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comparison flexbar.xml @ 31:d43903772a88 draft

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author jtilman
date Tue, 19 Jun 2018 09:58:57 -0400
parents 18acb52de258
children 4a095317caca
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30:18acb52de258 31:d43903772a88
1 1
2 <!-- Flexbar tool definition for Galaxy, version 2.5 --> 2 <!-- Flexbar tool definition for Galaxy, version 3.4 -->
3 <!-- Author: Johannes Roehr --> 3 <!-- Author: Johannes Roehr -->
4 4
5 5
6 <tool id="flexbar" name="Flexbar" version="2.5" force_history_refresh="True"> 6 <tool id="flexbar" name="Flexbar" version="3.4" force_history_refresh="True">
7 7
8 <description>flexible barcode and adapter removal</description> 8 <description>flexible barcode and adapter removal</description>
9 9
10 <requirements> 10 <requirements>
11 <requirement type="binary" version="2.5">flexbar</requirement> 11 <requirement type="binary" version="3.4">flexbar</requirement>
12 </requirements> 12 </requirements>
13 13
14 <version_command>flexbar --version</version_command> 14 <version_command>flexbar --versions</version_command>
15 15
16 <command interpreter="perl"> 16 <command interpreter="perl">
17 17
18 flexbar.pl flexbar 18 flexbar.pl flexbar
19 19
25 #if $cReads2.reads2.ext == $reads.ext: 25 #if $cReads2.reads2.ext == $reads.ext:
26 --reads2 $cReads2.reads2 26 --reads2 $cReads2.reads2
27 #end if 27 #end if
28 #end if 28 #end if
29 29
30 #if $reads.ext == "fastqsanger":
31 --format sanger
32 #end if
33 #if $reads.ext == "fastqsolexa":
34 --format solexa
35 #end if
36 #if $reads.ext == "fastqillumina":
37 --format i1.3
38 #end if
39 #if $reads.ext == "csfasta":
40 --color-space
41 #end if
42 #if $reads.ext == "fastqcssanger":
43 --color-space
44 #end if
45
46
47 --max-uncalled $maxUncalled 30 --max-uncalled $maxUncalled
48 --min-read-length $minReadLen 31 --min-read-length $minReadLen
49 32
50 #if $trimEnds.select == "on": 33 #if $trimEnds.select == "on":
51 --pre-trim-left $trimEnds.trimLeft 34 --pre-trim-left $trimEnds.trimLeft
52 --pre-trim-right $trimEnds.trimRight 35 --pre-trim-right $trimEnds.trimRight
53 #end if 36 #end if
54 37
55 #if $cTrimPhred.select == "on": 38 #if $cTrimPhred.select == "on":
56 --pre-trim-phred $cTrimPhred.trimPhred 39 --qtrim TAIL --qtrim-threshold $cTrimPhred.trimPhred
40
41 #if $reads.ext == "fastqsanger":
42 --qtrim-format sanger
43 #end if
44 #if $reads.ext == "fastqsolexa":
45 --qtrim-format solexa
46 #end if
47 #if $reads.ext == "fastqillumina":
48 --qtrim-format i1.3
49 #end if
57 #end if 50 #end if
58 51
59 #if $cTrimLen.select == "on": 52 #if $cTrimLen.select == "on":
60 --post-trim-length $cTrimLen.trimLen 53 --post-trim-length $cTrimLen.trimLen
61 #end if 54 #end if
82 75
83 #if $cBarcodes.cbMinOverlap.select == "yes": 76 #if $cBarcodes.cbMinOverlap.select == "yes":
84 --barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap 77 --barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap
85 #end if 78 #end if
86 79
87 --barcode-threshold $cBarcodes.bThresh 80 --barcode-error-rate $cBarcodes.bThresh
88 81
89 #if $cBarcodes.cbAlignScores.select == "yes": 82 #if $cBarcodes.cbAlignScores.select == "yes":
90 --barcode-match $bMatch 83 --barcode-match $bMatch
91 --barcode-mismatch $bMismatch 84 --barcode-mismatch $bMismatch
92 --barcode-gap $bGap 85 --barcode-gap $bGap
111 #end if 104 #end if
112 105
113 $cAdapters.aReadSet 106 $cAdapters.aReadSet
114 107
115 --adapter-min-overlap $cAdapters.aMinOverlap 108 --adapter-min-overlap $cAdapters.aMinOverlap
116 --adapter-threshold $cAdapters.aThresh 109 --adapter-error-rate $cAdapters.aThresh
117 110
118 #if $cAdapters.caAlignScores.select == "yes": 111 #if $cAdapters.caAlignScores.select == "yes":
119 --adapter-match $aMatch 112 --adapter-match $aMatch
120 --adapter-mismatch $aMismatch 113 --adapter-mismatch $aMismatch
121 --adapter-gap $aGap 114 --adapter-gap $aGap
142 </command> 135 </command>
143 136
144 137
145 <inputs> 138 <inputs>
146 139
147 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/> 140 <param format="fastq,fastqsanger,fastqsolexa,fastqillumina" name="reads" type="data" label="Reads fastq file" optional="false"/>
148 141
149 142
150 <conditional name="cReads2"> 143 <conditional name="cReads2">
