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comparison trim_galore.xml @ 17:eefb644655a5 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 48a5b169f1ea3d98761bfeaae135a808506e6cbb
author bgruening
date Wed, 05 Mar 2025 18:50:58 +0000
parents cd7e644cae1d
children
comparison
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16:cd7e644cae1d 17:eefb644655a5
1 <tool id="trim_galore" name="Trim Galore!" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="trim_galore" name="Trim Galore!" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>Quality and adapter trimmer of reads</description> 2 <description>Quality and adapter trimmer of reads</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/>
6 <expand macro="requirements" /> 7 <expand macro="requirements" />
7 <expand macro="xrefs"/>
8 <version_command> 8 <version_command>
9 trim_galore --version 9 trim_galore --version
10 </version_command> 10 </version_command>
11 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
12 #set compressed = 'no' 12 #set compressed = 'no'
289 </when> 289 </when>
290 </conditional> 290 </conditional>
291 </inputs> 291 </inputs>
292 292
293 <outputs> 293 <outputs>
294 <data format_source="input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads"> 294 <data format_source="singlePaired|input_singles" default_identifier_source="singlePaired|input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
295 <filter>singlePaired['sPaired'] == "single"</filter> 295 <filter>singlePaired['sPaired'] == "single"</filter>
296 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter> 296 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter>
297 </data> 297 </data>
298 298
299 <data format_source="input_singles" name="hardtrim_reads_single" from_work_dir="input_1_hardtrim.fq" label="${tool.name} on ${on_string}: hard-trimmed reads"> 299 <data format_source="singlePaired|input_singles" name="hardtrim_reads_single" from_work_dir="input_1_hardtrim.fq" label="${tool.name} on ${on_string}: hard-trimmed reads">
300 <filter>singlePaired['sPaired'] == "single"</filter> 300 <filter>singlePaired['sPaired'] == "single"</filter>
301 <filter>trimming['settingsType'] == "custom"</filter> 301 <filter>trimming['settingsType'] == "custom"</filter>
302 <filter>trimming['hardtrim3'] != '' or trimming['hardtrim5'] != ''</filter> 302 <filter>trimming['hardtrim3'] != '' or trimming['hardtrim5'] != ''</filter>
303 </data> 303 </data>
304 304
338 <filter>trimming['settingsType'] == "custom"</filter> 338 <filter>trimming['settingsType'] == "custom"</filter>
339 <filter>trimming['clock']</filter> 339 <filter>trimming['clock']</filter>
340 </collection> 340 </collection>
341 341
342 342
343 <data format_source="input_mate1" name="trimmed_reads_pair1" from_work_dir="input_1_val_1.fq" 343 <data format_source="singlePaired|input_mate1" default_identifier_source="singlePaired|input_mate1" name="trimmed_reads_pair1" from_work_dir="input_1_val_1.fq"
344 label="${tool.name} on ${on_string}: trimmed reads pair 1"> 344 label="${tool.name} on ${on_string}: trimmed reads pair 1">
345 <filter>singlePaired['sPaired'] == "paired"</filter> 345 <filter>singlePaired['sPaired'] == "paired"</filter>
346 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter> 346 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter>
347 <filter>trimming['clock'] == False</filter> 347 <filter>trimming['clock'] == False</filter>
348 </data> 348 </data>
349 349
350 <data format_source="input_mate2" name="trimmed_reads_pair2" from_work_dir="input_2_val_2.fq" 350 <data format_source="singlePaired|input_mate2" default_identifier_source="singlePaired|input_mate2" name="trimmed_reads_pair2" from_work_dir="input_2_val_2.fq"
351 label="${tool.name} on ${on_string}: trimmed reads pair 2"> 351 label="${tool.name} on ${on_string}: trimmed reads pair 2">
352 <filter>singlePaired['sPaired'] == "paired"</filter> 352 <filter>singlePaired['sPaired'] == "paired"</filter>
353 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter> 353 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter>
354 <filter>trimming['clock'] == False</filter> 354 <filter>trimming['clock'] == False</filter>
355 </data> 355 </data>
356 356
357 <data format_source="input_mate1" name="unpaired_reads_1" from_work_dir="input_1_unpaired_1.fq" 357 <data format_source="singlePaired|input_mate1" default_identifier_source="singlePaired|input_mate1" name="unpaired_reads_1" from_work_dir="input_1_unpaired_1.fq"
358 label="${tool.name} on ${on_string}: unpaired reads (1)"> 358 label="${tool.name} on ${on_string}: unpaired reads (1)">
359 <filter>params['settingsType'] == "custom"</filter> 359 <filter>params['settingsType'] == "custom"</filter>
