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comparison flye.xml @ 11:291923e6f276 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
author bgruening
date Mon, 18 Mar 2024 12:44:09 +0000
parents cb8dfd28c16f
children 3e4f8642c77e
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10:cb8dfd28c16f 11:291923e6f276
1 <tool id="flye" name="Flye" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01"> 1 <tool id="flye" name="Flye" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
2 <description>de novo assembler for single molecule sequencing reads</description> 2 <description>de novo assembler for single molecule sequencing reads</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/>
7 <expand macro="xrefs"/>
6 <expand macro="requirements" /> 8 <expand macro="requirements" />
7 <expand macro="edam_ontology"/>
8 <version_command>flye --version</version_command> 9 <version_command>flye --version</version_command>
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 #for $counter, $input in enumerate($inputs): 11 #for $counter, $input in enumerate($inputs):
11 #if $input.is_of_type('fastqsanger', 'fastq'): 12 #if $input.is_of_type('fastqsanger', 'fastq'):
12 #set $ext = 'fastq' 13 #set $ext = 'fastq'
15 #elif $input.is_of_type('fasta.gz'): 16 #elif $input.is_of_type('fasta.gz'):
16 #set $ext = 'fasta.gz' 17 #set $ext = 'fasta.gz'
17 #elif $input.is_of_type('fasta'): 18 #elif $input.is_of_type('fasta'):
18 #set $ext = 'fasta' 19 #set $ext = 'fasta'
19 #end if 20 #end if
20 ln -s '$input' ./input_${counter}.${ext} && 21 ln -sf '$input' ./input_${counter}.${ext} &&
21 #end for 22 #end for
22 flye 23 flye
23 $mode_conditional.mode 24 $mode_conditional.mode
24 #for $counter, $input in enumerate($inputs): 25 #for $counter, $input in enumerate($inputs):
25 ./input_${counter}.$ext 26 ./input_${counter}.$ext
226 <has_size value="1248" delta="100"/> 227 <has_size value="1248" delta="100"/>
227 </assert_contents> 228 </assert_contents>
228 </output> 229 </output>
229 <output name="assembly_gfa" ftype="txt"> 230 <output name="assembly_gfa" ftype="txt">
230 <assert_contents> 231 <assert_contents>
231 <has_size value="420252" delta="100"/> 232 <has_size value="419414" delta="100"/>
232 </assert_contents> 233 </assert_contents>
233 </output> 234 </output>
234 <output name="consensus" ftype="fasta"> 235 <output name="consensus" ftype="fasta">
235 <assert_contents> 236 <assert_contents>
236 <has_size value="427129" delta="100"/> 237 <has_size value="426277" delta="100"/>
237 </assert_contents> 238 </assert_contents>
238 </output> 239 </output>
239 </test> 240 </test>
240 <!--Test 06: hifi error option--> 241 <!--Test 06: hifi error option-->
241 <test expect_num_outputs="4"> 242 <test expect_num_outputs="4">
250 <has_size value="286" delta="100"/> 251 <has_size value="286" delta="100"/>
251 </assert_contents> 252 </assert_contents>
252 </output> 253 </output>
253 <output name="assembly_graph" ftype="graph_dot"> 254 <output name="assembly_graph" ftype="graph_dot">
254 <assert_contents> 255 <assert_contents>
255 <has_size value="1273" delta="100"/> 256 <has_size value="1500" delta="100"/>
256 </assert_contents> 257 </assert_contents>
257 </output> 258 </output>
258 <output name="assembly_gfa" ftype="txt"> 259 <output name="assembly_gfa" ftype="txt">
259 <assert_contents> 260 <assert_contents>
260 <has_size value="420252" delta="100"/> 261 <has_size value="418422" delta="100"/>
261 </assert_contents> 262 </assert_contents>
262 </output> 263 </output>
263 <output name="consensus" ftype="fasta"> 264 <output name="consensus" ftype="fasta">
264 <assert_contents> 265 <assert_contents>
