Mercurial > repos > bgruening > hifiasm
comparison hifiasm.xml @ 10:2061fb3b81b4 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
author | bgruening |
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date | Tue, 24 Jan 2023 17:46:39 +0000 |
parents | c388a21dcbf1 |
children | cd7936c5a9a5 |
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9:c388a21dcbf1 | 10:2061fb3b81b4 |
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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@">0.18.5</token> | 4 <token name="@TOOL_VERSION@">0.18.5</token> |
5 <token name="@VERSION_SUFFIX@">0</token> | 5 <token name="@VERSION_SUFFIX@">1</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> |
19 #set $input_files = list() | 19 #set $input_files = list() |
20 #set $hap1_inputs = list() | 20 #set $hap1_inputs = list() |
21 #set $hap2_inputs = list() | 21 #set $hap2_inputs = list() |
22 #set $hic1_inputs = list() | 22 #set $hic1_inputs = list() |
23 #set $hic2_inputs = list() | 23 #set $hic2_inputs = list() |
24 #set $ultralong_inputs = list() | |
24 #for idx, read in enumerate($mode.reads): | 25 #for idx, read in enumerate($mode.reads): |
25 #set $inputfile = 'input_%d.%s' % ($idx, $read.dataset.extension) | 26 #set $inputfile = 'input_%d.%s' % ($idx, $read.dataset.extension) |
26 ln -s '$read' $inputfile && | 27 ln -s '$read' $inputfile && |
27 $input_files.append($inputfile) | 28 $input_files.append($inputfile) |
28 #end for | 29 #end for |
38 #set $inputfile = './HiCR/input_%d.%s' % ($idx, $read.dataset.extension) | 39 #set $inputfile = './HiCR/input_%d.%s' % ($idx, $read.dataset.extension) |
39 ln -s '$read' $inputfile && | 40 ln -s '$read' $inputfile && |
40 $hic2_inputs.append($inputfile) | 41 $hic2_inputs.append($inputfile) |
41 #end for | 42 #end for |
42 #end if | 43 #end if |
44 #if str($ont_integration.ont_integration_selector) == 'set' | |
45 mkdir ultralong && | |
46 #for idx, read in enumerate($ont_integration.ul): | |
47 #set $inputfile = './ultralong/input_%d.%s' % ($idx, $read.dataset.extension) | |
48 ln -s '$read' $inputfile && | |
49 $ultralong_inputs.append($inputfile) | |
50 #end for | |
51 #end if | |
43 #if str($mode.mode_selector) == 'trio': | 52 #if str($mode.mode_selector) == 'trio': |
44 #for idx, read in enumerate($mode.hap1_reads): | 53 #for idx, read in enumerate($mode.hap1_reads): |
45 #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension) | 54 #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension) |
46 ln -s '$read' $inputfile && | 55 ln -s '$read' $inputfile && |
47 $hap1_inputs.append($inputfile) | 56 $hap1_inputs.append($inputfile) |
106 --n-hap $purge_options.n_hap | 115 --n-hap $purge_options.n_hap |
107 #end if | 116 #end if |
108 #end if | 117 #end if |
109 | 118 |
110 #if str($hic_partition.hic_partition_selector) == 'set': | 119 #if str($hic_partition.hic_partition_selector) == 'set': |
111 --h1 '${ ' '.join(["%s" % $x for $x in $hic1_inputs]) }' | 120 --h1 ${ ' '.join(["'%s'" % $x for $x in $hic1_inputs]) } |
112 --h2 '${ ' '.join(["%s" % $x for $x in $hic2_inputs]) }' | 121 --h2 ${ ' '.join(["'%s'" % $x for $x in $hic2_inputs]) } |
113 #if $hic_partition.seed: | 122 #if $hic_partition.seed: |
114 --seed $hic_partition.seed | 123 --seed $hic_partition.seed |
115 #end if | 124 #end if |
116 #if $hic_partition.n_weight: | 125 #if $hic_partition.n_weight: |
117 --n-weight $hic_partition.n_weight | 126 --n-weight $hic_partition.n_weight |
121 #end if | 130 #end if |
122 #if $hic_partition.f_perturb: | 131 #if $hic_partition.f_perturb: |
123 --f-perturb $hic_partition.f_perturb | 132 --f-perturb $hic_partition.f_perturb |
124 #end if | 133 #end if |
125 --l-msjoin $hic_partition.l_msjoin | 134 --l-msjoin $hic_partition.l_msjoin |
135 #end if | |
136 | |
137 #if str($ont_integration.ont_integration_selector) == 'set': | |
138 --ul ${ ' '.join(["'%s'" % $x for $x in $ultralong_inputs]) } | |
139 #if $ont_integration.ul_rate: | |
140 --ul-rate $ont_integration.ul_rate | |
141 #end if | |
