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comparison hifiasm.xml @ 9:c388a21dcbf1 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024
author bgruening
date Fri, 20 Jan 2023 22:27:43 +0000
parents 5f625c63b8bc
children 2061fb3b81b4
comparison
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8:5f625c63b8bc 9:c388a21dcbf1
1 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description> 2 <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.16.1</token> 4 <token name="@TOOL_VERSION@">0.18.5</token>
5 <token name="@VERSION_SUFFIX@">4</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token> 6 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
7 <xml name="reads"> 7 <xml name="reads">
8 <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" /> 8 <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />
9 </xml> 9 </xml>
10 </macros> 10 </macros>
291 </data> 291 </data>
292 <!--Log output--> 292 <!--Log output-->
293 <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}: log file"> 293 <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}: log file">
294 <filter>log_out</filter> 294 <filter>log_out</filter>
295 </data> 295 </data>
296 <collection name="noseq files" type="list" label="${tool.name} on ${on_string}: noseq files"> 296 <collection name="noseq_files" type="list" label="${tool.name} on ${on_string}: noseq files">
297 <discover_datasets pattern="__name_and_ext__" format="gfa1" directory="noseq_files" /> 297 <discover_datasets pattern="__name_and_ext__" format="gfa1" directory="noseq_files" />
298 </collection> 298 </collection>
299 </outputs> 299 </outputs>
300 <tests> 300 <tests>
301 <test expect_num_outputs="5"> 301 <test expect_num_outputs="5">
303 <param name="filter_bits" value="0" /> 303 <param name="filter_bits" value="0" />
304 <param name="mode_selector" value="standard" /> 304 <param name="mode_selector" value="standard" />
305 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" /> 305 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
306 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" /> 306 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
307 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" /> 307 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />
308 <output name="alternate_contig_graph" ftype="gfa1">
309 <assert_contents>
310 <has_size value="0"/>
311 </assert_contents>
312 </output>
313 </test> 308 </test>
314 <test expect_num_outputs="5"> 309 <test expect_num_outputs="5">
315 <param name="reads" value="hifiasm-in2-0.fa.gz,hifiasm-in2-1.fa.gz,hifiasm-in2-2.fa.gz,hifiasm-in2-3.fa.gz,hifiasm-in2-4.fa.gz" ftype="fasta.gz" /> 310 <param name="reads" value="hifiasm-in2-0.fa.gz,hifiasm-in2-1.fa.gz,hifiasm-in2-2.fa.gz,hifiasm-in2-3.fa.gz,hifiasm-in2-4.fa.gz" ftype="fasta.gz" />
316 <param name="filter_bits" value="0" /> 311 <param name="filter_bits" value="0" />
317 <param name="mode_selector" value="standard" /> 312 <param name="mode_selector" value="standard" />
318 <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1" /> 313 <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1" />
319 <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1" /> 314 <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1" />
320 <output name="primary_contig_graph" file="hifiasm-out2-primary.gfa" ftype="gfa1" /> 315 <output name="primary_contig_graph" file="hifiasm-out2-primary.gfa" ftype="gfa1" />
321 <output name="alternate_contig_graph" ftype="gfa1">
322 <assert_contents>
323 <has_size value="0"/>
324 </assert_contents>
325 </output>
326 </test> 316 </test>
327 <!-- Test logfile out--> 317 <!-- Test logfile out-->
328 <test expect_num_outputs="6"> 318 <test expect_num_outputs="6">