265 <has_size value="427129" delta="100"/> 266 <has_size value="425147" delta="200"/>
266 </assert_contents> 267 </assert_contents>
267 </output> 268 </output>
268 </test> 269 </test>
269 <!--Test 07: keep haplotypes--> 270 <!--Test 07: keep haplotypes-->
270 <test expect_num_outputs="4"> 271 <test expect_num_outputs="4">
285 <has_size value="1273" delta="100"/> 286 <has_size value="1273" delta="100"/>
286 </assert_contents> 287 </assert_contents>
287 </output> 288 </output>
288 <output name="assembly_gfa" ftype="txt"> 289 <output name="assembly_gfa" ftype="txt">
289 <assert_contents> 290 <assert_contents>
290 <has_size value="420252" delta="100"/> 291 <has_size value="418511" delta="100"/>
291 </assert_contents> 292 </assert_contents>
292 </output> 293 </output>
293 <output name="consensus" ftype="fasta"> 294 <output name="consensus" ftype="fasta">
294 <assert_contents> 295 <assert_contents>
295 <has_size value="427129" delta="100"/> 296 <has_size value="425267" delta="100"/>
296 </assert_contents> 297 </assert_contents>
297 </output> 298 </output>
298 </test> 299 </test>
299 <!--Test 08: scaffolding mode--> 300 <!--Test 08: scaffolding mode-->
300 <test expect_num_outputs="4"> 301 <test expect_num_outputs="4">
301 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/> 302 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
302 <param name="mode" value="--nano-hq"/> 303 <param name="mode" value="--nano-hq"/>
303 <param name="min_overlap" value="1000"/> 304 <param name="min_overlap" value="1000"/>
304 <param name="scaffolding" value="true"/> 305 <param name="scaffold" value="true"/>
305 <output name="assembly_info" ftype="tabular"> 306 <output name="assembly_info" ftype="tabular">
306 <assert_contents> 307 <assert_contents>
307 <has_size value="286" delta="100"/> 308 <has_size value="286" delta="100"/>
308 </assert_contents> 309 </assert_contents>
309 </output> 310 </output>
312 <has_size value="1248" delta="100"/> 313 <has_size value="1248" delta="100"/>
313 </assert_contents> 314 </assert_contents>
314 </output> 315 </output>
315 <output name="assembly_gfa" ftype="txt"> 316 <output name="assembly_gfa" ftype="txt">
316 <assert_contents> 317 <assert_contents>
317 <has_size value="420252" delta="100"/> 318 <has_size value="419414" delta="1000"/>
318 </assert_contents> 319 </assert_contents>
319 </output> 320 </output>
320 <output name="consensus" ftype="fasta"> 321 <output name="consensus" ftype="fasta">
321 <assert_contents> 322 <assert_contents>
322 <has_size value="427129" delta="100"/> 323 <has_size value="426277" delta="1000"/>
323 </assert_contents> 324 </assert_contents>
324 </output> 325 </output>
325 </test> 326 </test>
326 <!--Test 09: test not-alt-contigs parameter w--> 327 <!--Test 09: test not-alt-contigs parameter w-->
327 <test expect_num_outputs="4"> 328 <test expect_num_outputs="4">
351 </output> 352 </output>
352 </test> 353 </test>
353 </tests> 354 </tests>
354 <help><![CDATA[ 355 <help><![CDATA[
355 356
356 .. class:: infomark
357
358 **Purpose** 357 **Purpose**
359 358
360 Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. 359 Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.
361 It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents 360 It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents
362 a complete pipeline: it takes raw PacBio/ONT reads as input and outputs polished contigs. Flye also has a special mode for metagenome 361 a complete pipeline: it takes raw PacBio/ONT reads as input and outputs polished contigs. Flye also has a special mode for metagenome
363 assembly. 362 assembly.