142 #if $ont_integration.ul_tip: | |
143 --ul-tip $ont_integration.ul_tip | |
144 #end if | |
126 #end if | 145 #end if |
127 | 146 |
128 ## Changed the default outputs of hifiasm. Hifiasm outputs a primary assembly and two balanced haplotypes in default. Incorporated the option '--primary' to output primary assembly and alternate assembly. | 147 ## Changed the default outputs of hifiasm. Hifiasm outputs a primary assembly and two balanced haplotypes in default. Incorporated the option '--primary' to output primary assembly and alternate assembly. |
129 --primary | 148 --primary |
130 $input_filenames | 149 $input_filenames |
203 <param argument="--seed" type="integer" min="1" value="" optional="true" label="RNG seed" /> | 222 <param argument="--seed" type="integer" min="1" value="" optional="true" label="RNG seed" /> |
204 <param argument="--n-weight" type="integer" min="1" value="" optional="true" label="Rounds of reweighting Hi-C links. Increasing this may improves phasing results but takes longer time" /> | 223 <param argument="--n-weight" type="integer" min="1" value="" optional="true" label="Rounds of reweighting Hi-C links. Increasing this may improves phasing results but takes longer time" /> |
205 <param argument="--n-perturb" type="integer" min="1" value="" optional="true" label="Rounds of perturbation. Increasing this may improves phasing results but takes longer time" /> | 224 <param argument="--n-perturb" type="integer" min="1" value="" optional="true" label="Rounds of perturbation. Increasing this may improves phasing results but takes longer time" /> |
206 <param argument="--f-perturb" type="float" min="0" max="1" value="" optional="true" label="Fraction to flip for perturbation. Increasing this may improves phasing results but takes longer time" /> | 225 <param argument="--f-perturb" type="float" min="0" max="1" value="" optional="true" label="Fraction to flip for perturbation. Increasing this may improves phasing results but takes longer time" /> |
207 <param argument="--l-msjoin" type="integer" min="0" value="500000" label="Detect misjoined unitigs of greater than or equal to specified size" help="A value of 0 disables this filter"/> | 226 <param argument="--l-msjoin" type="integer" min="0" value="500000" label="Detect misjoined unitigs of greater than or equal to specified size" help="A value of 0 disables this filter"/> |
227 </when> | |
228 </conditional> | |
229 <conditional name="ont_integration"> | |
230 <param name="ont_integration_selector" type="select" label="Options for ONT integration"> | |
231 <option value="blank">Leave default</option> | |
232 <option value="set">Specify</option> | |
233 </param> | |
234 <when value="blank" /> | |
235 <when value="set"> | |
236 <param argument="--ul" type="data" format="fastq,fastq.gz,fasta,fasta.gz" multiple="true" label="Ultra-long (>10kb) reads" /> | |
237 <param argument="--ul-rate" type="float" value="0.2" optional="true" label="error rate of ultra-long reads (default 0.2)" /> | |
238 <param argument="--ul-tip" type="integer" value="6" optional="true" label="remove tip unitigs composed of less than (INT) reads for the UL assembly (default 6)" /> | |
208 </when> | 239 </when> |
209 </conditional> | 240 </conditional> |
210 <conditional name="advanced_options"> | 241 <conditional name="advanced_options"> |
211 <param name="advanced_selector" type="select" label="Advanced options"> | 242 <param name="advanced_selector" type="select" label="Advanced options"> |
212 <option value="blank">Leave default</option> | 243 <option value="blank">Leave default</option> |
296 <collection name="noseq_files" type="list" label="${tool.name} on ${on_string}: noseq files"> | 327 <collection name="noseq_files" type="list" label="${tool.name} on ${on_string}: noseq files"> |
297 <discover_datasets pattern="__name_and_ext__" format="gfa1" directory="noseq_files" /> | 328 <discover_datasets pattern="__name_and_ext__" format="gfa1" directory="noseq_files" /> |
298 </collection> | 329 </collection> |