360 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> 360 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
361 <filter>singlePaired['sPaired'] == "paired"</filter> 361 <filter>singlePaired['sPaired'] == "paired"</filter>
362 </data> 362 </data>
363 363
364 <data format_source="input_mate2" name="unpaired_reads_2" from_work_dir="input_2_unpaired_2.fq" 364 <data format_source="singlePaired|input_mate2" default_identifier_source="singlePaired|input_mate2" name="unpaired_reads_2" from_work_dir="input_2_unpaired_2.fq"
365 label="${tool.name} on ${on_string}: unpaired reads (2)"> 365 label="${tool.name} on ${on_string}: unpaired reads (2)">
366 <filter>params['settingsType'] == "custom"</filter> 366 <filter>params['settingsType'] == "custom"</filter>
367 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> 367 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
368 <filter>singlePaired['sPaired'] == "paired"</filter> 368 <filter>singlePaired['sPaired'] == "paired"</filter>
369 </data> 369 </data>
370
370 <!--Hard-trimmed paired reads--> 371 <!--Hard-trimmed paired reads-->
371 <data format_source="input_mate1" name="hardtrimmed_reads_pair1" from_work_dir="input_1_hardtrim.fq" 372 <data format_source="singlePaired|input_mate1" default_identifier_source="singlePaired|input_mate1" name="hardtrimmed_reads_pair1" from_work_dir="input_1_hardtrim.fq"
372 label="${tool.name} on ${on_string}: hard-trimmed reads pair 1"> 373 label="${tool.name} on ${on_string}: hard-trimmed reads pair 1">
373 <filter>singlePaired['sPaired'] == "paired"</filter> 374 <filter>singlePaired['sPaired'] == "paired"</filter>
374 <filter>trimming['settingsType'] == 'custom'</filter> 375 <filter>trimming['settingsType'] == 'custom'</filter>
375 <filter>trimming['hardtrim3'] or trimming['hardtrim5']</filter> 376 <filter>trimming['hardtrim3'] or trimming['hardtrim5']</filter>
376 </data> 377 </data>
377 378
378 <data format_source="input_mate2" name="hardtrimmed_reads_pair2" from_work_dir="input_2_hardtrim.fq" 379 <data format_source="singlePaired|input_mate2" default_identifier_source="singlePaired|input_mate2" name="hardtrimmed_reads_pair2" from_work_dir="input_2_hardtrim.fq"
379 label="${tool.name} on ${on_string}: hard-trimmed reads pair 2"> 380 label="${tool.name} on ${on_string}: hard-trimmed reads pair 2">
380 <filter>singlePaired['sPaired'] == "paired"</filter> 381 <filter>singlePaired['sPaired'] == "paired"</filter>
381 <filter>trimming['settingsType'] == 'custom'</filter> 382 <filter>trimming['settingsType'] == 'custom'</filter>
382 <filter>trimming['hardtrim3'] or trimming['hardtrim5']</filter> 383 <filter>trimming['hardtrim3'] or trimming['hardtrim5']</filter>
383 </data> 384 </data>
384 385
385 <!--Mouse epigenetic mode paired reads--> 386 <!--Mouse epigenetic mode paired reads-->
386 <data format_source="input_mate1" name="mec_reads_pair1" from_work_dir="input_1.clock_UMI.R1.fq" 387 <data format_source="singlePaired|input_mate1" default_identifier_source="singlePaired|input_mate1" name="mec_reads_pair1" from_work_dir="input_1.clock_UMI.R1.fq"
387 label="${tool.name} on ${on_string}: MEC reads pair 1"> 388 label="${tool.name} on ${on_string}: MEC reads pair 1">
388 <filter>singlePaired['sPaired'] == "paired"</filter> 389 <filter>singlePaired['sPaired'] == "paired"</filter>
389 <filter>trimming['settingsType'] == 'custom'</filter> 390 <filter>trimming['settingsType'] == 'custom'</filter>
390 <filter>trimming['clock']</filter> 391 <filter>trimming['clock']</filter>
391 </data> 392 </data>
392 393
393 <data format_source="input_mate2" name="mec_reads_pair2" from_work_dir="input_2.clock_UMI.R2.fq" 394 <data format_source="singlePaired|input_mate2" default_identifier_source="singlePaired|input_mate2" name="mec_reads_pair2" from_work_dir="input_2.clock_UMI.R2.fq"
394 label="${tool.name} on ${on_string}: MEC reads pair 2"> 395 label="${tool.name} on ${on_string}: MEC reads pair 2">
395 <filter>singlePaired['sPaired'] == "paired"</filter> 396 <filter>singlePaired['sPaired'] == "paired"</filter>
396 <filter>trimming['settingsType'] == 'custom'</filter> 397 <filter>trimming['settingsType'] == 'custom'</filter>
397 <filter>trimming['clock']</filter> 398 <filter>trimming['clock']</filter>
398 </data> 399 </data>
403 </data> 404 </data>
404 </outputs> 405 </outputs>
405 406
406 <tests> 407 <tests>
407 <test expect_num_outputs="2"> 408 <test expect_num_outputs="2">
408 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 409 <conditional name="singlePaired">
409 <param name="sPaired" value="single" /> 410 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
410 <param name="settingsType" value="custom" /> 411 <param name="sPaired" value="single" />
411 <param name="report" value="true" /> 412 </conditional>
413 <conditional name="params">