151 <param name="select" type="select" label="2nd read set (paired)"> 144 <param name="select" type="select" label="Paired reads file">
152 <option value="off" selected="true">Off</option> 145 <option value="off" selected="true">Off</option>
153 <option value="on">On</option> 146 <option value="on">On</option>
154 </param> 147 </param>
155 <when value="off"> 148 <when value="off">
156 </when> 149 </when>
157 <when value="on"> 150 <when value="on">
158 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/> 151 <param format="fastq,fastqsanger,fastqsolexa,fastqillumina" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/>
159 </when> 152 </when>
160 </conditional> 153 </conditional>
161 154
162 155
163 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/> 156 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/>
174 <param name="trimRight" size="4" type="integer" value="0" label="Right" optional="false" help="trims specified number of bases from read ends"/> 167 <param name="trimRight" size="4" type="integer" value="0" label="Right" optional="false" help="trims specified number of bases from read ends"/>
175 </when> 168 </when>
176 </conditional> 169 </conditional>
177 170
178 <conditional name="cTrimPhred"> 171 <conditional name="cTrimPhred">
179 <param name="select" type="select" label="3) Phred-trimming"> 172 <param name="select" type="select" label="3) Quality-based trimming">
180 <option value="off" selected="true">Off</option> 173 <option value="off" selected="true">Off</option>
181 <option value="on">On</option> 174 <option value="on">On</option>
182 </param> 175 </param>
183 <when value="off"> 176 <when value="off">
184 </when> 177 </when>
202 <param name="select" type="select" label="Separate barcode reads"> 195 <param name="select" type="select" label="Separate barcode reads">
203 <option value="no" selected="true">No</option> 196 <option value="no" selected="true">No</option>
204 <option value="yes">Yes</option> 197 <option value="yes">Yes</option>
205 </param> 198 </param>
206 <when value="yes"> 199 <when value="yes">
207 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/> 200 <param format="fastq,fastqsanger,fastqsolexa,fastqillumina" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
208 </when> 201 </when>
209 <when value="no"> 202 <when value="no">
210 <param name="bKeep" type="select" label="Remove barcodes within reads"> 203 <param name="bKeep" type="select" label="Remove barcodes within reads">
211 <option value="" selected="true">Yes</option> 204 <option value="" selected="true">Yes</option>
212 <option value="--barcode-keep">No</option> 205 <option value="--barcode-keep">No</option>
220 </param> 213 </param>
221 214
222 <param name="bTrimEnd" type="select" label="Trim-end mode" optional="false"> 215 <param name="bTrimEnd" type="select" label="Trim-end mode" optional="false">
223 <option value="ANY" selected="true">Any</option> 216 <option value="ANY" selected="true">Any</option>
224 <option value="RIGHT">Right</option> 217 <option value="RIGHT">Right</option>
225 <option value="RIGHT_TAIL">Right tail</option> 218 <option value="RTAIL">Right tail</option>
226 <option value="LEFT">Left</option> 219 <option value="LEFT">Left</option>
227 <option value="LEFT_TAIL">Left tail</option> 220 <option value="LTAIL">Left tail</option>
228 </param> 221 </param>
229 222
230 <conditional name="cbTailLen"> 223 <conditional name="cbTailLen">
231 <param name="select" type="select" label="Change tail length"> 224 <param name="select" type="select" label="Change tail length">
232 <option value="no" selected="true">No</option> 225 <option value="no" selected="true">No</option>
297 </conditional> 290 </conditional>
298 291
299 <param name="aTrimEnd" type="select" label="Trim-end mode" optional="false"> 292 <param name="aTrimEnd" type="select" label="Trim-end mode" optional="false">
300 <option value="ANY">Any</option> 293 <option value="ANY">Any</option>
301 <option value="RIGHT" selected="true">Right</option> 294 <option value="RIGHT" selected="true">Right</option>
302 <option value="RIGHT_TAIL">Right tail</option> 295 <option value="RTAIL">Right tail</option>
303 <option value="LEFT">Left</option> 296 <option value="LEFT">Left</option>
304 <option value="LEFT_TAIL">Left tail</option> 297 <option value="LTAIL">Left tail</option>
305 </param> 298 </param>
