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author rnateam
date Fri, 27 Nov 2015 04:33:02 -0500
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12:55b539a509f0 13:258b6f9e19ab
1
2 <!-- Flexbar tool definition for Galaxy, version 2.5 -->
3 <!-- Author: Johannes Roehr -->
4 <!-- Modified by Daniel Maticzka -->
5 <!-- * changed dependency to use separate flexbar package -->
6
7 <tool id="flexbar" name="Flexbar" version="2.5" force_history_refresh="True">
8
9 <description>flexible barcode and adapter removal</description>
10
11 <requirements>
12 <requirement type="package" version="2.5">flexbar</requirement>
13 </requirements>
14
15 <version_command>flexbar --version</version_command>
16
17 <command interpreter="perl">
18
19 flexbar.pl flexbar
20
21 --threads \${GALAXY_SLOTS:-1}
22
23 --reads $reads
24
25 #if $cReads2.select == "on":
26 #if $cReads2.reads2.ext == $reads.ext:
27 --reads2 $cReads2.reads2
28 #end if
29 #end if
30
31 #if $reads.ext == "fastqsanger":
32 --format sanger
33 #end if
34 #if $reads.ext == "fastqsolexa":
35 --format solexa
36 #end if
37 #if $reads.ext == "fastqillumina":
38 --format i1.3
39 #end if
40 #if $reads.ext == "csfasta":
41 --color-space
42 #end if
43 #if $reads.ext == "fastqcssanger":
44 --color-space
45 #end if
46
47
48 --max-uncalled $maxUncalled
49 --min-read-length $minReadLen
50
51 #if $trimEnds.select == "on":
52 --pre-trim-left $trimEnds.trimLeft
53 --pre-trim-right $trimEnds.trimRight
54 #end if
55
56 #if $cTrimPhred.select == "on":
57 --pre-trim-phred $cTrimPhred.trimPhred
58 #end if
59
60 #if $cTrimLen.select == "on":
61 --post-trim-length $cTrimLen.trimLen
62 #end if
63
64
65 #if $cBarcodes.select == "on":
66 --barcodes $cBarcodes.barcodes
67
68 #if $cBarcodes.cbReads.select == "yes":
69 --barcode-reads $cBarcodes.cbReads.bReads
70 #end if
71
72 #if $cBarcodes.cbReads.select == "no":
73 $cBarcodes.cbReads.bKeep
74 #end if
75
76 $cBarcodes.bUnassigned
77
78 --barcode-trim-end $cBarcodes.bTrimEnd
79
80 #if $cBarcodes.cbTailLen.select == "yes":
81 --barcode-tail-length $cBarcodes.cbTailLen.bTailLen
82 #end if
83
84 #if $cBarcodes.cbMinOverlap.select == "yes":
85 --barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap
86 #end if
87
88 --barcode-threshold $cBarcodes.bThresh
89
90 #if $cBarcodes.cbAlignScores.select == "yes":
91 --barcode-match $bMatch
92 --barcode-mismatch $bMismatch
93 --barcode-gap $bGap
94 #end if
95 #end if
96
97
98 #if $cAdapters.select == "on":
99
100 #if $cAdapters.ccAdapters.select == "data":
101 --adapters $cAdapters.ccAdapters.adaptersData
102 #end if
103
104 #if $cAdapters.ccAdapters.select == "seq":
105 --adapter-seq $cAdapters.ccAdapters.adapterSeq
106 #end if
107
108 --adapter-trim-end $cAdapters.aTrimEnd
109
110 #if $cAdapters.caTailLen.select == "yes":
111 --adapter-tail-length $cAdapters.caTailLen.aTailLen
112 #end if
113
114 $cAdapters.aReadSet
115
116 --adapter-min-overlap $cAdapters.aMinOverlap
117 --adapter-threshold $cAdapters.aThresh
118
119 #if $cAdapters.caAlignScores.select == "yes":
120 --adapter-match $aMatch
121 --adapter-mismatch $aMismatch
122 --adapter-gap $aGap
123 #end if
124 #end if
125
126
127 #if $cOutput.select == "show":
128 $cOutput.fastaOutput
129 $cOutput.lenDist
130 $cOutput.singleReads
131 #end if
132
133 #if $cLogging.select == "show":
134 $cLogging.logLevel
135 $cLogging.numTags
136 $cLogging.remTags
137 $cLogging.rndTags
138 #end if
139
140
141 $output $output.id $__new_file_path__ $reads.ext
142
143 </command>
144
145
146 <inputs>
147
148 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
149
150
151 <conditional name="cReads2">
152 <param name="select" type="select" label="2nd read set (paired)">
153 <option value="off" selected="true">Off</option>
154 <option value="on">On</option>
155 </param>
156 <when value="off">
157 </when>
158 <when value="on">
159 <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"/>
160 </when>
161 </conditional>
162
163
164 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/>
165
166 <conditional name="trimEnds">
167 <param name="select" type="select" label="2) Trimming of ends">
168 <option value="off" selected="true">Off</option>
169 <option value="on">On</option>
170 </param>
171 <when value="off">
172 </when>
173 <when value="on">
174 <param name="trimLeft" size="4" type="integer" value="0" label="Left" optional="false"/>
175 <param name="trimRight" size="4" type="integer" value="0" label="Right" optional="false" help="trims specified number of bases from read ends"/>
176 </when>
177 </conditional>
178
179 <conditional name="cTrimPhred">
180 <param name="select" type="select" label="3) Phred-trimming">
181 <option value="off" selected="true">Off</option>
182 <option value="on">On</option>
183 </param>
