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comparison cutadapt.xml @ 23:c4b82dce8335 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
author iuc
date Fri, 30 Apr 2021 10:13:37 +0000
parents 093678460093
children 288f97432497
comparison
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22:093678460093 23:c4b82dce8335
1 <tool id="cutadapt" name="Cutadapt" version="1.16.8" profile="17.09"> 1 <tool id="cutadapt" name="Cutadapt" version="1.16.9" profile="17.09">
2 <description>Remove adapter sequences from Fastq/Fasta</description> 2 <description>Remove adapter sequences from Fastq/Fasta</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
91 --output='$out1' 91 --output='$out1'
92 #end if 92 #end if
93 #else: 93 #else:
94 @read1_options@ 94 @read1_options@
95 @read2_options@ 95 @read2_options@
96 --output='$out1' 96 #if $library.type == "paired"
97 --paired-output='$out2' 97 --output='$out1'
98 --paired-output='$out2'
99 #else
100 --output='$out_pairs.forward'
101 --paired-output='$out_pairs.reverse'
102 #end if
98 #end if 103 #end if
99 104
100 --error-rate=$adapter_options.error_rate 105 --error-rate=$adapter_options.error_rate
101 --times=$adapter_options.count 106 --times=$adapter_options.count
102 --overlap=$adapter_options.overlap 107 --overlap=$adapter_options.overlap
238 243
239 </inputs> 244 </inputs>
240 245
241 <outputs> 246 <outputs>
242 <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output"> 247 <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output">
243 <filter>(output_options['multiple_output'] is False)</filter> 248 <filter>(output_options['multiple_output'] is False and library['type'] != 'paired_collection')</filter>
244 <expand macro="inherit_format_1" /> 249 <expand macro="inherit_format_1" />
245 </data> 250 </data>
246 <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2*" label="${tool.name} on ${on_string}: Read 2 Output" > 251 <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2*" label="${tool.name} on ${on_string}: Read 2 Output" >
247 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter> 252 <filter>(output_options['multiple_output'] is False and library['type'] == 'paired')</filter>
248 <expand macro="inherit_format_2" /> 253 <expand macro="inherit_format_2" />
249 </data> 254 </data>
255
256 <collection name="out_pairs" type="paired" format_source="input_1" label="${tool.name} on ${on_string}: Reads">
257 <filter>(output_options['multiple_output'] is False and library['type'] == 'paired_collection')</filter>
258 </collection>
250 259
251 <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report"> 260 <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report">
252 <filter>(output_options['report'] is True)</filter> 261 <filter>(output_options['report'] is True)</filter>
253 </data> 262 </data>
254 263
302 311
303 </outputs> 312 </outputs>
304 313
305 <tests> 314 <tests>
306 <!-- Ensure fastq works --> 315 <!-- Ensure fastq works -->
307 <test> 316 <test expect_num_outputs="1">
308 <param name="type" value="single" /> 317 <param name="type" value="single" />
309 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> 318 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
310 <param name="adapter_source_list" value="user"/> 319 <param name="adapter_source_list" value="user"/>
311 <param name="adapter" value="AGATCGGAAGAGC"/> 320 <param name="adapter" value="AGATCGGAAGAGC"/>
312 <output name="out1" file="cutadapt_small.out" ftype="fastq"/> 321 <output name="out1" file="cutadapt_small.out" ftype="fastq"/>
313 </test> 322 </test>
314 <!-- Ensure single end fastq.gz works --> 323 <!-- Ensure single end fastq.gz works -->
315 <test> 324 <test expect_num_outputs="1">
316 <param name="type" value="single" /> 325 <param name="type" value="single" />
317 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" /> 326 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
318 <param name="adapter_source_list" value="user"/> 327 <param name="adapter_source_list" value="user"/>
319 <param name="adapter" value="AGATCGGAAGAGC"/> 328 <param name="adapter" value="AGATCGGAAGAGC"/>
320 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/> 329 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
321 </test> 330 </test>
322 <!-- Ensure paired end fastq.gz works --> 331 <!-- Ensure paired end fastq.gz works -->
323 <test> 332 <test expect_num_outputs="2">
324 <param name="type" value="paired" /> 333 <param name="type" value="paired" />
325 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" /> 334 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
326 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" /> 335 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
327 <param name="adapter_source_list" value="user"/> 336 <param name="adapter_source_list" value="user"/>
328 <param name="adapter" value="AGATCGGAAGAGC"/> 337 <param name="adapter" value="AGATCGGAAGAGC"/>
338 <not_has_text text="--max-n"/> 347 <not_has_text text="--max-n"/>
