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comparison minimap2.xml @ 12:037c6e54df11 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
author iuc
date Fri, 28 May 2021 21:09:55 +0000
parents f54f5baedfdd
children 1f06dccdc5d1
comparison
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11:f54f5baedfdd 12:037c6e54df11
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy4" profile="17.01"> 2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description> 3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
4 <macros> 4 <macros>
5 <token name="@TOOL_VERSION@">2.17</token> 5 <import>macros.xml</import>
6 <xml name="pe_anaylsis_fixed_selector">
7 <param name="analysis_type_selector" type="select"
8 label="Presets for PE reads alignment"
9 help="These are the minimap2 preset options for PE alignment of short reads. You can customize these and other settings in the indexing, mapping and alignment options sections below.">
10 <option value="sr">Short reads without splicing (-k21 -w11 --sr -F800 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no) (sr)</option>
11 </param>
12 </xml>
13 </macros> 6 </macros>
14 <requirements> 7 <expand macro="edam_ontology"/>
15 <requirement type="package" version="@TOOL_VERSION@">minimap2</requirement> 8 <expand macro="requirements"/>
16 <requirement type="package" version="1.9">samtools</requirement> 9 <expand macro="pe_anaylsis_fixed_selector"/>
17 </requirements>
18 <stdio> 10 <stdio>
19 <exit_code range="1:" level="fatal" /> 11 <exit_code range="1:" level="fatal" />
20 <regex match="\[ERROR\]" source="stderr" level="fatal" /> 12 <regex match="\[ERROR\]" source="stderr" level="fatal" />
21 </stdio> 13 </stdio>
22 <version_command>minimap2 --version</version_command> 14 <version_command>minimap2 --version</version_command>
76 -p $mapping_options.p 68 -p $mapping_options.p
77 #end if 69 #end if
78 #if str($mapping_options.N): 70 #if str($mapping_options.N):
79 -N $mapping_options.N 71 -N $mapping_options.N
80 #end if 72 #end if
81 73 #if str($mapping_options.mask_len):
74 --mask-len $mapping_options.mask_len
75 #end if
76 #if str($mapping_options.kmer_ocurrence_interval.interval):
77 -U $mapping_options.kmer_ocurrence_interval.lower_limit,$mapping_options.kmer_ocurrence_interval.upper_limit
78 #end if
82 ## Alignment options 79 ## Alignment options
83 #if str($alignment_options.splicing.splice_mode) == '--splice': 80 #if str($alignment_options.splicing.splice_mode) == '--splice':
84 --frag=no --splice 81 --frag=no --splice
85 #if str($alignment_options.splicing.G): 82 #if str($alignment_options.splicing.G):
86 -G $alignment_options.splicing.G 83 -G $alignment_options.splicing.G
207 <param name="analysis_type_selector" type="select" optional="True" 204 <param name="analysis_type_selector" type="select" optional="True"
208 label="Select a profile of preset options" 205 label="Select a profile of preset options"
209 help="Each profile comes with the preconfigured settings mentioned in parentheses. You can customize each profile further in the indexing, mapping and alignment options sections below. If you do not select a profile here, the tool will use the per-parameter defaults listed in the below sections unless you customize them." > 206 help="Each profile comes with the preconfigured settings mentioned in parentheses. You can customize each profile further in the indexing, mapping and alignment options sections below. If you do not select a profile here, the tool will use the per-parameter defaults listed in the below sections unless you customize them." >
210 <option value="map-pb">PacBio/Oxford Nanopore read to reference mapping (-Hk19) (map-pb)</option> 207 <option value="map-pb">PacBio/Oxford Nanopore read to reference mapping (-Hk19) (map-pb)</option>
211 <option value="map-ont">Oxford Nanopore read to reference mapping. Slightly more sensitive for Oxford Nanopore to reference mapping (-k15). For PacBio reads, HPC minimizers consistently leads to faster performance and more sensitive results in comparison to normal minimizers. For Oxford Nanopore data, normal minimizers are better, though not much. The effectiveness of HPC is determined by the sequencing error mode. (map-ont)</option> 208 <option value="map-ont">Oxford Nanopore read to reference mapping. Slightly more sensitive for Oxford Nanopore to reference mapping (-k15). For PacBio reads, HPC minimizers consistently leads to faster performance and more sensitive results in comparison to normal minimizers. For Oxford Nanopore data, normal minimizers are better, though not much. The effectiveness of HPC is determined by the sequencing error mode. (map-ont)</option>
209 <option value="map-hifi">PacBio HiFi reads vs reference mapping (-k19 -w19 -U50,500 -g10k -A1 -B4 -O6,26 -E2,1 -s200 ) (map-hifi)</option>
