="output_format">
733 <param name="oformat" value="bam" /> 865 <param name="oformat" value="input" />
734 </conditional> 866 </conditional>
735 </conditional> 867 </conditional>
736 </conditional> 868 </conditional>
737 <output name="outputsam" file="test_ds.bam" ftype="bam" /> 869 <output name="outputsam" file="test_ds.bam" ftype="bam" />
738 </test> 870 </test>