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comparison cutadapt.xml @ 21:104d86c98776 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
author iuc
date Thu, 05 Mar 2020 06:45:31 -0500
parents e4691e1589d3
children 093678460093
comparison
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20:e4691e1589d3 21:104d86c98776
1 <tool id="cutadapt" name="Cutadapt" version="1.16.6" profile="17.09"> 1 <tool id="cutadapt" name="Cutadapt" version="1.16.7" 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>
105 $adapter_options.no_trim 105 $adapter_options.no_trim
106 $adapter_options.mask_adapter 106 $adapter_options.mask_adapter
107 107
108 $filter_options.discard 108 $filter_options.discard
109 $filter_options.discard_untrimmed 109 $filter_options.discard_untrimmed
110 #if str($filter_options.min) != '0': 110 #if str($filter_options.min):
111 --minimum-length=$filter_options.min 111 --minimum-length=$filter_options.min
112 #end if 112 #end if
113 #if str($filter_options.max) != '0': 113 #if str($filter_options.max):
114 --maximum-length=$filter_options.max 114 --maximum-length=$filter_options.max
115 #end if 115 #end if
116 #if $filter_options.max_n: 116 #if $filter_options.max_n:
117 --max-n=$filter_options.max_n 117 --max-n=$filter_options.max_n
118 #end if 118 #end if
195 <param name="mask_adapter" argument="--mask-adapter" type="boolean" value="False" truevalue="--mask-adapter" falsevalue="" label="Mask Adapters" help="Mask adapter bases with 'N' instead of trimming them (default: trim adapters)." /> 195 <param name="mask_adapter" argument="--mask-adapter" type="boolean" value="False" truevalue="--mask-adapter" falsevalue="" label="Mask Adapters" help="Mask adapter bases with 'N' instead of trimming them (default: trim adapters)." />
196 </section> 196 </section>
197 197
198 <!-- Filter Options --> 198 <!-- Filter Options -->
199 <section name="filter_options" title="Filter Options"> 199 <section name="filter_options" title="Filter Options">
200 <param name="discard" argument="--discard-trimmed" type="boolean" value="False" truevalue="--discard" falsevalue="" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" /> 200 <param name="discard" argument="--discard-trimmed" type="boolean" value="False" truevalue="--discard-trimmed" falsevalue="" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" />
201 <param name="discard_untrimmed" argument="--discard_untrimmed" type="boolean" value="False" truevalue="--discard-untrimmed" falsevalue="" label="Discard Untrimmed Reads" help="Discard reads that do not contain the adapter." /> 201 <param name="discard_untrimmed" argument="--discard_untrimmed" type="boolean" value="False" truevalue="--discard-untrimmed" falsevalue="" label="Discard Untrimmed Reads" help="Discard reads that do not contain the adapter." />
202 <param name="min" argument="--minimum-length" type="integer" min="0" optional="True" value="0" label="Minimum length" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Value of 0 means no minimum length." /> 202 <param name="min" argument="--minimum-length" type="integer" min="0" optional="True" value="" label="Minimum length" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded. In colorspace, an initial primer is not counted." />
203 <param name="max" argument="--maximum-length" type="integer" min="0" optional="True" value="0" label="Maximum length" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Value of 0 means no maximum length." /> 203 <param name="max" argument="--maximum-length" type="integer" min="0" optional="True" value="" label="Maximum length" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted." />
204 <param name="max_n" argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." /> 204 <param name="max_n" argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." />
205 <param name="pair_filter" argument="--pair-filter" type="select" optional="True" label="Pair filter" help="Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any"> 205 <param name="pair_filter" argument="--pair-filter" type="select" optional="True" label="Pair filter" help="Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any">
206 <option value="any" selected="True">any</option> 206 <option value="any" selected="True">any</option>
207 <option value="both">both</option> 207 <option value="both">both</option>
208 </param> 208 </param>
328 <param name="adapter" value="AGATCGGAAGAGC"/> 328 <param name="adapter" value="AGATCGGAAGAGC"/>
329 <param name="adapter_source_list2" value="user"/> 329 <param name="adapter_source_list2" value="user"/>
330 <param name="adapter2" value="AGATCGGAAGAGC"/> 330 <param name="adapter2" value="AGATCGGAAGAGC"/>
331 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/> 331 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
332 <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/> 332 <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>
333 <assert_command>
334 <not_has_text text="--discard-trimmed"/>
335 <not_has_text text="--discard-untrimmed"/>
336 <not_has_text text="--minimum-length"/>
337 <not_has_text text="--maximum-length"/>
338 <not_has_text text="--max-n"/>
339 <has_text text="--pair-filter=any"/>
340 </assert_command>
333 </test> 341 </test>
334 <!-- Ensure paired collection works --> 342 <!-- Ensure paired collection works -->
335 <test> 343 <test>
336 <param name="type" value="paired_collection" /> 344 <param name="type" value="paired_collection" />
337 <param name="input_1"> 345 <param name="input_1">
359 <test> 367 <test>
360 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> 368 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
