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Updated tool definition for Flexbar 2.33 release
author jtilman
date Mon, 18 Mar 2013 18:18:28 +0100
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children 83e3813084f2
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18:702ac01fbef8 19:621fa3daa2a1
1
2 <!-- Flexbar tool definition for Galaxy, version 2.33 -->
3 <!-- Author: Johannes Roehr -->
4
5 <tool id="flexbar" name="Flexbar" version="2.33" force_history_refresh="True">
6
7 <description>flexible barcode and adapter removal</description>
8
9 <requirements>
10 <requirement type="binary" version="2.33">flexbar</requirement>
11 </requirements>
12
13 <version_command>flexbar --version</version_command>
14
15 <command interpreter="perl">
16
17 flexbar.pl flexbar
18
19 --threads $threads
20
21 --reads $reads
22
23 #if $cReads2.select == "on":
24 #if $cReads2.reads2.ext == $reads.ext:
25 --reads2 $cReads2.reads2
26 #end if
27 #end if
28
29
30 #if $reads.ext == "fasta":
31 --format fasta
32 #end if
33 #if $reads.ext == "fastq":
34 --format fastq
35 #end if
36 #if $reads.ext == "fastqsanger":
37 --format fastq-sanger
38 #end if
39 #if $reads.ext == "fastqsolexa":
40 --format fastq-solexa
41 #end if
42 #if $reads.ext == "fastqillumina":
43 --format fastq-i1.3
44 #end if
45 #if $reads.ext == "csfasta":
46 --format csfasta
47 #end if
48 #if $reads.ext == "fastqcssanger":
49 --format csfastq
50 #end if
51
52
53 --max-uncalled $maxUncalled
54 --min-readlength $minReadLen
55
56 #if $trimEnds.select == "on":
57 --pre-trim-left $trimEnds.trimLeft
58 --pre-trim-right $trimEnds.trimRight
59 #end if
60
61 #if $cTrimPhred.select == "on":
62 --pre-trim-phred $cTrimPhred.trimPhred
63 #end if
64
65 #if $cTrimLen.select == "on":
66 --post-trim-length $cTrimLen.trimLen
67 #end if
68
69
70 #if $cBarcodes.select == "on":
71 --barcodes $cBarcodes.barcodes
72
73 #if $cBarcodes.cbReads.select == "yes":
74 --barcode-reads $cBarcodes.cbReads.bReads
75 #end if
76
77 #if $cBarcodes.cbReads.select == "no":
78 $cBarcodes.cbReads.bKeep
79 #end if
80
81 --barcode-trim-end $cBarcodes.bTrimEnd
82
83 #if $cBarcodes.cbTailLen.select == "yes":
84 --barcode-tail-length $cBarcodes.cbTailLen.bTailLen
85 #end if
86
87 #if $cBarcodes.cbMinOverlap.select == "yes":
88 --barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap
89 #end if
90
91 --barcode-threshold $cBarcodes.bThresh
92
93 #if $cBarcodes.cbAlignScores.select == "yes":
94 --barcode-match $bMatch
95 --barcode-mismatch $bMismatch
96 --barcode-gap $bGap
97 #end if
98 #end if
99
100
101 #if $cAdapters.select == "on":
102
103 #if $cAdapters.ccAdapters.select == "data":
104 --adapters $cAdapters.ccAdapters.adaptersData
105 #end if
106
107 #if $cAdapters.ccAdapters.select == "seq":
108 --adapter-seq $cAdapters.ccAdapters.adapterSeq
109 #end if
110
111 --adapter-trim-end $cAdapters.aTrimEnd
112
113 #if $cAdapters.caTailLen.select == "yes":
114 --adapter-tail-length $cAdapters.caTailLen.aTailLen
115 #end if
116
117 --adapter-min-overlap $cAdapters.aMinOverlap
118 --adapter-threshold $cAdapters.aThresh
119
120 #if $cAdapters.caAlignScores.select == "yes":
121 --adapter-match $aMatch
122 --adapter-mismatch $aMismatch
123 --adapter-gap $aGap
124 #end if
125 #end if
126
127
128 #if $cLogging.select == "show":
129 $cLogging.logLevel
130 $cLogging.singleReads
131 $cLogging.lenDist
132 $cLogging.fastaOutput
133 $cLogging.numTags
134 $cLogging.remTags
135 $cLogging.rndTags
136 #end if
137
138
139 $output $output.id $__new_file_path__ $reads.ext
140
141 </command>
142
143 <inputs>
144
145 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
146
147
148 <conditional name="cReads2">
149 <param name="select" type="select" label="2nd read set (paired)">
150 <option value="off" selected="true">Off</option>
151 <option value="on">On</option>
152 </param>
153 <when value="on">
154 <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"/>
155 </when>
156 </conditional>
157
158
159 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/>
160
161 <conditional name="trimEnds">
162 <param name="select" type="select" label="2) Trimming of ends">
163 <option value="off" selected="true">Off</option>
164 <option value="on">On</option>
165 </param>
166 <when value="on">
167 <param name="trimLeft" size="4" type="integer" value="0" label="Left" optional="false"/>
168 <param name="trimRight" size="4" type="integer" value="0" label="Right" optional="false" help="trims specified number of bases from read ends"/>
169 </when>
