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Adjusted tool definition to Flexbar release 2.4
author jtilman
date Tue, 06 Aug 2013 16:49:33 +0200
parents d62311a7bac6
children 0ef7736004bb
comparison
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21:d62311a7bac6 22:12e4b3bb38c6
1 1
2 <!-- Flexbar tool definition for Galaxy, version 2.34 --> 2 <!-- Flexbar tool definition for Galaxy, version 2.4 -->
3 <!-- Author: Johannes Roehr --> 3 <!-- Author: Johannes Roehr -->
4 4
5 <tool id="flexbar" name="Flexbar" version="2.34" force_history_refresh="True"> 5
6 6 <tool id="flexbar" name="Flexbar" version="2.4" force_history_refresh="True">
7
7 <description>flexible barcode and adapter removal</description> 8 <description>flexible barcode and adapter removal</description>
8 9
9 <requirements> 10 <requirements>
10 <requirement type="binary" version="2.34">flexbar</requirement> 11 <requirement type="binary" version="2.4">flexbar</requirement>
11 </requirements> 12 </requirements>
12 13
13 <version_command>flexbar --version</version_command> 14 <version_command>flexbar --version</version_command>
14 15
15 <command interpreter="perl"> 16 <command interpreter="perl">
24 #if $cReads2.reads2.ext == $reads.ext: 25 #if $cReads2.reads2.ext == $reads.ext:
25 --reads2 $cReads2.reads2 26 --reads2 $cReads2.reads2
26 #end if 27 #end if
27 #end if 28 #end if
28 29
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": 30 #if $reads.ext == "fastqsanger":
37 --format fastq-sanger 31 --format sanger
38 #end if 32 #end if
39 #if $reads.ext == "fastqsolexa": 33 #if $reads.ext == "fastqsolexa":
40 --format fastq-solexa 34 --format solexa
41 #end if 35 #end if
42 #if $reads.ext == "fastqillumina": 36 #if $reads.ext == "fastqillumina":
43 --format fastq-i1.3 37 --format i1.3
44 #end if 38 #end if
45 #if $reads.ext == "csfasta": 39 #if $reads.ext == "csfasta":
46 --format csfasta 40 --color-space
47 #end if 41 #end if
48 #if $reads.ext == "fastqcssanger": 42 #if $reads.ext == "fastqcssanger":
49 --format csfastq 43 --color-space
50 #end if 44 #end if
51 45
52 46
53 --max-uncalled $maxUncalled 47 --max-uncalled $maxUncalled
54 --min-readlength $minReadLen 48 --min-read-length $minReadLen
55 49
56 #if $trimEnds.select == "on": 50 #if $trimEnds.select == "on":
57 --pre-trim-left $trimEnds.trimLeft 51 --pre-trim-left $trimEnds.trimLeft
58 --pre-trim-right $trimEnds.trimRight 52 --pre-trim-right $trimEnds.trimRight
59 #end if 53 #end if
76 70
77 #if $cBarcodes.cbReads.select == "no": 71 #if $cBarcodes.cbReads.select == "no":
78 $cBarcodes.cbReads.bKeep 72 $cBarcodes.cbReads.bKeep
79 #end if 73 #end if
80 74
75 $cBarcodes.bUnassigned
76
81 --barcode-trim-end $cBarcodes.bTrimEnd 77 --barcode-trim-end $cBarcodes.bTrimEnd
82 78
83 #if $cBarcodes.cbTailLen.select == "yes": 79 #if $cBarcodes.cbTailLen.select == "yes":
84 --barcode-tail-length $cBarcodes.cbTailLen.bTailLen 80 --barcode-tail-length $cBarcodes.cbTailLen.bTailLen
85 #end if 81 #end if
86 82
87 #if $cBarcodes.cbMinOverlap.select == "yes": 83 #if $cBarcodes.cbMinOverlap.select == "yes":
88 --barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap 84 --barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap
89 #end if 85 #end if
90 86
91 --barcode-threshold $cBarcodes.bThresh 87 --barcode-threshold $cBarcodes.bThresh
92 88
93 #if $cBarcodes.cbAlignScores.select == "yes": 89 #if $cBarcodes.cbAlignScores.select == "yes":
94 --barcode-match $bMatch 90 --barcode-match $bMatch
95 --barcode-mismatch $bMismatch 91 --barcode-mismatch $bMismatch
96 --barcode-gap $bGap 92 --barcode-gap $bGap
112 108
113 #if $cAdapters.caTailLen.select == "yes": 109 #if $cAdapters.caTailLen.select == "yes":
114 --adapter-tail-length $cAdapters.caTailLen.aTailLen 110 --adapter-tail-length $cAdapters.caTailLen.aTailLen
115 #end if 111 #end if
116 112
113 $cAdapters.aReadSet
114
117 --adapter-min-overlap $cAdapters.aMinOverlap 115 --adapter-min-overlap $cAdapters.aMinOverlap
118 --adapter-threshold $cAdapters.aThresh 116 --adapter-threshold $cAdapters.aThresh
119 117
120 #if $cAdapters.caAlignScores.select == "yes": 118 #if $cAdapters.caAlignScores.select == "yes":
121 --adapter-match $aMatch 119 --adapter-match $aMatch
123 --adapter-gap $aGap 121 --adapter-gap $aGap
124 #end if 122 #end if
125 #end if 123 #end if
126 124
127 125
126 #if $cOutput.select == "show":
127 $cOutput.fastaOutput
128 $cOutput.lenDist
129 $cOutput.singleReads
130 #end if
131
128 #if $cLogging.select == "show": 132 #if $cLogging.select == "show":
129 $cLogging.logLevel 133 $cLogging.logLevel
130 $cLogging.singleReads
131 $cLogging.lenDist
132 $cLogging.fastaOutput
133 $cLogging.numTags 134 $cLogging.numTags