299 </outputs> | 330 </outputs> |
300 <tests> | 331 <tests> |
332 <!-- TEST 1 --> | |
301 <test expect_num_outputs="5"> | 333 <test expect_num_outputs="5"> |
302 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> | 334 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> |
303 <param name="filter_bits" value="0" /> | 335 <param name="filter_bits" value="0" /> |
304 <param name="mode_selector" value="standard" /> | 336 <param name="mode_selector" value="standard" /> |
305 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" /> | 337 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" /> |
306 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" /> | 338 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" /> |
307 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" /> | 339 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" /> |
308 </test> | 340 </test> |
341 <!-- TEST 2 --> | |
309 <test expect_num_outputs="5"> | 342 <test expect_num_outputs="5"> |
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" /> | 343 <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" /> |
311 <param name="filter_bits" value="0" /> | 344 <param name="filter_bits" value="0" /> |
312 <param name="mode_selector" value="standard" /> | 345 <param name="mode_selector" value="standard" /> |
313 <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1" /> | 346 <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1" /> |
314 <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1" /> | 347 <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1" /> |
315 <output name="primary_contig_graph" file="hifiasm-out2-primary.gfa" ftype="gfa1" /> | 348 <output name="primary_contig_graph" file="hifiasm-out2-primary.gfa" ftype="gfa1" /> |
316 </test> | 349 </test> |
317 <!-- Test logfile out--> | 350 <!-- TEST 3: Test logfile out--> |
318 <test expect_num_outputs="6"> | 351 <test expect_num_outputs="6"> |
319 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> | 352 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> |
320 <param name="filter_bits" value="0" /> | 353 <param name="filter_bits" value="0" /> |
321 <param name="mode_selector" value="standard" /> | 354 <param name="mode_selector" value="standard" /> |
322 <param name="log_out" value="yes"/> | 355 <param name="log_out" value="yes"/> |
327 <assert_contents> | 360 <assert_contents> |
328 <has_text text="-o output -f 0 --primary input_0.fasta.gz"/> | 361 <has_text text="-o output -f 0 --primary input_0.fasta.gz"/> |
329 </assert_contents> | 362 </assert_contents> |
330 </output> | 363 </output> |
331 </test> | 364 </test> |
332 <!--Test Hi-C reads--> | 365 <!--TEST 4: Test Hi-C reads--> |
333 <test expect_num_outputs="6"> | 366 <test expect_num_outputs="6"> |
334 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> | 367 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> |
335 <param name="filter_bits" value="0" /> | 368 <param name="filter_bits" value="0" /> |
336 <param name="mode_selector" value="standard" /> | 369 <param name="mode_selector" value="standard" /> |
337 <conditional name="hic_partition"> | 370 <conditional name="hic_partition"> |
362 <has_text_matching expression="^S" /> | 395 <has_text_matching expression="^S" /> |
363 <has_size value="83904" delta="500"/> | 396 <has_size value="83904" delta="500"/> |
364 </assert_contents> | 397 </assert_contents> |
365 </output> | 398 </output> |
366 </test> | 399 </test> |
367 <!-- Test trio mode --> | 400 <!-- TEST 5: Test trio mode --> |
368 <test expect_num_outputs="5"> | 401 <test expect_num_outputs="5"> |
369 <param name="filter_bits" value="0"/> | 402 <param name="filter_bits" value="0"/> |
370 <conditional name="mode"> | 403 <conditional name="mode"> |
371 <param name="mode_selector" value="trio"/> | 404 <param name="mode_selector" value="trio"/> |
372 <param name="reads" value="child.fasta.gz"/> | 405 <param name="reads" value="child.fasta.gz"/> |
379 <has_text text="-1 hap1.yak" /> | 412 <has_text text="-1 hap1.yak" /> |