364 363
365 ---- 364 ----
366 365
367 .. class:: infomark
368
369 **Quick usage** 366 **Quick usage**
370 367
371 Input reads can be in FASTA or FASTQ format, uncompressed or compressed with gz. Currently, PacBio (raw, corrected, HiFi) and ONT reads 368 Input reads can be in FASTA or FASTQ format, uncompressed or compressed with gz. Currently, PacBio (raw, corrected, HiFi) and ONT reads
372 (raw, corrected) are supported. Expected error rates are <30% for raw, <3% for corrected, and <1% for HiFi. Note that Flye was primarily 369 (raw, corrected) are supported. Expected error rates are <30% for raw, <3% for corrected, and <1% for HiFi. Note that Flye was primarily
373 developed to run on raw reads. You may specify multiple files with reads (separated by spaces). Mixing different read types is not yet supported. The *--meta* o 370 developed to run on raw reads. You may specify multiple files with reads (separated by spaces). Mixing different read types is not yet supported. The *--meta* o
378 To reduce memory consumption for large genome assemblies, you can use a subset of the longest reads for initial disjointig assembly by 375 To reduce memory consumption for large genome assemblies, you can use a subset of the longest reads for initial disjointig assembly by
379 specifying *--asm-coverage* and *--genome-size* options. Typically, 40x coverage is enough to produce good disjointigs. 376 specifying *--asm-coverage* and *--genome-size* options. Typically, 40x coverage is enough to produce good disjointigs.
380 377
381 ---- 378 ----
382 379
383 .. class:: infomark
384
385 **Outputs** 380 **Outputs**
386 381
387 The main output files are: 382 The main output files are:
388 383
389 :: 384 * Final assembly: contains contigs and possibly scaffolds (see below).
390 385 * Final repeat graph: note that the edge sequences might be different (shorter) than contig sequences, because contigs might include multiple graph edges.
391 - Final assembly: contains contigs and possibly scaffolds (see below). 386 * Extra information about contigs (such as length or coverage).
392 - Final repeat graph: note that the edge sequences might be different (shorter) than contig sequences, because contigs might include multiple graph edges.
393 - Extra information about contigs (such as length or coverage).
394 387
395 Each contig is formed by a single unique graph edge. If possible, unique contigs are extended with the sequence from flanking unresolved repeats on the graph. Thus, 388 Each contig is formed by a single unique graph edge. If possible, unique contigs are extended with the sequence from flanking unresolved repeats on the graph. Thus,
396 a contig fully contains the corresponding graph edge (with the same id), but might be longer then this edge. This is somewhat similar to unitig-contig relation in 389 a contig fully contains the corresponding graph edge (with the same id), but might be longer then this edge. This is somewhat similar to unitig-contig relation in
397 OLC assemblers. In a rare case when a repetitive graph edge is not covered by the set of "extended" contigs, it will be also output in the assembly file. 390 OLC assemblers. In a rare case when a repetitive graph edge is not covered by the set of "extended" contigs, it will be also output in the assembly file.
398 391
400 the assembly file (with a scaffold prefix). Since it is hard to give a reliable estimate of the gap size, those gaps are represented with the default 100 Ns. 393 the assembly file (with a scaffold prefix). Since it is hard to give a reliable estimate of the gap size, those gaps are represented with the default 100 Ns.
401 assembly_info.txt file (below) contains additional information about how scaffolds were formed. 394 assembly_info.txt file (below) contains additional information about how scaffolds were formed.
402 395
403 Extra information about contigs/scaffolds is output into the assembly_info.txt file. It is a tab-delimited table with the columns as follows: 396 Extra information about contigs/scaffolds is output into the assembly_info.txt file. It is a tab-delimited table with the columns as follows:
404 397
405 :: 398 * Contig/scaffold id
406 399 * Length
407 - Contig/scaffold id 400 * Coverage
408 - Length 401 * Is circular, (Y)es or (N)o
409 - Coverage 402 * Is repetitive, (Y)es or (N)o
410 - Is circular, (Y)es or (N)o 403 * Multiplicity (based on coverage)
411 - Is repetitive, (Y)es or (N)o 404 * Alternative group
412 - Multiplicity (based on coverage) 405 * Graph path (graph path corresponding to this contig/scaffold).