414 <param name="settingsType" value="custom" />
415 <param name="report" value="true" />
416 </conditional>
412 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/> 417 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/>
413 <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="12" /> 418 <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="12" />
414 </test> 419 </test>
415 <test expect_num_outputs="2"> 420 <test expect_num_outputs="2">
416 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" /> 421 <conditional name="singlePaired">
417 <param name="sPaired" value="single" /> 422 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
418 <param name="settingsType" value="custom" /> 423 <param name="sPaired" value="single" />
419 <param name="report" value="true" /> 424 </conditional>
425 <conditional name="params">
426 <param name="settingsType" value="custom" />
427 <param name="report" value="true" />
428 </conditional>
420 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> 429 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
421 <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="12" /> 430 <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="12" />
422 </test> 431 </test>
423 432
424 <test expect_num_outputs="1"> 433 <test expect_num_outputs="1">
425 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 434 <conditional name="singlePaired">
426 <param name="sPaired" value="single" /> 435 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
427 <param name="trimming_select" value="--illumina" /> 436 <param name="sPaired" value="single" />
437 <conditional name="trimming">
438 <param name="trimming_select" value="--illumina" />
439 </conditional>
440 </conditional>
428 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastqsanger" ftype="fastqsanger"/> 441 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastqsanger" ftype="fastqsanger"/>
429 </test> 442 </test>
430 <test expect_num_outputs="1"> 443 <test expect_num_outputs="1">
431 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" /> 444 <conditional name="singlePaired">
432 <param name="sPaired" value="single" /> 445 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
433 <param name="trimming_select" value="--illumina" /> 446 <param name="sPaired" value="single" />
447 <conditional name="trimming">
448 <param name="trimming_select" value="--illumina" />
449 </conditional>
450 </conditional>
434 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> 451 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
435 </test> 452 </test>
436 453
437 <test expect_num_outputs="1"> 454 <test expect_num_outputs="1">
438 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 455 <conditional name="singlePaired">
439 <param name="sPaired" value="single" /> 456 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
440 <param name="adapter" value="AAAGAGC" /> 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>
441 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/> 463 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/>
442 </test> 464 </test>
443 <test expect_num_outputs="1"> 465 <test expect_num_outputs="1">
444 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" /> 466 <conditional name="singlePaired">
445 <param name="sPaired" value="single" /> 467 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
446 <param name="adapter" value="AAAGAGC" /> 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>
447 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> 474 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
448 </test> 475 </test>
449 476
450 <test expect_num_outputs="3"> 477 <test expect_num_outputs="3">
451 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> 478 <conditional name="singlePaired">
452 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> 479 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
453 <param name="sPaired" value="paired" /> 480 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
454 <param name="settingsType" value="custom" /> 481 <param name="sPaired" value="paired" />
455 <param name="report" value="true" /> 482 </conditional>
483 <conditional name="params">
484 <param name="settingsType" value="custom" />
485 <param name="report" value="true" />
486 </conditional>
456 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/> 487 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/>
457 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/> 488 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/>
458 <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="24" /> 489 <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="24" />
459 </test> 490 </test>
460 <test expect_num_outputs="3"> 491 <test expect_num_outputs="3">