339 <has_text text="--pair-filter=any"/> 348 <has_text text="--pair-filter=any"/>
340 </assert_command> 349 </assert_command>
341 </test> 350 </test>
342 <!-- Ensure paired collection works --> 351 <!-- Ensure paired collection works -->
343 <test> 352 <test expect_num_outputs="3">
344 <param name="type" value="paired_collection" /> 353 <param name="type" value="paired_collection" />
345 <param name="input_1"> 354 <param name="input_1">
346 <collection type="paired"> 355 <collection type="paired">
347 <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" /> 356 <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
348 <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" /> 357 <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
350 </param> 359 </param>
351 <param name="adapter_source_list" value="user"/> 360 <param name="adapter_source_list" value="user"/>
352 <param name="adapter" value="AGATCGGAAGAGC"/> 361 <param name="adapter" value="AGATCGGAAGAGC"/>
353 <param name="adapter_source_list2" value="user"/> 362 <param name="adapter_source_list2" value="user"/>
354 <param name="adapter2" value="AGATCGGAAGAGC"/> 363 <param name="adapter2" value="AGATCGGAAGAGC"/>
355 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/> 364 <output_collection name="out_pairs" type="paired">
356 <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/> 365 <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
366 <element name="reverse" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz" />
367 </output_collection>
357 </test> 368 </test>
358 <!-- Ensure built-in adapters work --> 369 <!-- Ensure built-in adapters work -->
359 <test> 370 <test expect_num_outputs="1">
360 <param name="type" value="single" /> 371 <param name="type" value="single" />
361 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> 372 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
362 <param name="adapter_source_list" value="builtin"/> 373 <param name="adapter_source_list" value="builtin"/>
363 <param name="adapter" value="TGTAGGCC"/> 374 <param name="adapter" value="TGTAGGCC"/>
364 <output name="out1" file="cutadapt_builtin.out" ftype="fastq"/> 375 <output name="out1" file="cutadapt_builtin.out" ftype="fastq"/>
365 </test> 376 </test>
366 <!-- Ensure discard file output works --> 377 <!-- Ensure discard file output works -->
367 <test> 378 <test expect_num_outputs="1">
368 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> 379 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
369 <param name="adapter_source_list" value="user"/> 380 <param name="adapter_source_list" value="user"/>
370 <param name="adapter" value="TTAGACATATCTCCGTCG"/> 381 <param name="adapter" value="TTAGACATATCTCCGTCG"/>
371 <param name="output_filtering" value="filter"/> 382 <param name="output_filtering" value="filter"/>
372 <section name="filter_options"> 383 <section name="filter_options">
378 <assert_command> 389 <assert_command>
379 <has_text text="--discard-trimmed"/> 390 <has_text text="--discard-trimmed"/>
380 </assert_command> 391 </assert_command>
381 </test> 392 </test>
382 <!-- Ensure rest file output works --> 393 <!-- Ensure rest file output works -->
383 <test> 394 <test expect_num_outputs="2">
384 <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" /> 395 <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" />
385 <param name="adapter_source_list" value="user"/> 396 <param name="adapter_source_list" value="user"/>
386 <param name="adapter" value="AAAGATG"/> 397 <param name="adapter" value="AAAGATG"/>
387 <param name="output_filtering" value="default"/> 398 <param name="output_filtering" value="default"/>
388 <param name="read_modification" value="none"/> 399 <param name="read_modification" value="none"/>
390 <param name="rest_file" value="True"/> 401 <param name="rest_file" value="True"/>
391 <output name="out1" file="cutadapt_rest.out" ftype="fasta"/> 402 <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
392 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/> 403 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
393 </test> 404 </test>
394 <!-- Ensure nextseq-trim option works --> 405 <!-- Ensure nextseq-trim option works -->
395 <test> 406 <test expect_num_outputs="1">
396 <param name="type" value="single" /> 407 <param name="type" value="single" />
397 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" /> 408 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
398 <param name="adapter_source_list" value="user"/> 409 <param name="adapter_source_list" value="user"/>
399 <param name="adapter" value="AGATCGGAAGAGC"/> 410 <param name="adapter" value="AGATCGGAAGAGC"/>
400 <param name="read_modification" value="modify"/> 411 <param name="read_modification" value="modify"/>
401 <param name="nextseq_trim" value="20" /> 412 <param name="nextseq_trim" value="20" />
402 <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/> 413 <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/>