413 - Alternative group 406
414 - Graph path (graph path corresponding to this contig/scaffold). 407 Scaffold gaps are marked with `??` symbols, and `*` symbol denotes a terminal graph node. Alternative contigs (representing alternative haplotypes) will have the same alt.
415 408 group ID. Primary contigs are marked by `*`.
416 Scaffold gaps are marked with ?? symbols, and * symbol denotes a terminal graph node. Alternative contigs (representing alternative haplotypes) will have the same alt.
417 group ID. Primary contigs are marked by *.
418 409
419 ---- 410 ----
420 411
421 .. class:: infomark
422
423 **Algorithm Description** 412 **Algorithm Description**
424 413
425 This is a brief description of the Flye algorithm. Please refer to the manuscript for more detailed information. The draft contig extension is organized as follows: 414 This is a brief description of the Flye algorithm. Please refer to the manuscript for more detailed information. The draft contig extension is organized as follows:
426 415
427 :: 416 * K-mer counting / erroneous k-mer pre-filtering
428 417 * Solid k-mer selection (k-mers with sufficient frequency, which are unlikely to be erroneous)
429 - K-mer counting / erroneous k-mer pre-filtering 418 * Contig extension. The algorithm starts from a single read and extends it with a next overlapping read (overlaps are dynamically detected using the selected solid k-mers).
430 - Solid k-mer selection (k-mers with sufficient frequency, which are unlikely to be erroneous)
431 - Contig extension. The algorithm starts from a single read and extends it with a next overlapping read (overlaps are dynamically detected using the selected solid k-mers).
432 419
433 Note that we do not attempt to resolve repeats at this stage, thus the reconstructed contigs might contain misassemblies. Flye then aligns the reads on these draft 420 Note that we do not attempt to resolve repeats at this stage, thus the reconstructed contigs might contain misassemblies. Flye then aligns the reads on these draft
434 contigs using minimap2 and calls a consensus. Afterwards, Flye performs repeat analysis as follows: 421 contigs using minimap2 and calls a consensus. Afterwards, Flye performs repeat analysis as follows:
435 422
436 :: 423 * Repeat graph is constructed from the (possibly misassembled) contigs
437 424 * In this graph all repeats longer than minimum overlap are collapsed
438 - Repeat graph is constructed from the (possibly misassembled) contigs 425 * The algorithm resolves repeats using the read information and graph structure
439 - In this graph all repeats longer than minimum overlap are collapsed 426 * The unbranching paths in the graph are output as contigs
440 - The algorithm resolves repeats using the read information and graph structure
441 - The unbranching paths in the graph are output as contigs
442 427
443 If enabled, after resolving bridged repeats, Trestle module attempts to resolve simple unbridged repeats (of multiplicity 2) using the heterogeneities between repeat copies. 428 If enabled, after resolving bridged repeats, Trestle module attempts to resolve simple unbridged repeats (of multiplicity 2) using the heterogeneities between repeat copies.
444 Finally, Flye performs polishing of the resulting assembly to correct the remaining errors: 429 Finally, Flye performs polishing of the resulting assembly to correct the remaining errors:
445 430
446 :: 431 * Alignment of all reads to the current assembly using minimap2
447 432 * Partition the alignment into mini-alignments (bubbles)
448 - Alignment of all reads to the current assembly using minimap2 433 * Error correction of each bubble using a maximum likelihood approach
449 - Partition the alignment into mini-alignments (bubbles)
450 - Error correction of each bubble using a maximum likelihood approach
451
452 434
453 The polishing steps could be repeated, which might slightly increase quality for some datasets. 435 The polishing steps could be repeated, which might slightly increase quality for some datasets.
454 436
455 437
456 ]]></help> 438 ]]></help>