461 <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" /> 492 <conditional name="singlePaired">
462 <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" /> 493 <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
463 <param name="sPaired" value="paired" /> 494 <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
464 <param name="settingsType" value="custom" /> 495 <param name="sPaired" value="paired" />
465 <param name="report" value="true" /> 496 </conditional>
497 <conditional name="params">
498 <param name="settingsType" value="custom" />
499 <param name="report" value="true" />
500 </conditional>
466 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> 501 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
467 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> 502 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
468 <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" /> 503 <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" />
469 </test> 504 </test>
470 505
471 <test expect_num_outputs="7"> 506 <test expect_num_outputs="7">
472 <param name="input_mate_pairs"> 507 <conditional name="singlePaired">
473 <collection type="paired"> 508 <param name="input_mate_pairs">
474 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> 509 <collection type="paired">
475 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> 510 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
476 </collection> 511 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
477 </param> 512 </collection>
478 513 </param>
479 <param name="sPaired" value="paired_collection" /> 514 <param name="sPaired" value="paired_collection" />
480 <param name="settingsType" value="custom" /> 515 </conditional>
481 <param name="report" value="true" /> 516 <conditional name="params">
482 <param name="retain_unpaired_select" value="retain_unpaired_output" /> 517 <param name="settingsType" value="custom" />
483 518 <param name="report" value="true" />
519 <conditional name="retain_unpaired">
520 <param name="retain_unpaired_select" value="retain_unpaired_output" />
521 </conditional>
522 </conditional>
484 <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="24" /> 523 <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="24" />
485
486 <output_collection name="trimmed_reads_paired_collection" type="paired"> 524 <output_collection name="trimmed_reads_paired_collection" type="paired">
487 <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/> 525 <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/>
488 <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/> 526 <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/>
489 </output_collection> 527 </output_collection>
490 528
492 <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/> 530 <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/>
493 <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/> 531 <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/>
494 </output_collection> 532 </output_collection>
495 </test> 533 </test>
496 <test expect_num_outputs="7"> 534 <test expect_num_outputs="7">
497 <param name="input_mate_pairs"> 535 <conditional name="singlePaired">
498 <collection type="paired"> 536 <param name="input_mate_pairs">
499 <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" /> 537 <collection type="paired">
500 <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" /> 538 <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
501 </collection> 539 <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
502 </param> 540 </collection>
503 541 </param>
504 <param name="sPaired" value="paired_collection" /> 542 <param name="sPaired" value="paired_collection" />
505 <param name="settingsType" value="custom" /> 543 </conditional>
506 <param name="report" value="true" /> 544 <conditional name="params">
507 <param name="retain_unpaired_select" value="retain_unpaired_output" /> 545 <param name="settingsType" value="custom" />
508 546 <param name="report" value="true" />
547 <conditional name="retain_unpaired">
548 <param name="retain_unpaired_select" value="retain_unpaired_output" />
549 </conditional>
550 </conditional>
509 <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" /> 551 <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />
510
511 <output_collection name="trimmed_reads_paired_collection" type="paired"> 552 <output_collection name="trimmed_reads_paired_collection" type="paired">
512 <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> 553 <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
513 <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> 554 <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
514 </output_collection> 555 </output_collection>
515 556