306 299
307 <conditional name="caTailLen"> 300 <conditional name="caTailLen">
308 <param name="select" type="select" label="Change tail length"> 301 <param name="select" type="select" label="Change tail length">
309 <option value="no" selected="true">No</option> 302 <option value="no" selected="true">No</option>
333 <when value="no"> 326 <when value="no">
334 </when> 327 </when>
335 <when value="yes"> 328 <when value="yes">
336 <param name="aMatch" size="3" type="integer" value="1" label="Match" optional="false"/> 329 <param name="aMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
337 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/> 330 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
338 <param name="aGap" size="3" type="integer" value="-7" label="Gap" optional="false"/> 331 <param name="aGap" size="3" type="integer" value="-6" label="Gap" optional="false"/>
339 </when> 332 </when>
340 </conditional> 333 </conditional>
341 </when> 334 </when>
342 </conditional> 335 </conditional>
343 336
389 <when value="off"> 382 <when value="off">
390 </when> 383 </when>
391 <when value="show"> 384 <when value="show">
392 <param name="logLevel" type="select" label="Alignment logging"> 385 <param name="logLevel" type="select" label="Alignment logging">
393 <option value="" selected="true">Off</option> 386 <option value="" selected="true">Off</option>
394 <option value="--log-level ALL">All</option> 387 <option value="--align-log ALL">All</option>
395 <option value="--log-level MOD">Modified</option> 388 <option value="--align-log MOD">Modified</option>
396 <option value="--log-level TAB">Tabular</option> 389 <option value="--align-log TAB">Tabular</option>
397 </param> 390 </param>
398 391
399 <param name="numTags" type="select" label="Number tags"> 392 <param name="numTags" type="select" label="Number tags">
400 <option value="" selected="true">Off</option> 393 <option value="" selected="true">Off</option>
401 <option value="--number-tags">On</option> 394 <option value="--number-tags">On</option>
404 <param name="remTags" type="select" label="Removal tags"> 397 <param name="remTags" type="select" label="Removal tags">
405 <option value="" selected="true">Off</option> 398 <option value="" selected="true">Off</option>
406 <option value="--removal-tags">On</option> 399 <option value="--removal-tags">On</option>
407 </param> 400 </param>
408 401
409 <param name="rndTags" type="select" label="Random tags"> 402 <param name="rndTags" type="select" label="UMI tags">
410 <option value="" selected="true">Off</option> 403 <option value="" selected="true">Off</option>
411 <option value="--random-tags">On</option> 404 <option value="--umi-tags">On</option>
412 </param> 405 </param>
413 </when> 406 </when>
414 </conditional> 407 </conditional>
415 408
416 </inputs> 409 </inputs>
426 419
427 <help> 420 <help>
428 421
429 **Description** 422 **Description**
430 423
431 Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform. Flexbar is available on the project_ page. 424 The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. Unique molecular identifiers can be extracted in a flexible way. The program supports sequencing data in fastq format, e.g. from the Illumina platform. Flexbar is available on the project_ page.
432 425
433 .. _project: https://github.com/seqan/flexbar 426 .. _project: https://github.com/seqan/flexbar
434 427
435 ------ 428 ------
436 429
448 441
449 ------ 442 ------
450 443
451 **Documentation** 444 **Documentation**
452 445
453 Further documentation is available on the `manual`__ wiki page and via the command line help screen. 446 Further documentation is available on the `manual`__ page and via the command line help screen.
454 447
455 .. __: https://github.com/seqan/flexbar/wiki 448 .. __: https://github.com/seqan/flexbar/wiki
456 449
457 ------ 450 ------
458 451
459 **Reference** 452 **References**
460 453
461 Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905. 454 Johannes T. Roehr, Christoph Dieterich, Knut Reinert:
455 Flexbar 3.0 – SIMD and multicore parallelization. Bioinformatics 2017.
456
457 Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich:
458 Flexbar – flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012.
462 459
463 </help> 460 </help>
464 461
465 </tool> 462 </tool>
466 463