Mercurial > repos > pimarin > recentrifuge

comparison recentrifuge.xml @ 2:b135c5908e8c draft

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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
author pimarin
date Wed, 06 Apr 2022 13:52:48 +0000
parents e5474449c35d
children 2890083b1a84
comparison
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1:856d50c93de9 2:b135c5908e8c
363 <output name="data_tsv" file="kraken_test/test3_rcf.data.tsv" lines_diff="2"/> 363 <output name="data_tsv" file="kraken_test/test3_rcf.data.tsv" lines_diff="2"/>
364 <output name="stat_tsv" file="kraken_test/test3_rcf.stat.tsv" lines_diff="2"/> 364 <output name="stat_tsv" file="kraken_test/test3_rcf.stat.tsv" lines_diff="2"/>
365 <output name="logfile" file="kraken_test/test3_tsv.log" lines_diff="20"/> 365 <output name="logfile" file="kraken_test/test3_tsv.log" lines_diff="20"/>
366 </test> 366 </test>
367 </tests> 367 </tests>
368 <help><![CDATA[ 368 <help>
369 <![CDATA[
369 =-= /home/pierre/anaconda3/envs/rcf/bin/rcf =-= v1.8.1 - Mar 2022 =-= by Jose Manuel Martí =-= 370 =-= /home/pierre/anaconda3/envs/rcf/bin/rcf =-= v1.8.1 - Mar 2022 =-= by Jose Manuel Martí =-=
370
371 usage: rcf [-h] [-V] [-n PATH] [--format GENERIC_FORMAT] 371 usage: rcf [-h] [-V] [-n PATH] [--format GENERIC_FORMAT]
372 (-f FILE | -g FILE | -l FILE | -r FILE | -k FILE) [-o FILE] 372 (-f FILE | -g FILE | -l FILE | -r FILE | -k FILE) [-o FILE]
373 [-e OUTPUT_TYPE] [-p] [--nohtml] [-a | -c CONTROLS_NUMBER] 373 [-e OUTPUT_TYPE] [-p] [--nohtml] [-a | -c CONTROLS_NUMBER]
374 [-s SCORING] [-y NUMBER] [-m INT] [-x TAXID] [-i TAXID] [-z NUMBER] 374 [-s SCORING] [-y NUMBER] [-m INT] [-x TAXID] [-i TAXID] [-z NUMBER]
375 [-w INT] [-u SUMMARY_BEHAVIOR] [-t] [--nokollapse] [-d] [--strain] 375 [-w INT] [-u SUMMARY_BEHAVIOR] [-t] [--nokollapse] [-d] [--strain]
376 [--sequential] 376 [--sequential]
377
378 Robust comparative analysis and contamination removal for metagenomics 377 Robust comparative analysis and contamination removal for metagenomics
379
380 options: 378 options:
381 -h, --help show this help message and exit 379 -h, --help show this help message and exit
382 -V, --version show program's version number and exit 380 -V, --version show program's version number and exit
383
384 input: 381 input:
385 Define Recentrifuge input files and formats 382 Define Recentrifuge input files and formats
386
387 -n PATH, --nodespath PATH 383 -n PATH, --nodespath PATH
388 path for the nodes information files (nodes.dmp and 384 path for the nodes information files (nodes.dmp and
389 names.dmp from NCBI) 385 names.dmp from NCBI)
390 --format GENERIC_FORMAT 386 --format GENERIC_FORMAT
391 format of the output files from a generic classifier 387 format of the output files from a generic classifier
417 -k FILE, --kraken FILE 413 -k FILE, --kraken FILE
418 Kraken output files; if a single directory is entered, 414 Kraken output files; if a single directory is entered,
419 every .krk file inside will be taken as a different 415 every .krk file inside will be taken as a different
420 sample; multiple -k is available to include several 416 sample; multiple -k is available to include several
421 Kraken (version 1 or 2) samples 417 Kraken (version 1 or 2) samples
422
423 output: 418 output:
424 Related to the Recentrifuge output files 419 Related to the Recentrifuge output files
425
426 -o FILE, --outprefix FILE 420 -o FILE, --outprefix FILE
427 output prefix; if not given, it will be inferred from 421 output prefix; if not given, it will be inferred from
428 input files; an HTML filename is still accepted for 422 input files; an HTML filename is still accepted for
429 backwards compatibility with legacy --outhtml option 423 backwards compatibility with legacy --outhtml option
430 -e OUTPUT_TYPE, --extra OUTPUT_TYPE 424 -e OUTPUT_TYPE, --extra OUTPUT_TYPE
432 of ['FULL', 'CSV', 'MULTICSV', 'TSV', 'DYNOMICS'] 426 of ['FULL', 'CSV', 'MULTICSV', 'TSV', 'DYNOMICS']
433 -p, --pickle pickle (serialize) statistics and data results in 427 -p, --pickle pickle (serialize) statistics and data results in
434 pandas DataFrames (format affected by selection of 428 pandas DataFrames (format affected by selection of
435 --extra) 429 --extra)
436 --nohtml suppress saving the HTML output file 430 --nohtml suppress saving the HTML output file
437
438 tuning: 431 tuning:
439 Coarse tuning of algorithm parameters 432 Coarse tuning of algorithm parameters