212 <option value="ava-pb">PacBio all-vs-all overlap mapping (-Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25) (ava-pb)</option> 210 <option value="ava-pb">PacBio all-vs-all overlap mapping (-Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25) (ava-pb)</option>
213 <option value="ava-ont">Oxford Nanopore all-vs-all overlap mapping (-k15 -Xw5 -m100 -g10000 -r2000 --max-chain-skip 25). Similarly, the major difference from ava-pb is that this preset is not using HPC minimizers. (ava-ont)</option> 211 <option value="ava-ont">Oxford Nanopore all-vs-all overlap mapping (-k15 -Xw5 -m100 -g10000 -r2000 --max-chain-skip 25). Similarly, the major difference from ava-pb is that this preset is not using HPC minimizers. (ava-ont)</option>
214 <option value="asm5">Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100). Typically, the alignment will not extend to regions with 5% or higher sequence divergence. Only use this preset if the average divergence is far below 5%. (asm5)</option> 212 <option value="asm5">Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100). Typically, the alignment will not extend to regions with 5% or higher sequence divergence. Only use this preset if the average divergence is far below 5%. (asm5)</option>
215 <option value="asm10">Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 10% sequence divergence. (asm10)</option> 213 <option value="asm10">Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 10% sequence divergence. (asm10)</option>
216 <option value="asm20">Long assembly to reference mapping (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence. (asm20)</option> 214 <option value="asm20">Long assembly to reference mapping (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence. (asm20)</option>
234 <expand macro="pe_anaylsis_fixed_selector" /> 232 <expand macro="pe_anaylsis_fixed_selector" />
235 </when> 233 </when>
236 </conditional> 234 </conditional>
237 <section name="indexing_options" title="Indexing options"> 235 <section name="indexing_options" title="Indexing options">
238 <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/> 236 <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
239 <param argument="-k" type="integer" min="4" max="28" optional="true" label="k-mer size" help=""/> 237 <param argument="-k" type="integer" min="4" max="28" optional="true" label="K-mer size" help=""/>
240 <param argument="-w" type="integer" min="1" optional="true" label="minimizer window size" help=""/> 238 <param argument="-w" type="integer" min="1" optional="true" label="Minimizer window size" help=""/>
241 <param argument="-I" type="integer" min="1" optional="true" label="split index for every N input gigabases" help=""/> 239 <param argument="-I" type="integer" min="1" optional="true" label="Split index for every N input gigabases" help=""/>
242 </section> 240 </section>
243 <section name="mapping_options" title="Mapping options" help="Sets -f, -g, -F, -r, -n, -m, -X, -p, -N and --min-occ-floor options." expanded="False"> 241 <section name="mapping_options" title="Mapping options" help="Sets -f, -g, -F, -r, -n, -m, -X, -p, -N and --min-occ-floor options." expanded="False">
244 <param argument="-N" type="integer" min="0" optional="true" label="retain at most INT secondary alignments" help="default=5"/> 242 <param argument="-N" type="integer" min="0" optional="true" label="Retain at most INT secondary alignments" help="default=5"/>
245 <param argument="-F" type="integer" min="0" value="" optional="true" 243 <param argument="-F" type="integer" min="0" value="" optional="true"
246 label="Max fragment length for PE alignment" 244 label="Max fragment length for PE alignment"
247 help="The maximum apparent fragment length up to which paired-end reads are aligned together; at higher fragment lengths the mates will be aligned independent of each other; effective only for paired-end data and when spliced alignment mode is turned off; default=800" /> 245 help="The maximum apparent fragment length up to which paired-end reads are aligned together; at higher fragment lengths the mates will be aligned independent of each other; effective only for paired-end data and when spliced alignment mode is turned off; default=800" />
248 <param argument="-f" type="float" value="" optional="true" label="filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/> 246 <param argument="-f" type="float" value="" optional="true" label="Filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/>
249 <param argument="--min-occ-floor" name="min_occ_floor" type="integer" label="force minimap2 to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" /> 247 <conditional name="kmer_ocurrence_interval">