170 </conditional>
171
172 <conditional name="cTrimPhred">
173 <param name="select" type="select" label="3) Phred-trimming">
174 <option value="off" selected="true">Off</option>
175 <option value="on">On</option>
176 </param>
177 <when value="on">
178 <param name="trimPhred" size="4" type="integer" value="10" label="Threshold" optional="false" help="trim right end until specified or higher quality reached"/>
179 </when>
180 </conditional>
181
182
183 <conditional name="cBarcodes">
184 <param name="select" type="select" label="4) Barcode detection">
185 <option value="off" selected="true">Off</option>
186 <option value="on">On</option>
187 </param>
188 <when value="on">
189 <param format="fasta" name="barcodes" type="data" label="Barcodes" optional="false"/>
190 <conditional name="cbReads">
191 <param name="select" type="select" label="Separate barcode reads">
192 <option value="no" selected="true">No</option>
193 <option value="yes">Yes</option>
194 </param>
195 <when value="yes">
196 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
197 </when>
198 <when value="no">
199 <param name="bKeep" type="select" label="Remove barcodes within reads">
200 <option value="" selected="true">Yes</option>
201 <option value="--barcode-keep">No</option>
202 </param>
203 </when>
204 </conditional>
205 <param name="bTrimEnd" type="select" label="Trim-end mode" optional="false">
206 <option value="ANY" selected="true">Any</option>
207 <option value="RIGHT">Right</option>
208 <option value="RIGHT_TAIL">Right tail</option>
209 <option value="LEFT">Left</option>
210 <option value="LEFT_TAIL">Left tail</option>
211 </param>
212 <conditional name="cbTailLen">
213 <param name="select" type="select" label="Change tail length">
214 <option value="no" selected="true">No</option>
215 <option value="yes">Yes</option>
216 </param>
217 <when value="yes">
218 <param name="bTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
219 </when>
220 </conditional>
221
222 <conditional name="cbMinOverlap">
223 <param name="select" type="select" label="Change min-overlap" help="default: barcode length">
224 <option value="no" selected="true">No</option>
225 <option value="yes">Yes</option>
226 </param>
227 <when value="yes">
228 <param name="bMinOverlap" size="4" type="integer" value="8" label="Min-overlap" optional="false"/>
229 </when>
230 </conditional>
231
232 <param name="bThresh" size="4" type="integer" value="1" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
233
234 <conditional name="cbAlignScores">
235 <param name="select" type="select" label="Modify alignment scores">
236 <option value="no" selected="true">No</option>
237 <option value="yes">Yes</option>
238 </param>
239 <when value="yes">
240 <param name="bMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
241 <param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
242 <param name="bGap" size="3" type="integer" value="-7" label="Gap" optional="false"/>
243 </when>
244 </conditional>
245 </when>
246 </conditional>
247
248
249 <conditional name="cAdapters">
250 <param name="select" type="select" label="5) Adapter removal">
251 <option value="off" selected="true">Off</option>
252 <option value="on">On</option>
253 </param>
254
255 <when value="on">
256 <conditional name="ccAdapters">
257 <param name="select" type="select" label="Adapter source">
258 <option value="data" selected="true">Fasta</option>
259 <option value="seq">Sequence</option>
260 <!-- <option value="file">File</option> -->
261 </param>
262 <when value="data">
263 <param format="fasta" name="adaptersData" type="data" label="Adapters" optional="false"/>
264 </when>
265 <when value="seq">
266 <param name="adapterSeq" size="40" label="Adapter" type="text" value="AAAAAAAAAAAAAA" optional="false"/>
267 </when>
268 <!-- <when value="file">
269 <param name="adaptersFile" type="file" label="Adapters file" optional="false"/>
270 </when> -->
271 </conditional>
272
273 <param name="aTrimEnd" type="select" label="Trim-end mode" optional="false">
274 <option value="ANY">Any</option>
275 <option value="RIGHT" selected="true">Right</option>
276 <option value="RIGHT_TAIL">Right tail</option>
277 <option value="LEFT">Left</option>
278 <option value="LEFT_TAIL">Left tail</option>
279 </param>
280
281 <conditional name="caTailLen">
282 <param name="select" type="select" label="Change tail length">
283 <option value="no" selected="true">No</option>
284 <option value="yes">Yes</option>
285 </param>
286 <when value="yes">