329 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 319 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
330 <param name="filter_bits" value="0" /> 320 <param name="filter_bits" value="0" />
331 <param name="mode_selector" value="standard" /> 321 <param name="mode_selector" value="standard" />
332 <param name="log_out" value="yes"/> 322 <param name="log_out" value="yes"/>
333 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" /> 323 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
334 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" /> 324 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
335 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" /> 325 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />
336 <output name="alternate_contig_graph" ftype="gfa1">
337 <assert_contents>
338 <has_size value="0"/>
339 </assert_contents>
340 </output>
341 <output name="log_file" ftype="txt"> 326 <output name="log_file" ftype="txt">
342 <assert_contents> 327 <assert_contents>
343 <has_line line="[M::main] CMD: hifiasm -t 1 -o output -f 0 --primary input_0.fasta.gz"/> 328 <has_text text="-o output -f 0 --primary input_0.fasta.gz"/>
344 </assert_contents> 329 </assert_contents>
345 </output> 330 </output>
346 </test> 331 </test>
347 <!--Test Hi-C reads--> 332 <!--Test Hi-C reads-->
348 <test expect_num_outputs="6"> 333 <test expect_num_outputs="6">
361 <output name="hic_pcontig_graph" file="hifiasm-out-hifi-p.gfa" ftype="gfa1" /> 346 <output name="hic_pcontig_graph" file="hifiasm-out-hifi-p.gfa" ftype="gfa1" />
362 <output name="hic_acontig_graph" file="hifiasm-out-hifi-a.gfa" ftype="gfa1" /> 347 <output name="hic_acontig_graph" file="hifiasm-out-hifi-a.gfa" ftype="gfa1" />
363 <output name="hic_balanced_contig_hap1_graph" ftype="gfa1"> 348 <output name="hic_balanced_contig_hap1_graph" ftype="gfa1">
364 <assert_contents> 349 <assert_contents>
365 <has_text_matching expression="^S" /> 350 <has_text_matching expression="^S" />
366 <has_size value="59529" delta="500"/> 351 <has_size value="83914" delta="500"/>
367 </assert_contents> 352 </assert_contents>
368 </output> 353 </output>
369 <output name="hic_balanced_contig_hap1_graph" ftype="gfa1" > 354 <output name="hic_balanced_contig_hap1_graph" ftype="gfa1" >
370 <assert_contents> 355 <assert_contents>
371 <has_text_matching expression="^S" /> 356 <has_text_matching expression="^S" />
372 <has_size value="59529" delta="500"/> 357 <has_size value="83914" delta="500"/>
373 </assert_contents> 358 </assert_contents>
374 </output> 359 </output>
375 <output name="hic_raw_initig" ftype="gfa1" > 360 <output name="hic_raw_initig" ftype="gfa1" >
376 <assert_contents> 361 <assert_contents>
377 <has_text_matching expression="^S" /> 362 <has_text_matching expression="^S" />
378 <has_size value="59522" delta="500"/> 363 <has_size value="83904" delta="500"/>
379 </assert_contents> 364 </assert_contents>
380 </output> 365 </output>
381 </test> 366 </test>
382 <!-- Test trio mode --> 367 <!-- Test trio mode -->
383 <test expect_num_outputs="5"> 368 <test expect_num_outputs="5">
388 <param name="hap1_reads" value="paternal.fasta.gz"/> 373 <param name="hap1_reads" value="paternal.fasta.gz"/>
389 <param name="hap2_reads" value="maternal.fasta.gz"/> 374 <param name="hap2_reads" value="maternal.fasta.gz"/>
390 <param name="max_kmers" value="2"/> 375 <param name="max_kmers" value="2"/>
391 <param name="min_kmers" value="5"/> 376 <param name="min_kmers" value="5"/>
392 </conditional> 377 </conditional>
393 <output name="raw_unitigs_trio" ftype="gfa1"> 378 <assert_command>
394 <assert_contents> 379 <has_text text="-1 hap1.yak" />
395 <has_size value="0"/> 380 <has_text text="-2 hap2.yak" />