134 $cLogging.remTags 135 $cLogging.remTags
135 $cLogging.rndTags 136 $cLogging.rndTags
136 #end if 137 #end if
137 138
138 139
139 $output $output.id $__new_file_path__ $reads.ext 140 $output $output.id $__new_file_path__ $reads.ext
140 141
141 </command> 142 </command>
142 143
144
143 <inputs> 145 <inputs>
144 146
145 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/> 147 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
146 148
147 149
193 </param> 195 </param>
194 <when value="off"> 196 <when value="off">
195 </when> 197 </when>
196 <when value="on"> 198 <when value="on">
197 <param format="fasta" name="barcodes" type="data" label="Barcodes" optional="false"/> 199 <param format="fasta" name="barcodes" type="data" label="Barcodes" optional="false"/>
200
198 <conditional name="cbReads"> 201 <conditional name="cbReads">
199 <param name="select" type="select" label="Separate barcode reads"> 202 <param name="select" type="select" label="Separate barcode reads">
200 <option value="no" selected="true">No</option> 203 <option value="no" selected="true">No</option>
201 <option value="yes">Yes</option> 204 <option value="yes">Yes</option>
202 </param> 205 </param>
208 <option value="" selected="true">Yes</option> 211 <option value="" selected="true">Yes</option>
209 <option value="--barcode-keep">No</option> 212 <option value="--barcode-keep">No</option>
210 </param> 213 </param>
211 </when> 214 </when>
212 </conditional> 215 </conditional>
216
217 <param name="bUnassigned" type="select" label="Include unassigned reads">
218 <option value="" selected="true">No</option>
219 <option value="--barcode-unassigned">Yes</option>
220 </param>
221
213 <param name="bTrimEnd" type="select" label="Trim-end mode" optional="false"> 222 <param name="bTrimEnd" type="select" label="Trim-end mode" optional="false">
214 <option value="ANY" selected="true">Any</option> 223 <option value="ANY" selected="true">Any</option>
215 <option value="RIGHT">Right</option> 224 <option value="RIGHT">Right</option>
216 <option value="RIGHT_TAIL">Right tail</option> 225 <option value="RIGHT_TAIL">Right tail</option>
217 <option value="LEFT">Left</option> 226 <option value="LEFT">Left</option>
218 <option value="LEFT_TAIL">Left tail</option> 227 <option value="LEFT_TAIL">Left tail</option>
219 </param> 228 </param>
229
220 <conditional name="cbTailLen"> 230 <conditional name="cbTailLen">
221 <param name="select" type="select" label="Change tail length"> 231 <param name="select" type="select" label="Change tail length">
222 <option value="no" selected="true">No</option> 232 <option value="no" selected="true">No</option>
223 <option value="yes">Yes</option> 233 <option value="yes">Yes</option>
224 </param> 234 </param>
251 <when value="no"> 261 <when value="no">
252 </when> 262 </when>
253 <when value="yes"> 263 <when value="yes">
254 <param name="bMatch" size="3" type="integer" value="1" label="Match" optional="false"/> 264 <param name="bMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
255 <param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/> 265 <param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
256 <param name="bGap" size="3" type="integer" value="-7" label="Gap" optional="false"/> 266 <param name="bGap" size="3" type="integer" value="-9" label="Gap" optional="false"/>
257 </when> 267 </when>
258 </conditional> 268 </conditional>
259 </when> 269 </when>
260 </conditional> 270 </conditional>
261 271
304 <when value="yes"> 314 <when value="yes">
305 <param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/> 315 <param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
306 </when> 316 </when>
307 </conditional> 317 </conditional>
308 318
319 <param name="aReadSet" type="select" label="Removal for single read set">
320 <option value="" selected="true">No</option>
321 <option value="--adapter-read-set 1">1st</option>
322 <option value="--adapter-read-set 2">2nd</option>
323 </param>
324
309 <param name="aMinOverlap" size="4" type="integer" value="1" label="Min-overlap" optional="false"/> 325 <param name="aMinOverlap" size="4" type="integer" value="1" label="Min-overlap" optional="false"/>
310 <param name="aThresh" size="4" type="integer" value="3" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/> 326 <param name="aThresh" size="4" type="integer" value="3" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
311 327
312 <conditional name="caAlignScores"> 328 <conditional name="caAlignScores">
313 <param name="select" type="select" label="Modify alignment scores"> 329 <param name="select" type="select" label="Modify alignment scores">
338 </when> 354 </when>
339 </conditional> 355 </conditional>
340 356