518 <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> 559 <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
519 </output_collection> 560 </output_collection>
520 </test> 561 </test>
521 <!--Test hard-trim option--> 562 <!--Test hard-trim option-->
522 <test expect_num_outputs="2"> 563 <test expect_num_outputs="2">
523 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> 564 <conditional name="singlePaired">
524 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> 565 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
525 <param name="sPaired" value="paired" /> 566 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
567 <param name="sPaired" value="paired" />
568 </conditional>
526 <conditional name="trimming"> 569 <conditional name="trimming">
527 <param name="settingsType" value="custom" /> 570 <param name="settingsType" value="custom" />
528 <param name="hardtrim3" value="20"/> 571 <param name="hardtrim3" value="20"/>
529 </conditional> 572 </conditional>
530 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed3_pair1_.fastqsanger" ftype="fastqsanger"/> 573 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed3_pair1_.fastqsanger" ftype="fastqsanger"/>
531 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed3_pair2_.fastqsanger" ftype="fastqsanger"/> 574 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed3_pair2_.fastqsanger" ftype="fastqsanger"/>
532 </test> 575 </test>
533 <test expect_num_outputs="2"> 576 <test expect_num_outputs="2">
534 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> 577 <conditional name="singlePaired">
535 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> 578 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
536 <param name="sPaired" value="paired" /> 579 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
580 <param name="sPaired" value="paired" />
581 </conditional>
537 <conditional name="trimming"> 582 <conditional name="trimming">
538 <param name="settingsType" value="custom" /> 583 <param name="settingsType" value="custom" />
539 <param name="hardtrim5" value="20"/> 584 <param name="hardtrim5" value="20"/>
540 </conditional> 585 </conditional>
541 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed5_pair1_.fastqsanger" ftype="fastqsanger"/> 586 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed5_pair1_.fastqsanger" ftype="fastqsanger"/>
542 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed5_pair2_.fastqsanger" ftype="fastqsanger"/> 587 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed5_pair2_.fastqsanger" ftype="fastqsanger"/>
543 </test> 588 </test>
544 589
545 <!--Test mouse epigenetic clock option--> 590 <!--Test mouse epigenetic clock option-->
546 <test expect_num_outputs="2"> 591 <test expect_num_outputs="2">
547 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> 592 <conditional name="singlePaired">
548 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> 593 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
549 <param name="sPaired" value="paired" /> 594 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
595 <param name="sPaired" value="paired" />
596 </conditional>
550 <conditional name="trimming"> 597 <conditional name="trimming">
551 <param name="settingsType" value="custom" /> 598 <param name="settingsType" value="custom" />
552 <param name="clock" value="true"/> 599 <param name="clock" value="true"/>
553 </conditional> 600 </conditional>
554 <output name="mec_reads_pair1" file="mec_reads_pair1.fastqsanger" ftype="fastqsanger"/> 601 <output name="mec_reads_pair1" file="mec_reads_pair1.fastqsanger" ftype="fastqsanger"/>
555 <output name="mec_reads_pair2" file="mec_reads_pair2.fastqsanger" ftype="fastqsanger"/> 602 <output name="mec_reads_pair2" file="mec_reads_pair2.fastqsanger" ftype="fastqsanger"/>
556 </test> 603 </test>
557 <!--Test polyA option--> 604 <!--Test polyA option-->
558 <test expect_num_outputs="2"> 605 <test expect_num_outputs="2">
559 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> 606 <conditional name="singlePaired">
560 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> 607 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
561 <param name="sPaired" value="paired" /> 608 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
609 <param name="sPaired" value="paired" />
610 </conditional>
562 <conditional name="trimming"> 611 <conditional name="trimming">
563 <param name="settingsType" value="custom" /> 612 <param name="settingsType" value="custom" />
564 <param name="polyA" value="true"/> 613 <param name="polyA" value="true"/>
565 </conditional> 614 </conditional>
566 <output name="trimmed_reads_pair1" file="trimmed_polyA_reads_pair1.fastqsanger" ftype="fastqsanger"/> 615 <output name="trimmed_reads_pair1" file="trimmed_polyA_reads_pair1.fastqsanger" ftype="fastqsanger"/>