287 <param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
288 </when>
289 </conditional>
290
291 <param name="aMinOverlap" size="4" type="integer" value="1" label="Min-overlap" optional="false"/>
292 <param name="aThresh" size="4" type="integer" value="3" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
293
294 <conditional name="caAlignScores">
295 <param name="select" type="select" label="Modify alignment scores">
296 <option value="no" selected="true">No</option>
297 <option value="yes">Yes</option>
298 </param>
299 <when value="yes">
300 <param name="aMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
301 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
302 <param name="aGap" size="3" type="integer" value="-7" label="Gap" optional="false"/>
303 </when>
304 </conditional>
305 </when>
306 </conditional>
307
308
309 <conditional name="cTrimLen">
310 <param name="select" type="select" label="6) Trimming to length">
311 <option value="off" selected="true">Off</option>
312 <option value="on">On</option>
313 </param>
314 <when value="on">
315 <param name="trimLen" size="4" type="integer" value="30" label="Length" optional="false" help="trim reads to certain length from right"/>
316 </when>
317 </conditional>
318
319 <param name="minReadLen" size="4" type="integer" value="18" label="7) Minimum read length" optional="false" help="shorter reads are discarded"/>
320
321
322 <conditional name="cLogging">
323 <param name="select" type="select" label="Logging and tagging options">
324 <option value="off" selected="true">Off</option>
325 <option value="show">Show</option>
326 </param>
327 <when value="show">
328 <param name="logLevel" type="select" label="Alignment logging">
329 <option value="" selected="true">Off</option>
330 <option value="--log-level ALL">All</option>
331 <option value="--log-level MOD">Modified</option>
332 <option value="--log-level TAB">Tabular</option>
333 </param>
334
335 <param name="singleReads" type="select" label="Single reads">
336 <option value="" selected="true">Off</option>
337 <option value="--single-reads">On</option>
338 </param>
339
340 <param name="lenDist" type="select" label="Read length distribution">
341 <option value="" selected="true">Off</option>
342 <option value="--length-dist">On</option>
343 </param>
344
345 <param name="fastaOutput" type="select" label="Fasta output">
346 <option value="" selected="true">Off</option>
347 <option value="--fasta-output">Always</option>
348 </param>
349
350 <param name="numTags" type="select" label="Number tags">
351 <option value="" selected="true">Off</option>
352 <option value="--number-tags">On</option>
353 </param>
354
355 <param name="remTags" type="select" label="Removal tags">
356 <option value="" selected="true">Off</option>
357 <option value="--removal-tags">On</option>
358 </param>
359
360 <param name="rndTags" type="select" label="Random tags">
361 <option value="" selected="true">Off</option>
362 <option value="--random-tags">On</option>
363 </param>
364 </when>
365 </conditional>
366
367 <param name="threads" type="select" label="Threads" help="check availability of cores">
368 <option value="1" selected="true">1</option>
369 <option value="2">2</option>
370 <option value="4">4</option>
371 </param>
372
373 </inputs>
374
375 <stdio>
376 <exit_code range="1:" level="fatal" description="Error!" />
377 </stdio>
378
379 <outputs>
380 <data format="txt" name="output" metadata_source="reads"/>
381 </outputs>
382
383
384 <help>
385
386 **Description**
387
388 Flexbar is a program to preprocess sequencing data. It demultiplexes barcoded runs and removes adapter sequences. Further, basic read trimming and filtering options are provided. Flexbar increases 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.
389
390 .. _project: https://sourceforge.net/projects/flexbar
391
392 ------
393
394 **Trim-end modes**
395
396 **Any:** longer part of read remains
397
398 **Left:** align before or at read end, right part remains
399
400 **Right:** align after or at read start, left part remains
401
402 **Left tail:** consider first n bases, see tail-length options
403
404 **Right tail:** use only last n bases of reads in alignment
405
406 ------
407
408 **Documentation**
409
410 Further documentation is available on the `manual`__ wiki page and via the command line help screen.
411
412 .. __: http://sourceforge.net/p/flexbar/wiki
413
414 ------
415
416 **Reference**
417
418 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.
419
420 </help>
421
422 </tool>
423