403 </test> 414 </test>
404 <!-- Ensure Report and Info file output work --> 415 <!-- Ensure Report and Info file output work -->
405 <test> 416 <test expect_num_outputs="3">
406 <param name="type" value="single" /> 417 <param name="type" value="single" />
407 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> 418 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
408 <param name="adapter_source_list" value="user"/> 419 <param name="adapter_source_list" value="user"/>
409 <param name="adapter" value="AGATCGGAAGAGC"/> 420 <param name="adapter" value="AGATCGGAAGAGC"/>
410 <param name="report" value="True" /> 421 <param name="report" value="True" />
417 </output> 428 </output>
418 <output name="info_file" value="cutadapt_info_out.txt" ftype="txt"/> 429 <output name="info_file" value="cutadapt_info_out.txt" ftype="txt"/>
419 </test> 430 </test>
420 431
421 432
422 <test> 433 <test expect_num_outputs="1">
423 <conditional name="library"> 434 <conditional name="library">
424 <param name="type" value="single" /> 435 <param name="type" value="single" />
425 <param name="input_1" ftype="fastq" value="cutadapt_in_split.fastq" /> 436 <param name="input_1" ftype="fastq" value="cutadapt_in_split.fastq" />
426 <section name="r1" > 437 <section name="r1" >
427 <repeat name="front_adapters"> 438 <repeat name="front_adapters">
451 <element name="unknown" value="unknown.fastq" ftype="fastq"> 462 <element name="unknown" value="unknown.fastq" ftype="fastq">
452 </element> 463 </element>
453 </output_collection> 464 </output_collection>
454 </test> 465 </test>
455 466
456 <test> 467 <test expect_num_outputs="1">
457 <conditional name="library"> 468 <conditional name="library">
458 <param name="type" value="single" /> 469 <param name="type" value="single" />
459 <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" /> 470 <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" />
460 <section name="r1" > 471 <section name="r1" >
461 <repeat name="front_adapters"> 472 <repeat name="front_adapters">
478 </element> 489 </element>
479 </output_collection> 490 </output_collection>
480 </test> 491 </test>
481 492
482 <!-- Ensure untrimmed file output works --> 493 <!-- Ensure untrimmed file output works -->
483 <test> 494 <test expect_num_outputs="2">
484 <param name="type" value="single" /> 495 <param name="type" value="single" />
485 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> 496 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
486 <param name="adapter_source_list" value="user"/> 497 <param name="adapter_source_list" value="user"/>
487 <param name="adapter" value="AAAT"/> 498 <param name="adapter" value="AAAT"/>
488 <param name="untrimmed_file" value="True" /> 499 <param name="untrimmed_file" value="True" />
489 <output name="out1" file="cutadapt_trimmed.out" ftype="fastq"/> 500 <output name="out1" file="cutadapt_trimmed.out" ftype="fastq"/>
490 <output name="untrimmed_output" file="cutadapt_untrimmed.out" ftype="fastq"/> 501 <output name="untrimmed_output" file="cutadapt_untrimmed.out" ftype="fastq"/>
491 </test> 502 </test>
492 <!-- Ensure untrimmed gzip file output works --> 503 <!-- Ensure untrimmed gzip file output works -->
493 <test> 504 <test expect_num_outputs="2">
494 <param name="type" value="single" /> 505 <param name="type" value="single" />
495 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" /> 506 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
496 <param name="adapter_source_list" value="user"/> 507 <param name="adapter_source_list" value="user"/>
497 <param name="adapter" value="AGATCGGAAGAGC"/> 508 <param name="adapter" value="AGATCGGAAGAGC"/>
498 <param name="untrimmed_file" value="True" /> 509 <param name="untrimmed_file" value="True" />
504 difference between level 1 compression and no compression 515 difference between level 1 compression and no compression
505 --> 516 -->
506 <output name="untrimmed_output" file="cutadapt_untrimmed.out.gz" compare="sim_size" delta="4000" ftype="fastq.gz"/> 517 <output name="untrimmed_output" file="cutadapt_untrimmed.out.gz" compare="sim_size" delta="4000" ftype="fastq.gz"/>
507 </test> 518 </test>
508 <!-- same as 1st test with paired data + filter options (because of discard_untrimmed no comparison is done) --> 519 <!-- same as 1st test with paired data + filter options (because of discard_untrimmed no comparison is done) -->
509 <test> 520 <test expect_num_outputs="2">
510 <param name="type" value="paired" /> 521 <param name="type" value="paired" />
511 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" /> 522 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
512 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" /> 523 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
513 <param name="adapter_source_list" value="user"/> 524 <param name="adapter_source_list" value="user"/>
514 <param name="adapter" value="AGATCGGAAGAGC"/> 525 <param name="adapter" value="AGATCGGAAGAGC"/>