341 <param name="minReadLen" size="4" type="integer" value="18" label="7) Minimum read length" optional="false" help="shorter reads are discarded"/> 357 <param name="minReadLen" size="4" type="integer" value="18" label="7) Minimum read length" optional="false" help="shorter reads are discarded"/>
342 358
359 <conditional name="cOutput">
360 <param name="select" type="select" label="Output selection">
361 <option value="off" selected="true">Off</option>
362 <option value="show">Show</option>
363 </param>
364 <when value="off">
365 </when>
366 <when value="show">
367 <param name="fastaOutput" type="select" label="Fasta output">
368 <option value="" selected="true">Off</option>
369 <option value="--fasta-output">Always</option>
370 </param>
371
372 <param name="lenDist" type="select" label="Read length distribution">
373 <option value="" selected="true">Off</option>
374 <option value="--length-dist">On</option>
375 </param>
376
377 <param name="singleReads" type="select" label="Single reads">
378 <option value="" selected="true">Off</option>
379 <option value="--single-reads">On</option>
380 </param>
381 </when>
382 </conditional>
343 383
344 <conditional name="cLogging"> 384 <conditional name="cLogging">
345 <param name="select" type="select" label="Logging and tagging options"> 385 <param name="select" type="select" label="Logging and tagging options">
346 <option value="off" selected="true">Off</option> 386 <option value="off" selected="true">Off</option>
347 <option value="show">Show</option> 387 <option value="show">Show</option>
354 <option value="--log-level ALL">All</option> 394 <option value="--log-level ALL">All</option>
355 <option value="--log-level MOD">Modified</option> 395 <option value="--log-level MOD">Modified</option>
356 <option value="--log-level TAB">Tabular</option> 396 <option value="--log-level TAB">Tabular</option>
357 </param> 397 </param>
358 398
359 <param name="singleReads" type="select" label="Single reads">
360 <option value="" selected="true">Off</option>
361 <option value="--single-reads">On</option>
362 </param>
363
364 <param name="lenDist" type="select" label="Read length distribution">
365 <option value="" selected="true">Off</option>
366 <option value="--length-dist">On</option>
367 </param>
368
369 <param name="fastaOutput" type="select" label="Fasta output">
370 <option value="" selected="true">Off</option>
371 <option value="--fasta-output">Always</option>
372 </param>
373
374 <param name="numTags" type="select" label="Number tags"> 399 <param name="numTags" type="select" label="Number tags">
375 <option value="" selected="true">Off</option> 400 <option value="" selected="true">Off</option>
376 <option value="--number-tags">On</option> 401 <option value="--number-tags">On</option>
377 </param> 402 </param>
378 403
385 <option value="" selected="true">Off</option> 410 <option value="" selected="true">Off</option>
386 <option value="--random-tags">On</option> 411 <option value="--random-tags">On</option>
387 </param> 412 </param>
388 </when> 413 </when>
389 </conditional> 414 </conditional>
390 415
391 <param name="threads" type="select" label="Threads" help="check availability of cores"> 416 <param name="threads" type="select" label="Threads" help="check availability of cores">
392 <option value="1" selected="true">1</option> 417 <option value="1" selected="true">1</option>
393 <option value="2">2</option> 418 <option value="2">2</option>
394 <option value="4">4</option> 419 <option value="4">4</option>
395 </param> 420 </param>
407 432
408 <help> 433 <help>
409 434
410 **Description** 435 **Description**
411 436
412 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. 437 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.
413 438
414 .. _project: https://sourceforge.net/projects/flexbar 439 .. _project: https://sourceforge.net/projects/flexbar
415 440
416 ------ 441 ------
417 442
418 **Trim-end modes** 443 **Trim-end modes**
419 444
420 **Any:** longer part of read remains 445 **Any:** longer side of read remains after overlap removal
421 446
422 **Left:** align before or at read end, right part remains 447 **Left:** right side remains after removal, align before or at read end
423 448
424 **Right:** align after or at read start, left part remains 449 **Right:** left part remains after removal, align after or at read start
425 450
426 **Left tail:** consider first n bases, see tail-length options 451 **Left tail:** consider first n bases of reads in alignment
427 452
428 **Right tail:** use only last n bases of reads in alignment 453 **Right tail:** use only last n bases, see tail-length options
429 454
430 ------ 455 ------
431 456
432 **Documentation** 457 **Documentation**
433 458