250 <param argument="-g" type="integer" value="" optional="true" label="stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/> 248 <param name="interval" argument="-U" type="select" label="Specify an interval of k-mer occurrences" help="Allows to specify an interval of k-mer occurrences with -U. For repeat-rich genomes, the automatic k-mer occurrence threshold determined by -f may be too large and makes alignment impractically slow. The new option protects against such cases. Enabled for asm* and map-hifi.">
251 <param argument="-r" type="integer" value="" optional="true" label="bandwidth used in chaining and DP-based alignment" help="default=500" /> 249 <option value="enabled">Enabled</option>
252 <param argument="-n" type="integer" value="" optional="true" label="minimal number of minimizers on a chain" help="default=3"/> 250 <option value="" selected="true">Disabled</option>
253 <param argument="-m" type="integer" value="" optional="true" label="minimal chaining score (matching bases minus log gap penalty)" help="default=40"/> 251 </param>
252 <when value="enabled">
253 <param name="lower_limit" type="integer" min="0" max="10000" value="" label="K-mer ocurrence lower limit"/>
254 <param name="upper_limit" type="integer" min="0" max="10000" value="" label="K-mer ocurrence upper limit"/>
255 </when>
256 <when value="">
257 </when>
258 </conditional>
259 <param argument="--min-occ-floor" name="min_occ_floor" type="integer" label="Force minimap2 to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" />
260 <param argument="-g" type="integer" value="" optional="true" label="Stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/>
261 <param argument="-r" type="integer" value="" optional="true" label="Bandwidth used in chaining and DP-based alignment" help="default=500" />
262 <param argument="-n" type="integer" value="" optional="true" label="Minimal number of minimizers on a chain" help="default=3"/>
263 <param argument="-m" type="integer" value="" optional="true" label="Minimal chaining score (matching bases minus log gap penalty)" help="default=40"/>
254 <param argument="--max-chain-skip" type="integer" value="" optional="true" 264 <param argument="--max-chain-skip" type="integer" value="" optional="true"
255 label="Maximum seed skips during chaining" 265 label="Maximum seed skips during chaining"
256 help="A heuristics that stops chaining early. Minimap2 uses dynamic programming for chaining. The time complexity is quadratic in the number of seeds. This option makes minimap2 exit the inner loop if it repeatedly sees seeds already on chains. Set to a large number to switch off this heurstics effectively. default=25" /> 266 help="A heuristics that stops chaining early. Minimap2 uses dynamic programming for chaining. The time complexity is quadratic in the number of seeds. This option makes minimap2 exit the inner loop if it repeatedly sees seeds already on chains. Set to a large number to switch off this heurstics effectively. default=25" />
257 <param argument="--max-chain-iter" type="integer" value="" optional="true" 267 <param argument="--max-chain-iter" type="integer" value="" optional="true"
258 label="Maximum number of partial chains checked during chaining" 268 label="Maximum number of partial chains checked during chaining"
259 help="A heuristics to avoid quadratic time complexity in the worst case. default=5000" /> 269 help="A heuristics to avoid quadratic time complexity in the worst case. default=5000" />
260 <param argument="-X" type="boolean" truevalue="-X" falsevalue="" optional="true" label="skip self and dual mappings (for the all-vs-all mode)"/> 270 <param argument="-X" type="boolean" truevalue="-X" falsevalue="" optional="true" label="Skip self and dual mappings (for the all-vs-all mode)"/>
261 <param argument="-p" type="float" value="" max="1" optional="true" label="min secondary-to-primary score ratio" help="default=0.8"/> 271 <param argument="-p" type="float" value="" max="1" optional="true" label="Min secondary-to-primary score ratio" help="default=0.8"/>
272 <param argument="--mask-len" type="integer" min="0" max="10000" value="" optional="true" label="Fine control the removal of redundant hits" help="Keep an alignment if dropping it leaves an unaligned region on query longer than INT"/>
262 </section> 273 </section>
263 <section name="alignment_options" title="Alignment options" help="Sets -A, -B, -O, -E, -z, -s, and spliced alignments options." expanded="False"> 274 <section name="alignment_options" title="Alignment options" help="Sets -A, -B, -O, -E, -z, -s, and spliced alignments options." expanded="False">
264 <conditional name="splicing"> 275 <conditional name="splicing">
265 <param name="splice_mode" type="select" 276 <param name="splice_mode" type="select"
266 label="Customize spliced alignment mode?" 277 label="Customize spliced alignment mode?"