184 <when value="off">
185 </when>
186 <when value="on">
187 <param name="trimPhred" size="4" type="integer" value="10" label="Threshold" optional="false" help="trim right end until specified or higher quality reached"/>
188 </when>
189 </conditional>
190
191
192 <conditional name="cBarcodes">
193 <param name="select" type="select" label="4) Barcode detection">
194 <option value="off" selected="true">Off</option>
195 <option value="on">On</option>
196 </param>
197 <when value="off">
198 </when>
199 <when value="on">
200 <param format="fasta" name="barcodes" type="data" label="Barcodes" optional="false"/>
201
202 <conditional name="cbReads">
203 <param name="select" type="select" label="Separate barcode reads">
204 <option value="no" selected="true">No</option>
205 <option value="yes">Yes</option>
206 </param>
207 <when value="yes">
208 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
209 </when>
210 <when value="no">
211 <param name="bKeep" type="select" label="Remove barcodes within reads">
212 <option value="" selected="true">Yes</option>
213 <option value="--barcode-keep">No</option>
214 </param>
215 </when>
216 </conditional>
217
218 <param name="bUnassigned" type="select" label="Include unassigned reads">
219 <option value="" selected="true">No</option>
220 <option value="--barcode-unassigned">Yes</option>
221 </param>
222
223 <param name="bTrimEnd" type="select" label="Trim-end mode" optional="false">
224 <option value="ANY" selected="true">Any</option>
225 <option value="RIGHT">Right</option>
226 <option value="RIGHT_TAIL">Right tail</option>
227 <option value="LEFT">Left</option>
228 <option value="LEFT_TAIL">Left tail</option>
229 </param>
230
231 <conditional name="cbTailLen">
232 <param name="select" type="select" label="Change tail length">
233 <option value="no" selected="true">No</option>
234 <option value="yes">Yes</option>
235 </param>
236 <when value="no">
237 </when>
238 <when value="yes">
239 <param name="bTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
240 </when>
241 </conditional>
242
243 <conditional name="cbMinOverlap">
244 <param name="select" type="select" label="Change min-overlap" help="default: barcode length">
245 <option value="no" selected="true">No</option>
246 <option value="yes">Yes</option>
247 </param>
248 <when value="no">
249 </when>
250 <when value="yes">
251 <param name="bMinOverlap" size="4" type="integer" value="8" label="Min-overlap" optional="false"/>
252 </when>
253 </conditional>
254
255 <param name="bThresh" size="4" type="integer" value="1" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
256
257 <conditional name="cbAlignScores">
258 <param name="select" type="select" label="Modify alignment scores">
259 <option value="no" selected="true">No</option>
260 <option value="yes">Yes</option>
261 </param>
262 <when value="no">
263 </when>
264 <when value="yes">
265 <param name="bMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
266 <param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
267 <param name="bGap" size="3" type="integer" value="-9" label="Gap" optional="false"/>
268 </when>
269 </conditional>
270 </when>
271 </conditional>
272
273
274 <conditional name="cAdapters">
275 <param name="select" type="select" label="5) Adapter removal">
276 <option value="off" selected="true">Off</option>
277 <option value="on">On</option>
278 </param>
279
280 <when value="off">
281 </when>
282 <when value="on">
283 <conditional name="ccAdapters">
284 <param name="select" type="select" label="Adapter source">
285 <option value="data" selected="true">Fasta</option>
286 <option value="seq">Sequence</option>
287 <!-- <option value="file">File</option> -->
288 </param>
289 <when value="data">
290 <param format="fasta" name="adaptersData" type="data" label="Adapters" optional="false"/>
291 </when>
292 <when value="seq">
293 <param name="adapterSeq" size="40" label="Adapter" type="text" value="AAAAAAAAAAAAAA" optional="false"/>
294 </when>
295 <!-- <when value="file">
296 <param name="adaptersFile" type="file" label="Adapters file" optional="false"/>
297 </when> -->
298 </conditional>
299
300 <param name="aTrimEnd" type="select" label="Trim-end mode" optional="false">
301 <option value="ANY">Any</option>
302 <option value="RIGHT" selected="true">Right</option>
303 <option value="RIGHT_TAIL">Right tail</option>
304 <option value="LEFT">Left</option>
305 <option value="LEFT_TAIL">Left tail</option>
306 </param>
307
308 <conditional name="caTailLen">
309 <param name="select" type="select" label="Change tail length">
310 <option value="no" selected="true">No</option>
311 <option value="yes">Yes</option>
312 </param>
313 <when value="no">
314 </when>
315 <when value="yes">
316 <param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