380 <has_text text="-2 hap2.yak" /> | 413 <has_text text="-2 hap2.yak" /> |
381 <has_text text="--primary" /> | 414 <has_text text="--primary" /> |
382 </assert_command> | 415 </assert_command> |
383 </test> | 416 </test> |
384 <!-- Test ignore-error-corrected option --> | 417 <!-- TEST 6: Test ignore-error-corrected option --> |
385 <test expect_num_outputs="5"> | 418 <test expect_num_outputs="5"> |
386 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> | 419 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> |
387 <param name="filter_bits" value="0" /> | 420 <param name="filter_bits" value="0" /> |
388 <param name="mode_selector" value="standard" /> | 421 <param name="mode_selector" value="standard" /> |
389 <conditional name="assembly_options"> | 422 <conditional name="assembly_options"> |
392 </conditional> | 425 </conditional> |
393 <output name="raw_unitigs" file="hifiasm-out3-raw.gfa" ftype="gfa1" /> | 426 <output name="raw_unitigs" file="hifiasm-out3-raw.gfa" ftype="gfa1" /> |
394 <output name="processed_unitigs" file="hifiasm-out3-processed.gfa" ftype="gfa1" /> | 427 <output name="processed_unitigs" file="hifiasm-out3-processed.gfa" ftype="gfa1" /> |
395 <output name="primary_contig_graph" file="hifiasm-out3-primary.gfa" ftype="gfa1" /> | 428 <output name="primary_contig_graph" file="hifiasm-out3-primary.gfa" ftype="gfa1" /> |
396 </test> | 429 </test> |
397 <!-- Test expected haplotype number --> | 430 <!-- TEST 7: Test expected haplotype number --> |
398 <test expect_num_outputs="5"> | 431 <test expect_num_outputs="5"> |
399 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> | 432 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> |
400 <param name="filter_bits" value="0" /> | 433 <param name="filter_bits" value="0" /> |
401 <param name="mode_selector" value="standard" /> | 434 <param name="mode_selector" value="standard" /> |
402 <conditional name="purge_options"> | 435 <conditional name="purge_options"> |
405 </conditional> | 438 </conditional> |
406 <output name="raw_unitigs" file="hifiasm-out4-raw.gfa" ftype="gfa1" /> | 439 <output name="raw_unitigs" file="hifiasm-out4-raw.gfa" ftype="gfa1" /> |
407 <output name="processed_unitigs" file="hifiasm-out4-processed.gfa" ftype="gfa1" /> | 440 <output name="processed_unitigs" file="hifiasm-out4-processed.gfa" ftype="gfa1" /> |
408 <output name="primary_contig_graph" file="hifiasm-out4-primary.gfa" ftype="gfa1" /> | 441 <output name="primary_contig_graph" file="hifiasm-out4-primary.gfa" ftype="gfa1" /> |
409 </test> | 442 </test> |
410 <!-- Test min_hist_cnt option --> | 443 <!-- TEST 8: Test min_hist_cnt option --> |
411 <test expect_num_outputs="5"> | 444 <test expect_num_outputs="5"> |
412 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> | 445 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> |
413 <param name="filter_bits" value="0" /> | 446 <param name="filter_bits" value="0" /> |
414 <param name="mode_selector" value="standard" /> | 447 <param name="mode_selector" value="standard" /> |
415 <conditional name="advanced_options"> | 448 <conditional name="advanced_options"> |
418 </conditional> | 451 </conditional> |
419 <output name="raw_unitigs" file="hifiasm-out5-raw.gfa" ftype="gfa1" /> | 452 <output name="raw_unitigs" file="hifiasm-out5-raw.gfa" ftype="gfa1" /> |
420 <output name="processed_unitigs" file="hifiasm-out5-processed.gfa" ftype="gfa1" /> | 453 <output name="processed_unitigs" file="hifiasm-out5-processed.gfa" ftype="gfa1" /> |
421 <output name="primary_contig_graph" file="hifiasm-out5-primary.gfa" ftype="gfa1" /> | 454 <output name="primary_contig_graph" file="hifiasm-out5-primary.gfa" ftype="gfa1" /> |
422 </test> | 455 </test> |
423 <!-- Test max_kooc option --> | 456 <!-- TEST 9: Test max_kooc option --> |
424 <test expect_num_outputs="5"> | 457 <test expect_num_outputs="5"> |
425 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> | 458 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> |
426 <param name="filter_bits" value="0" /> | 459 <param name="filter_bits" value="0" /> |