277 help="Higher values cause slower spliced alignment. When in use, this option causes -r (in mapping options) to be set to the same value. default=200k" /> 288 help="Higher values cause slower spliced alignment. When in use, this option causes -r (in mapping options) to be set to the same value. default=200k" />
278 <param argument="-C" type="integer" min="0" optional="true" 289 <param argument="-C" type="integer" min="0" optional="true"
279 label="Cost of non-canonical (non-GT-AG) splicing" 290 label="Cost of non-canonical (non-GT-AG) splicing"
280 help="default=0" /> 291 help="default=0" />
281 <param argument="-u" type="select" optional="true" 292 <param argument="-u" type="select" optional="true"
282 label="how to find GT-AG" 293 label="How to find GT-AG"
283 help="default=n (don't match GT-AG)"> 294 help="default=n (don't match GT-AG)">
284 <option value="n">don't match GT-AG (-un)</option> 295 <option value="n">Don't match GT-AG (-un)</option>
285 <option value="f">transcript strand (-uf)</option> 296 <option value="f">Transcript strand (-uf)</option>
286 <option value="b">both strands (-ub)</option> 297 <option value="b">Both strands (-ub)</option>
287 </param> 298 </param>
288 <param argument="--splice-flank" type="boolean" truevalue="--splice-flank=yes" falsevalue="--splice-flank=no" checked="true" 299 <param argument="--splice-flank" type="boolean" truevalue="--splice-flank=yes" falsevalue="--splice-flank=no" checked="true"
289 label="Assume conserved flanking region of splice sites?" 300 label="Assume conserved flanking region of splice sites?"
290 help="Assume the next base to a GT donor site tends to be A/G (91% in human and 92% in mouse) and the preceding base to a AG acceptor tends to be C/T. This trend is evolutionarily conserved, all the way to S. cerevisiae (PMID:18688272). Specifying this option generally leads to higher junction accuracy by several percents, so it is applied by default with --splice. However, the SIRV control does not honor this trend (only ~60%) so this option reduces accuracy. If you are benchmarking minimap2 on SIRV data, please disable this option." /> 301 help="Assume the next base to a GT donor site tends to be A/G (91% in human and 92% in mouse) and the preceding base to a AG acceptor tends to be C/T. This trend is evolutionarily conserved, all the way to S. cerevisiae (PMID:18688272). Specifying this option generally leads to higher junction accuracy by several percents, so it is applied by default with --splice. However, the SIRV control does not honor this trend (only ~60%) so this option reduces accuracy. If you are benchmarking minimap2 on SIRV data, please disable this option." />
291 <conditional name="splice_site_annotations"> 302 <conditional name="splice_site_annotations">
326 help="Increase to improve the contiguity of alignments at the cost of poorer alignments in the middle. default=400" /> 337 help="Increase to improve the contiguity of alignments at the cost of poorer alignments in the middle. default=400" />
327 <param name="z2" type="integer" min="0" optional="true" 338 <param name="z2" type="integer" min="0" optional="true"
328 label="Z-drop threshold for reverse-complementing the query" 339 label="Z-drop threshold for reverse-complementing the query"
329 help="Decrease to find small inversions at the cost of performance and false positives. default=200" /> 340 help="Decrease to find small inversions at the cost of performance and false positives. default=200" />
330 <param argument="-s" type="integer" min="0" optional="true" 341 <param argument="-s" type="integer" min="0" optional="true"
331 label="minimal peak DP alignment score" help="default=80"/> 342 label="Minimal peak DP alignment score" help="default=80"/>
332 <param name="no_end_flt" type="boolean" falsevalue="--no-end-flt" truevalue="" checked="true" 343 <param name="no_end_flt" type="boolean" falsevalue="--no-end-flt" truevalue="" checked="true"
333 label="Filter seeds towards the ends of chains before performing base-level alignment?" /> 344 label="Filter seeds towards the ends of chains before performing base-level alignment?" />