361 <param name="adapter_source_list" value="user"/> 369 <param name="adapter_source_list" value="user"/>
362 <param name="adapter" value="TTAGACATATCTCCGTCG"/> 370 <param name="adapter" value="TTAGACATATCTCCGTCG"/>
363 <param name="output_filtering" value="filter"/> 371 <param name="output_filtering" value="filter"/>
364 <param name="discard" value="True"/> 372 <section name="filter_options">
373 <param name="discard" value="True"/>
374 </section>
365 <param name="read_modification" value="none"/> 375 <param name="read_modification" value="none"/>
366 <param name="output_type" value="default"/> 376 <param name="output_type" value="default"/>
367 <output name="out1" file="cutadapt_discard.out" ftype="fastq"/> 377 <output name="out1" file="cutadapt_discard.out" ftype="fastq"/>
378 <assert_command>
379 <has_text text="--discard-trimmed"/>
380 </assert_command>
368 </test> 381 </test>
369 <!-- Ensure rest file output works --> 382 <!-- Ensure rest file output works -->
370 <test> 383 <test>
371 <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" /> 384 <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" />
372 <param name="adapter_source_list" value="user"/> 385 <param name="adapter_source_list" value="user"/>
438 <element name="unknown" value="unknown.fastq" ftype="fastq"> 451 <element name="unknown" value="unknown.fastq" ftype="fastq">
439 </element> 452 </element>
440 </output_collection> 453 </output_collection>
441 </test> 454 </test>
442 455
443 456 <test>
444 <test> 457 <conditional name="library">
445 <conditional name="library"> 458 <param name="type" value="single" />
446 <param name="type" value="single" /> 459 <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" />
447 <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" /> 460 <section name="r1" >
448 <section name="r1" > 461 <repeat name="front_adapters">
449 <repeat name="front_adapters"> 462 <conditional name="front_adapter_source">
450 <conditional name="front_adapter_source"> 463 <param name="front_adapter_source_list" value="file"/>
451 <param name="front_adapter_source_list" value="file"/> 464 <param name="front_adapter_file" ftype="fasta" value="barcodes.fasta" />
452 <param name="front_adapter_file" ftype="fasta" value="barcodes.fasta" /> 465 </conditional>
453 </conditional> 466 </repeat>
454 </repeat> 467 </section>
455 </section> 468 </conditional>
456 </conditional> 469 <param name="report" value="False" />
457 <param name="report" value="False" /> 470 <param name="info_file" value="False" />
458 <param name="info_file" value="False" /> 471 <param name="multiple_output" value="True" />
459 <param name="multiple_output" value="True" /> 472 <output_collection name="split_output" type="list" count="3">
460 <output_collection name="split_output" type="list" count="3"> 473 <element name="A1" decompress="True" file="A1.fastq.gz" ftype="fastq.gz">
461 <element name="A1" decompress="True" file="A1.fastq.gz" ftype="fastq.gz"> 474 </element>
462 </element> 475 <element name="A2" decompress="True" file="A2.fastq.gz" ftype="fastq.gz">
463 <element name="A2" decompress="True" file="A2.fastq.gz" ftype="fastq.gz"> 476 </element>
464 </element> 477 <element name="unknown" decompress="True" file="unknown.fastq.gz" ftype="fastq.gz">
465 <element name="unknown" decompress="True" file="unknown.fastq.gz" ftype="fastq.gz"> 478 </element>
466 </element> 479 </output_collection>
467 </output_collection> 480 </test>
468 </test>
469 481
470 <!-- Ensure untrimmed file output works --> 482 <!-- Ensure untrimmed file output works -->
471 <test> 483 <test>
472 <param name="type" value="single" /> 484 <param name="type" value="single" />
473 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> 485 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
490 See discussion at https://github.com/galaxyproject/galaxy/issues/7671 502 See discussion at https://github.com/galaxyproject/galaxy/issues/7671
491 `delta="4000" is more than the difference between gzip level 1 and gzip level 9, but much less than the 503 `delta="4000" is more than the difference between gzip level 1 and gzip level 9, but much less than the
492 difference between level 1 compression and no compression 504 difference between level 1 compression and no compression
493 --> 505 -->
494 <output name="untrimmed_output" file="cutadapt_untrimmed.out.gz" compare="sim_size" delta="4000" ftype="fastq.gz"/> 506 <output name="untrimmed_output" file="cutadapt_untrimmed.out.gz" compare="sim_size" delta="4000" ftype="fastq.gz"/>
507 </test>
508 <!-- same as 1st test with paired data + filter options (because of discard_untrimmed no comparison is done) -->
509 <test>
510 <param name="type" value="paired" />
511 <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" />
513 <param name="adapter_source_list" value="user"/>
514 <param name="adapter" value="AGATCGGAAGAGC"/>
515 <param name="adapter_source_list2" value="user"/>
516 <param name="adapter2" value="AGATCGGAAGAGC"/>
517 <section name="filter_options">
518 <param name="discard_untrimmed" value="true"/>
519 <param name="min" value="1"/>
520 <param name="max" value="1000"/>
521 <param name="max_n" value="1"/>
522 <param name="pair_filter" value="both"/>
523 </section>
524 <assert_command>
525 <has_text text="--discard-untrimmed"/>
526 <has_text text="--minimum-length=1"/>
527 <has_text text="--maximum-length=1000"/>
528 <has_text text="--max-n=1"/>
529 <has_text text="--pair-filter=both"/>
530 </assert_command>
495 </test> 531 </test>
496 </tests> 532 </tests>
497 533
498 <help><![CDATA[ 534 <help><![CDATA[
499 535