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bernt-matthiasbernt-matthias
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fix linter errors
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‎tools/trim_galore/trim_galore.xml‎

Lines changed: 117 additions & 69 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,8 @@
33
<macros>
44
<import>macros.xml</import>
55
</macros>
6-
<expand macro="requirements" />
76
<expand macro="xrefs"/>
7+
<expand macro="requirements" />
88
<version_command>
99
trim_galore --version
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</version_command>
@@ -406,84 +406,121 @@
406406

407407
<tests>
408408
<test expect_num_outputs="2">
409-
<param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
410-
<param name="sPaired" value="single" />
411-
<param name="settingsType" value="custom" />
412-
<param name="report" value="true" />
409+
<conditional name="singlePaired">
410+
<param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
411+
<param name="sPaired" value="single" />
412+
</conditional>
413+
<conditional name="params">
414+
<param name="settingsType" value="custom" />
415+
<param name="report" value="true" />
416+
</conditional>
413417
<output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/>
414418
<output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="12" />
415419
</test>
416420
<test expect_num_outputs="2">
417-
<param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
418-
<param name="sPaired" value="single" />
419-
<param name="settingsType" value="custom" />
420-
<param name="report" value="true" />
421+
<conditional name="singlePaired">
422+
<param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
423+
<param name="sPaired" value="single" />
424+
</conditional>
425+
<conditional name="params">
426+
<param name="settingsType" value="custom" />
427+
<param name="report" value="true" />
428+
</conditional>
421429
<output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
422430
<output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="12" />
423431
</test>
424432

425433
<test expect_num_outputs="1">
426-
<param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
427-
<param name="sPaired" value="single" />
428-
<param name="trimming_select" value="--illumina" />
434+
<conditional name="singlePaired">
435+
<param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
436+
<param name="sPaired" value="single" />
437+
<conditional name="trimming">
438+
<param name="trimming_select" value="--illumina" />
439+
</conditional>
440+
</conditional>
429441
<output name="trimmed_reads_single" file="sanger_full_range_results2.fastqsanger" ftype="fastqsanger"/>
430442
</test>
431443
<test expect_num_outputs="1">
432-
<param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
433-
<param name="sPaired" value="single" />
434-
<param name="trimming_select" value="--illumina" />
444+
<conditional name="singlePaired">
445+
<param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
446+
<param name="sPaired" value="single" />
447+
<conditional name="trimming">
448+
<param name="trimming_select" value="--illumina" />
449+
</conditional>
450+
</conditional>
435451
<output name="trimmed_reads_single" file="sanger_full_range_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
436452
</test>
437453

438454
<test expect_num_outputs="1">
439-
<param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
440-
<param name="sPaired" value="single" />
441-
<param name="adapter" value="AAAGAGC" />
455+
<conditional name="singlePaired">
456+
<param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
457+
<param name="sPaired" value="single" />
458+
<conditional name="trimming">
459+
<param name="trimming_select" value="user" />
460+
<param name="adapter" value="AAAGAGC" />
461+
</conditional>
462+
</conditional>
442463
<output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/>
443464
</test>
444465
<test expect_num_outputs="1">
445-
<param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
446-
<param name="sPaired" value="single" />
447-
<param name="adapter" value="AAAGAGC" />
466+
<conditional name="singlePaired">
467+
<param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
468+
<param name="sPaired" value="single" />
469+
<conditional name="trimming">
470+
<param name="trimming_select" value="user" />
471+
<param name="adapter" value="AAAGAGC" />
472+
</conditional>
473+
</conditional>
448474
<output name="trimmed_reads_single" file="sanger_full_range_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
449475
</test>
450476

451477
<test expect_num_outputs="3">
452-
<param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
453-
<param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
454-
<param name="sPaired" value="paired" />
455-
<param name="settingsType" value="custom" />
456-
<param name="report" value="true" />
478+
<conditional name="singlePaired">
479+
<param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
480+
<param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
481+
<param name="sPaired" value="paired" />
482+
</conditional>
483+
<conditional name="params">
484+
<param name="settingsType" value="custom" />
485+
<param name="report" value="true" />
486+
</conditional>
457487
<output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/>
458488
<output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/>
459489
<output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="24" />
460490
</test>
461491
<test expect_num_outputs="3">
462-
<param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
463-
<param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
464-
<param name="sPaired" value="paired" />
465-
<param name="settingsType" value="custom" />
466-
<param name="report" value="true" />
492+
<conditional name="singlePaired">
493+
<param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
494+
<param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
495+
<param name="sPaired" value="paired" />
496+
</conditional>
497+
<conditional name="params">
498+
<param name="settingsType" value="custom" />
499+
<param name="report" value="true" />
500+
</conditional>
467501
<output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
468502
<output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
469503
<output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" />
470504
</test>
471505