334 </section> 345 </section>
335 <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False"> 346 <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False">
336 <param name="output_format" type="select" label="Select an output format"> 347 <param name="output_format" type="select" label="Select an output format">
337 <option value="BAM">BAM</option> 348 <option value="BAM">BAM</option>
338 <option value="CRAM">CRAM</option> 349 <option value="CRAM">CRAM</option>
339 <option value="paf">paf</option> 350 <option value="paf">PAF</option>
340 </param> 351 </param>
341 <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" label="don't output base quality"/> 352 <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" label="Don't output base quality"/>
342 <param argument="-L" type="boolean" truevalue="-L" falsevalue="" label="write CIGAR with >65535 ops to the CG tag" help="Useful for very long reads in SAM/BAM format"/> 353 <param argument="-L" type="boolean" truevalue="-L" falsevalue="" label="Write CIGAR with >65535 ops to the CG tag" help="Useful for very long reads in SAM/BAM format"/>
343 <param argument="-K" type="integer" optional="true" label="minibatch size for mapping (in megabyte)" help="default=500M"/> 354 <param argument="-K" type="integer" optional="true" label="Minibatch size for mapping (in megabyte)" help="default=500M"/>
344 <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below."> 355 <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below.">
345 <option value="none">no</option> 356 <option value="none">no</option>
346 <option value="short">short</option> 357 <option value="short">short</option>
347 <option value="long">long</option> 358 <option value="long">long</option>
348 </param> 359 </param>
349 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" label="Generate CIGAR" 360 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" label="Generate CIGAR"
350 help="In PAF, the CIGAR is written to the ‘cg’ custom tag." /> 361 help="In PAF, the CIGAR is written to the ‘cg’ custom tag." />
351 362
352 <param argument="--eqx" type="boolean" truevalue="--eqx" falsevalue="" label="write =/X CIGAR operators"/> 363 <param argument="--eqx" type="boolean" truevalue="--eqx" falsevalue="" label="Write =/X CIGAR operators"/>
353 <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="use soft clipping for supplementary alignments ?"/> 364 <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="Use soft clipping for supplementary alignments ?"/>
354 </section> 365 </section>
355 </inputs> 366 </inputs>
356 <outputs> 367 <outputs>
357 <data format="bam" name="alignment_output" label="${tool.name} on ${on_string} (mapped reads in ${io_options.output_format} format)"> 368 <data format="bam" name="alignment_output" label="${tool.name} on ${on_string} (mapped reads in ${io_options.output_format} format)">
358 <actions> 369 <actions>
478 <param name="fastq_input_selector" value="single" /> 489 <param name="fastq_input_selector" value="single" />
479 <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" /> 490 <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" />
480 <param name="analysis_type_selector" value="self-homology" /> 491 <param name="analysis_type_selector" value="self-homology" />
481 <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="2" /> 492 <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="2" />
482 </test> 493 </test>
494 <test>
495 <!-- test mask-len option -->
496 <param name="reference_source_selector" value="history" />
497 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
498 <param name="fastq_input_selector" value="single"/>
499 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
500 <param name="analysis_type_selector" value="sr"/>
501 <section name="mapping_options">
502 <param name="mask_len" value="100"/>
503 </section>
504 <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="2" />
505 </test>
506 <test>
507 <!-- test map-hifi -->