440
441 -a, --avoidcross avoid cross analysis 433 -a, --avoidcross avoid cross analysis
442 -c CONTROLS_NUMBER, --controls CONTROLS_NUMBER 434 -c CONTROLS_NUMBER, --controls CONTROLS_NUMBER
443 this number of first samples will be treated as 435 this number of first samples will be treated as
444 negative controls; default is no controls 436 negative controls; default is no controls
445 -s SCORING, --scoring SCORING 437 -s SCORING, --scoring SCORING
458 (multiple -x is available to exclude several taxid) 450 (multiple -x is available to exclude several taxid)
459 -i TAXID, --include TAXID 451 -i TAXID, --include TAXID
460 NCBI taxid code to include a taxon and all underneath 452 NCBI taxid code to include a taxon and all underneath
461 (multiple -i is available to include several taxid); 453 (multiple -i is available to include several taxid);
462 by default, all the taxa are considered for inclusion 454 by default, all the taxa are considered for inclusion
463
464 fine tuning: 455 fine tuning:
465 Fine tuning of algorithm parameters 456 Fine tuning of algorithm parameters
466
467 -z NUMBER, --ctrlminscore NUMBER 457 -z NUMBER, --ctrlminscore NUMBER
468 minimum score/confidence of the classification of a 458 minimum score/confidence of the classification of a
469 read in control samples to pass the quality filter; it 459 read in control samples to pass the quality filter; it
470 defaults to "minscore" 460 defaults to "minscore"
471 -w INT, --ctrlmintaxa INT 461 -w INT, --ctrlmintaxa INT
475 -u SUMMARY_BEHAVIOR, --summary SUMMARY_BEHAVIOR 465 -u SUMMARY_BEHAVIOR, --summary SUMMARY_BEHAVIOR
476 choice for summary behaviour, and can be one of 466 choice for summary behaviour, and can be one of
477 ['ADD', 'ONLY', 'AVOID'] 467 ['ADD', 'ONLY', 'AVOID']
478 -t, --takeoutroot remove counts directly assigned to the "root" level 468 -t, --takeoutroot remove counts directly assigned to the "root" level
479 --nokollapse show the "cellular organisms" taxon 469 --nokollapse show the "cellular organisms" taxon
480
481 advanced: 470 advanced:
482 Advanced modes of running 471 Advanced modes of running
483
484 -d, --debug increase output verbosity and perform additional 472 -d, --debug increase output verbosity and perform additional
485 checks 473 checks
486 --strain set strain level instead of species as the resolution 474 --strain set strain level instead of species as the resolution
487 limit for the robust contamination removal algorithm; 475 limit for the robust contamination removal algorithm;
488 use with caution, this is an experimental feature 476 use with caution, this is an experimental feature
489 --sequential deactivate parallel processing 477 --sequential deactivate parallel processing
490
491 rcf - Release 1.8.1 - Mar 2022 478 rcf - Release 1.8.1 - Mar 2022
492
493 Copyright (C) 2017–2022, Jose Manuel Martí Martínez 479 Copyright (C) 2017–2022, Jose Manuel Martí Martínez
494
495 This program is free software: you can redistribute it and/or modify 480 This program is free software: you can redistribute it and/or modify
496 it under the terms of the GNU Affero General Public License as 481 it under the terms of the GNU Affero General Public License as
497 published by the Free Software Foundation, either version 3 of the 482 published by the Free Software Foundation, either version 3 of the
498 License, or (at your option) any later version. 483 License, or (at your option) any later version.
499
500 This program is distributed in the hope that it will be useful, 484 This program is distributed in the hope that it will be useful,
501 but WITHOUT ANY WARRANTY; without even the implied warranty of 485 but WITHOUT ANY WARRANTY; without even the implied warranty of
502 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 486 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
503 GNU Affero General Public License for more details. 487 GNU Affero General Public License for more details.
504
505 You should have received a copy of the GNU Affero General Public License 488 You should have received a copy of the GNU Affero General Public License
506 along with this program. If not, see <https://www.gnu.org/licenses/>. 489 along with this program. If not, see <https://www.gnu.org/licenses/>.
507 ]]></help> 490
508 <expand macro="citations"/> 491 ]]>
509 </tool> 492 </help>
493 <expand macro="citations"/>
494 </tool>