317 </when>
318 </conditional>
319
320 <param name="aReadSet" type="select" label="Removal for single read set">
321 <option value="" selected="true">No</option>
322 <option value="--adapter-read-set 1">1st</option>
323 <option value="--adapter-read-set 2">2nd</option>
324 </param>
325
326 <param name="aMinOverlap" size="4" type="integer" value="1" label="Min-overlap" optional="false"/>
327 <param name="aThresh" size="4" type="integer" value="3" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
328
329 <conditional name="caAlignScores">
330 <param name="select" type="select" label="Modify alignment scores">
331 <option value="no" selected="true">No</option>
332 <option value="yes">Yes</option>
333 </param>
334 <when value="no">
335 </when>
336 <when value="yes">
337 <param name="aMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
338 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
339 <param name="aGap" size="3" type="integer" value="-7" label="Gap" optional="false"/>
340 </when>
341 </conditional>
342 </when>
343 </conditional>
344
345
346 <conditional name="cTrimLen">
347 <param name="select" type="select" label="6) Trimming to length">
348 <option value="off" selected="true">Off</option>
349 <option value="on">On</option>
350 </param>
351 <when value="off">
352 </when>
353 <when value="on">
354 <param name="trimLen" size="4" type="integer" value="30" label="Length" optional="false" help="trim reads to certain length from right"/>
355 </when>
356 </conditional>
357
358 <param name="minReadLen" size="4" type="integer" value="18" label="7) Minimum read length" optional="false" help="shorter reads are discarded"/>
359
360 <conditional name="cOutput">
361 <param name="select" type="select" label="Output selection">
362 <option value="off" selected="true">Off</option>
363 <option value="show">Show</option>
364 </param>
365 <when value="off">
366 </when>
367 <when value="show">
368 <param name="fastaOutput" type="select" label="Fasta output">
369 <option value="" selected="true">Off</option>
370 <option value="--fasta-output">Always</option>
371 </param>
372
373 <param name="lenDist" type="select" label="Read length distribution">
374 <option value="" selected="true">Off</option>
375 <option value="--length-dist">On</option>
376 </param>
377
378 <param name="singleReads" type="select" label="Single reads">
379 <option value="" selected="true">Off</option>
380 <option value="--single-reads">On</option>
381 </param>
382 </when>
383 </conditional>
384
385 <conditional name="cLogging">
386 <param name="select" type="select" label="Logging and tagging options">
387 <option value="off" selected="true">Off</option>
388 <option value="show">Show</option>
389 </param>
390 <when value="off">
391 </when>
392 <when value="show">
393 <param name="logLevel" type="select" label="Alignment logging">
394 <option value="" selected="true">Off</option>
395 <option value="--log-level ALL">All</option>
396 <option value="--log-level MOD">Modified</option>
397 <option value="--log-level TAB">Tabular</option>
398 </param>
399
400 <param name="numTags" type="select" label="Number tags">
401 <option value="" selected="true">Off</option>
402 <option value="--number-tags">On</option>
403 </param>
404
405 <param name="remTags" type="select" label="Removal tags">
406 <option value="" selected="true">Off</option>
407 <option value="--removal-tags">On</option>
408 </param>
409
410 <param name="rndTags" type="select" label="Random tags">
411 <option value="" selected="true">Off</option>
412 <option value="--random-tags">On</option>
413 </param>
414 </when>
415 </conditional>
416
417 </inputs>
418
419 <stdio>
420 <exit_code range="1:" level="fatal" description="Error!" />
421 </stdio>
422
423 <outputs>
424 <data format="txt" name="output" metadata_source="reads"/>
425 </outputs>
426
427
428 <help>
429
430 **Description**
431
432 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.
433
434 .. _project: https://github.com/seqan/flexbar
435
436 ------
437
438 **Trim-end modes**
439
440 **Any:** longer side of read remains after overlap removal
441
442 **Left:** right side remains after removal, align before or at read end
443
444 **Right:** left part remains after removal, align after or at read start
445
446 **Left tail:** consider first n bases of reads in alignment
447
448 **Right tail:** use only last n bases, see tail-length options
449
450 ------
451
452 **Documentation**
453
454 Further documentation is available on the `manual`__ wiki page and via the command line help screen.
455
456 .. __: https://github.com/seqan/flexbar/wiki
457
458 ------
459
460 **Reference**
461
462 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.
463
464 </help>
465
466 </tool>