508 <param name="reference_source_selector" value="history" />
509 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/>
510 <param name="fastq_input_selector" value="single"/>
511 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
512 <param name="analysis_type_selector" value="map-hifi"/>
513 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="2" />
514 </test>
515 <test>
516 <!-- test kmer ocurrence interval option -->
517 <param name="reference_source_selector" value="history" />
518 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
519 <param name="fastq_input_selector" value="single"/>
520 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
521 <param name="analysis_type_selector" value="sr"/>
522 <conditional name="kmer_ocurrence_interval">
523 <param name="interval" value="enabled"/>
524 <param name="lower_limit" value="10"/>
525 <param name="upper_limit" value="30"/>
526 </conditional>
527 <output name="alignment_output" ftype="bam" file="minimap2-test-kmer_ocurrence.bam" lines_diff="2" />
528 </test>
483 </tests> 529 </tests>
484 <help> 530 <help>
485 531
486 Users’ Guide 532 Users’ Guide
487 ------------ 533 ------------
543 minimizers improve performance and sensitivity when aligning PacBio 589 minimizers improve performance and sensitivity when aligning PacBio
544 reads, but hurt when aligning Nanopore reads. 590 reads, but hurt when aligning Nanopore reads.
545 591
546 Map long mRNA/cDNA reads 592 Map long mRNA/cDNA reads
547 ^^^^^^^^^^^^^^^^^^^^^^^^ 593 ^^^^^^^^^^^^^^^^^^^^^^^^
548
549 594
550 There are different long-read RNA-seq technologies, including 595 There are different long-read RNA-seq technologies, including
551 tranditional full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq 596 tranditional full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq
552 and Direct RNA-seq. They produce data of varying quality and properties. 597 and Direct RNA-seq. They produce data of varying quality and properties.
553 By default, ``-x splice`` assumes the read orientation relative to the 598 By default, ``-x splice`` assumes the read orientation relative to the
579 may try to add ``-a`` or ``-c`` anyway. 624 may try to add ``-a`` or ``-c`` anyway.
580 625
581 Map short accurate genomic reads 626 Map short accurate genomic reads
582 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 627 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
583 628
584
585 When two read files are specified, minimap2 reads from each file in turn 629 When two read files are specified, minimap2 reads from each file in turn
586 and merge them into an interleaved stream internally. Two reads are 630 and merge them into an interleaved stream internally. Two reads are
587 considered to be paired if they are adjacent in the input stream and 631 considered to be paired if they are adjacent in the input stream and
588 have the same name (with the ``/[0-9]`` suffix trimmed if present). 632 have the same name (with the ``/[0-9]`` suffix trimmed if present).
589 Single- and paired-end reads can be mixed. 633 Single- and paired-end reads can be mixed.
709 - Minimap2 may produce suboptimal alignments through long 753 - Minimap2 may produce suboptimal alignments through long
710 low-complexity regions where seed positions may be suboptimal. This 754 low-complexity regions where seed positions may be suboptimal. This
711 should not be a big concern because even the optimal alignment may be 755 should not be a big concern because even the optimal alignment may be
712 wrong in such regions. 756 wrong in such regions.
713 </help> 757 </help>
714 <citations> 758 <expand macro="citations"/>
715 <citation type="doi">10.1093/bioinformatics/btp324</citation>
716 <citation type="doi">10.1093/bioinformatics/btp698</citation>
717 <citation type="bibtex">@misc{1303.3997,
718 Author = {Heng Li},
719 Title = {Minimap2: fast pairwise alignment for long nucleotide sequences},
720 Year = {2017},
721 Eprint = {arXiv:1708.01492},
722 url = {https://arxiv.org/abs/1708.01492},
723 }</citation>
724 </citations>
725 </tool> 759 </tool>