396 </assert_contents> 381 <has_text text="--primary" />
397 </output> 382 </assert_command>
398 <output name="processed_unitigs_trio" ftype="gfa1">
399 <assert_contents>
400 <has_size value="0"/>
401 </assert_contents>
402 </output>
403 <output name="hap1_contigs">
404 <assert_contents>
405 <has_size value="0"/>
406 </assert_contents>
407 </output>
408 <output name="hap2_contigs">
409 <assert_contents>
410 <has_size value="0"/>
411 </assert_contents>
412 </output>
413 </test> 383 </test>
414 <!-- Test ignore-error-corrected option --> 384 <!-- Test ignore-error-corrected option -->
415 <test expect_num_outputs="5"> 385 <test expect_num_outputs="5">
416 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 386 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
417 <param name="filter_bits" value="0" /> 387 <param name="filter_bits" value="0" />
421 <param name="ignore_error_corrected" value="True"/> 391 <param name="ignore_error_corrected" value="True"/>
422 </conditional> 392 </conditional>
423 <output name="raw_unitigs" file="hifiasm-out3-raw.gfa" ftype="gfa1" /> 393 <output name="raw_unitigs" file="hifiasm-out3-raw.gfa" ftype="gfa1" />
424 <output name="processed_unitigs" file="hifiasm-out3-processed.gfa" ftype="gfa1" /> 394 <output name="processed_unitigs" file="hifiasm-out3-processed.gfa" ftype="gfa1" />
425 <output name="primary_contig_graph" file="hifiasm-out3-primary.gfa" ftype="gfa1" /> 395 <output name="primary_contig_graph" file="hifiasm-out3-primary.gfa" ftype="gfa1" />
426 <output name="alternate_contig_graph" ftype="gfa1">
427 <assert_contents>
428 <has_size value="0"/>
429 </assert_contents>
430 </output>
431 </test> 396 </test>
432 <!-- Test expected haplotype number --> 397 <!-- Test expected haplotype number -->
433 <test expect_num_outputs="5"> 398 <test expect_num_outputs="5">
434 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 399 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
435 <param name="filter_bits" value="0" /> 400 <param name="filter_bits" value="0" />
439 <param name="n_hap" value="1"/> 404 <param name="n_hap" value="1"/>
440 </conditional> 405 </conditional>
441 <output name="raw_unitigs" file="hifiasm-out4-raw.gfa" ftype="gfa1" /> 406 <output name="raw_unitigs" file="hifiasm-out4-raw.gfa" ftype="gfa1" />
442 <output name="processed_unitigs" file="hifiasm-out4-processed.gfa" ftype="gfa1" /> 407 <output name="processed_unitigs" file="hifiasm-out4-processed.gfa" ftype="gfa1" />
443 <output name="primary_contig_graph" file="hifiasm-out4-primary.gfa" ftype="gfa1" /> 408 <output name="primary_contig_graph" file="hifiasm-out4-primary.gfa" ftype="gfa1" />
444 <output name="alternate_contig_graph" ftype="gfa1">
445 <assert_contents>
446 <has_size value="0"/>
447 </assert_contents>
448 </output>
449 </test> 409 </test>
450 <!-- Test min_hist_cnt option --> 410 <!-- Test min_hist_cnt option -->
451 <test expect_num_outputs="5"> 411 <test expect_num_outputs="5">
452 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 412 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
453 <param name="filter_bits" value="0" /> 413 <param name="filter_bits" value="0" />
457 <param name="min_hist_cnt" value="1"/> 417 <param name="min_hist_cnt" value="1"/>
458 </conditional> 418 </conditional>
459 <output name="raw_unitigs" file="hifiasm-out5-raw.gfa" ftype="gfa1" /> 419 <output name="raw_unitigs" file="hifiasm-out5-raw.gfa" ftype="gfa1" />
460 <output name="processed_unitigs" file="hifiasm-out5-processed.gfa" ftype="gfa1" /> 420 <output name="processed_unitigs" file="hifiasm-out5-processed.gfa" ftype="gfa1" />
461 <output name="primary_contig_graph" file="hifiasm-out5-primary.gfa" ftype="gfa1" /> 421 <output name="primary_contig_graph" file="hifiasm-out5-primary.gfa" ftype="gfa1" />