427 <param name="mode_selector" value="standard" /> | 460 <param name="mode_selector" value="standard" /> |
428 <conditional name="advanced_options"> | 461 <conditional name="advanced_options"> |
431 </conditional> | 464 </conditional> |
432 <output name="raw_unitigs" file="hifiasm-out6-raw.gfa" ftype="gfa1" /> | 465 <output name="raw_unitigs" file="hifiasm-out6-raw.gfa" ftype="gfa1" /> |
433 <output name="processed_unitigs" file="hifiasm-out6-processed.gfa" ftype="gfa1" /> | 466 <output name="processed_unitigs" file="hifiasm-out6-processed.gfa" ftype="gfa1" /> |
434 <output name="primary_contig_graph" file="hifiasm-out6-primary.gfa" ftype="gfa1" /> | 467 <output name="primary_contig_graph" file="hifiasm-out6-primary.gfa" ftype="gfa1" /> |
435 </test> | 468 </test> |
436 <!-- Test hg-size option --> | 469 <!-- TEST 10: Test hg-size option --> |
437 <test expect_num_outputs="5"> | 470 <test expect_num_outputs="5"> |
438 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> | 471 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> |
439 <param name="filter_bits" value="0" /> | 472 <param name="filter_bits" value="0" /> |
440 <param name="mode_selector" value="standard" /> | 473 <param name="mode_selector" value="standard" /> |
441 <conditional name="advanced_options"> | 474 <conditional name="advanced_options"> |
444 </conditional> | 477 </conditional> |
445 <output name="raw_unitigs" file="hifiasm-out7-raw.gfa" ftype="gfa1" /> | 478 <output name="raw_unitigs" file="hifiasm-out7-raw.gfa" ftype="gfa1" /> |
446 <output name="processed_unitigs" file="hifiasm-out7-processed.gfa" ftype="gfa1" /> | 479 <output name="processed_unitigs" file="hifiasm-out7-processed.gfa" ftype="gfa1" /> |
447 <output name="primary_contig_graph" file="hifiasm-out7-primary.gfa" ftype="gfa1" /> | 480 <output name="primary_contig_graph" file="hifiasm-out7-primary.gfa" ftype="gfa1" /> |
448 </test> | 481 </test> |
449 <!-- Test ignore-error-corrected option --> | 482 <!-- TEST 11: Test ignore-error-corrected option --> |
450 <test expect_num_outputs="5"> | 483 <test expect_num_outputs="5"> |
451 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> | 484 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> |
452 <param name="filter_bits" value="0" /> | 485 <param name="filter_bits" value="0" /> |
453 <param name="mode_selector" value="standard" /> | 486 <param name="mode_selector" value="standard" /> |
454 <conditional name="assembly_options"> | 487 <conditional name="assembly_options"> |
456 <param name="hom-cov" value="1000"/> | 489 <param name="hom-cov" value="1000"/> |
457 </conditional> | 490 </conditional> |
458 <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1" /> | 491 <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1" /> |
459 <output name="processed_unitigs" file="hifiasm-out8-processed.gfa" ftype="gfa1" /> | 492 <output name="processed_unitigs" file="hifiasm-out8-processed.gfa" ftype="gfa1" /> |
460 <output name="primary_contig_graph" file="hifiasm-out8-primary.gfa" ftype="gfa1" /> | 493 <output name="primary_contig_graph" file="hifiasm-out8-primary.gfa" ftype="gfa1" /> |
494 </test> | |
495 <!-- TEST 12: test nanopore input --> | |
496 <test expect_num_outputs="5"> | |
497 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> | |
498 <param name="mode_selector" value="standard" /> | |
499 <param name="filter_bits" value="0" /> | |
500 <conditional name="ont_integration"> | |
501 <param name="ont_integration_selector" value="set" /> | |
502 <param name="ul" value="nanopore.first5.fasta.gz" /> | |
503 <param name="ul_tip" value="1" /> | |
504 </conditional> | |
505 <output name="primary_contig_graph" file="hifiasm-out-hifiul.bp.p_ctg.gfa" ftype="gfa1" /> | |
506 <output name="raw_unitigs" file="hifiasm-out-hifiul.bp.r_utg.gfa" ftype="gfa1" /> | |
461 </test> | 507 </test> |
462 </tests> | 508 </tests> |
463 <help><![CDATA[ | 509 <help><![CDATA[ |
464 .. class:: infomark | 510 .. class:: infomark |
465 | 511 |