472506
<test expect_num_outputs="7">
473-
<param name="input_mate_pairs">
474-
<collection type="paired">
475-
<element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
476-
<element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
477-
</collection>
478-
</param>
479-
480-
<param name="sPaired" value="paired_collection" />
481-
<param name="settingsType" value="custom" />
482-
<param name="report" value="true" />
483-
<param name="retain_unpaired_select" value="retain_unpaired_output" />
484-
507+
<conditional name="singlePaired">
508+
<param name="input_mate_pairs">
509+
<collection type="paired">
510+
<element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
511+
<element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
512+
</collection>
513+
</param>
514+
<param name="sPaired" value="paired_collection" />
515+
</conditional>
516+
<conditional name="params">
517+
<param name="settingsType" value="custom" />
518+
<param name="report" value="true" />
519+
<conditional name="retain_unpaired">
520+
<param name="retain_unpaired_select" value="retain_unpaired_output" />
521+
</conditional>
522+
</conditional>
485523
<output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="24" />
486-
487524
<output_collection name="trimmed_reads_paired_collection" type="paired">
488525
<element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/>
489526
<element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/>
@@ -495,20 +532,23 @@
495532
</output_collection>
496533
</test>
497534
<test expect_num_outputs="7">
498-
<param name="input_mate_pairs">
499-
<collection type="paired">
500-
<element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
501-
<element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
502-
</collection>
503-
</param>
504-
505-
<param name="sPaired" value="paired_collection" />
506-
<param name="settingsType" value="custom" />
507-
<param name="report" value="true" />
508-
<param name="retain_unpaired_select" value="retain_unpaired_output" />
509-
535+
<conditional name="singlePaired">
536+
<param name="input_mate_pairs">
537+
<collection type="paired">
538+
<element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
539+
<element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
540+
</collection>
541+
</param>
542+
<param name="sPaired" value="paired_collection" />
543+
</conditional>
544+
<conditional name="params">
545+
<param name="settingsType" value="custom" />
546+
<param name="report" value="true" />
547+
<conditional name="retain_unpaired">
548+
<param name="retain_unpaired_select" value="retain_unpaired_output" />
549+
</conditional>
550+
</conditional>
510551
<output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />
511-
512552
<output_collection name="trimmed_reads_paired_collection" type="paired">
513553
<element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
514554
<element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
@@ -521,9 +561,11 @@
521561
</test>
522562
<!--Test hard-trim option-->
523563
<test expect_num_outputs="2">
524-
<param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
525-
<param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
526-
<param name="sPaired" value="paired" />
564+
<conditional name="singlePaired">
565+
<param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
566+
<param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
567+
<param name="sPaired" value="paired" />
568+
</conditional>
527569
<conditional name="trimming">
528570
<param name="settingsType" value="custom" />
529571
<param name="hardtrim3" value="20"/>
@@ -532,9 +574,11 @@
532574
<output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed3_pair2_.fastqsanger" ftype="fastqsanger"/>
533575
</test>
534576
<test expect_num_outputs="2">
535-
<param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
536-
<param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
537-
<param name="sPaired" value="paired" />
577+
<conditional name="singlePaired">
578+
<param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
579+
<param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
580+
<param name="sPaired" value="paired" />
581+
</conditional>
538582
<conditional name="trimming">
539583
<param name="settingsType" value="custom" />
540584
<param name="hardtrim5" value="20"/>
@@ -545,9 +589,11 @@
545589

546590
<!--Test mouse epigenetic clock option-->
547591
<test expect_num_outputs="2">
548-
<param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
549-
<param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
550-
<param name="sPaired" value="paired" />
592+
<conditional name="singlePaired">
593+
<param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
594+
<param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
595+
<param name="sPaired" value="paired" />
596+
</conditional>
551597
<conditional name="trimming">
552598
<param name="settingsType" value="custom" />
553599
<param name="clock" value="true"/>
@@ -557,9 +603,11 @@
557603
</test>
558604
<!--Test polyA option-->
559605
<test expect_num_outputs="2">
560-
<param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
561-
<param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
562-
<param name="sPaired" value="paired" />
606+
<conditional name="singlePaired">
607+
<param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
608+
<param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
609+
<param name="sPaired" value="paired" />
610+
</conditional>
563611
<conditional name="trimming">
564612
<param name="settingsType" value="custom" />
565613
<param name="polyA" value="true"/>

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