462 <output name="alternate_contig_graph" ftype="gfa1">
463 <assert_contents>
464 <has_size value="0"/>
465 </assert_contents>
466 </output>
467 </test> 422 </test>
468 <!-- Test max_kooc option --> 423 <!-- Test max_kooc option -->
469 <test expect_num_outputs="5"> 424 <test expect_num_outputs="5">
470 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 425 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
471 <param name="filter_bits" value="0" /> 426 <param name="filter_bits" value="0" />
475 <param name="max_kooc" value="21000"/> 430 <param name="max_kooc" value="21000"/>
476 </conditional> 431 </conditional>
477 <output name="raw_unitigs" file="hifiasm-out6-raw.gfa" ftype="gfa1" /> 432 <output name="raw_unitigs" file="hifiasm-out6-raw.gfa" ftype="gfa1" />
478 <output name="processed_unitigs" file="hifiasm-out6-processed.gfa" ftype="gfa1" /> 433 <output name="processed_unitigs" file="hifiasm-out6-processed.gfa" ftype="gfa1" />
479 <output name="primary_contig_graph" file="hifiasm-out6-primary.gfa" ftype="gfa1" /> 434 <output name="primary_contig_graph" file="hifiasm-out6-primary.gfa" ftype="gfa1" />
480 <output name="alternate_contig_graph" ftype="gfa1">
481 <assert_contents>
482 <has_size value="0"/>
483 </assert_contents>
484 </output>
485 </test> 435 </test>
486 <!-- Test hg-size option --> 436 <!-- Test hg-size option -->
487 <test expect_num_outputs="5"> 437 <test expect_num_outputs="5">
488 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 438 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
489 <param name="filter_bits" value="0" /> 439 <param name="filter_bits" value="0" />
493 <param name="hg_size" value="1k"/> 443 <param name="hg_size" value="1k"/>
494 </conditional> 444 </conditional>
495 <output name="raw_unitigs" file="hifiasm-out7-raw.gfa" ftype="gfa1" /> 445 <output name="raw_unitigs" file="hifiasm-out7-raw.gfa" ftype="gfa1" />
496 <output name="processed_unitigs" file="hifiasm-out7-processed.gfa" ftype="gfa1" /> 446 <output name="processed_unitigs" file="hifiasm-out7-processed.gfa" ftype="gfa1" />
497 <output name="primary_contig_graph" file="hifiasm-out7-primary.gfa" ftype="gfa1" /> 447 <output name="primary_contig_graph" file="hifiasm-out7-primary.gfa" ftype="gfa1" />
498 <output name="alternate_contig_graph" ftype="gfa1">
499 <assert_contents>
500 <has_size value="0"/>
501 </assert_contents>
502 </output>
503 </test> 448 </test>
504 <!-- Test ignore-error-corrected option --> 449 <!-- Test ignore-error-corrected option -->
505 <test expect_num_outputs="5"> 450 <test expect_num_outputs="5">
506 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 451 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
507 <param name="filter_bits" value="0" /> 452 <param name="filter_bits" value="0" />
511 <param name="hom-cov" value="1000"/> 456 <param name="hom-cov" value="1000"/>
512 </conditional> 457 </conditional>
513 <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1" /> 458 <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1" />
514 <output name="processed_unitigs" file="hifiasm-out8-processed.gfa" ftype="gfa1" /> 459 <output name="processed_unitigs" file="hifiasm-out8-processed.gfa" ftype="gfa1" />
515 <output name="primary_contig_graph" file="hifiasm-out8-primary.gfa" ftype="gfa1" /> 460 <output name="primary_contig_graph" file="hifiasm-out8-primary.gfa" ftype="gfa1" />
516 <output name="alternate_contig_graph" ftype="gfa1">
517 <assert_contents>
518 <has_size value="0"/>
519 </assert_contents>
520 </output>
521 </test> 461 </test>
522 </tests> 462 </tests>
523 <help><![CDATA[ 463 <help><![CDATA[
524 .. class:: infomark 464 .. class:: infomark
525 465