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comparison flexbar.xml @ 34:4a095317caca draft

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author jtilman
date Wed, 27 Jun 2018 06:41:36 -0400
parents d43903772a88
children 4e47e1caf21a
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33:3b010ddcea2a 34:4a095317caca
1 1
2 <!-- Flexbar tool definition for Galaxy, version 3.4 --> 2 <!-- Flexbar tool definition for Galaxy, version 3.4.1 -->
3 <!-- Author: Johannes Roehr --> 3 <!-- Author: Johannes Roehr -->
4 4
5 5
6 <tool id="flexbar" name="Flexbar" version="3.4" force_history_refresh="True"> 6 <tool id="flexbar" name="Flexbar" version="3.4.1">
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="3.4">flexbar</requirement> 11 <requirement type="package" version="3.4.0">flexbar</requirement>
12 </requirements> 12 </requirements>
13 13
14 <version_command>flexbar --versions</version_command> 14 <version_command>flexbar --versions</version_command>
15 15
16 <command interpreter="perl"> 16 <command detect_errors="aggressive">
17 17
18 flexbar.pl flexbar 18 <![CDATA[
19
20 flexbar
19 21
20 --threads \${GALAXY_SLOTS:-1} 22 --threads \${GALAXY_SLOTS:-1}
21 23
22 --reads $reads 24 #if $reads.mode == "se":
23 25 --reads '$reads.rs'
24 #if $cReads2.select == "on": 26 #elif $reads.mode == "pe":
25 #if $cReads2.reads2.ext == $reads.ext: 27 --reads '$reads.r1'
26 --reads2 $cReads2.reads2 28 --reads2 '$reads.r2'
27 #end if 29 #else:
30 --reads '$reads.rc.forward'
31 --reads2 '$reads.rc.reverse'
28 #end if 32 #end if
29 33
30 --max-uncalled $maxUncalled 34 --max-uncalled $maxUncalled
31 --min-read-length $minReadLen 35 --min-read-length $minReadLen
32 36
33 #if $trimEnds.select == "on": 37 #if $trimEnds.select == "on":
34 --pre-trim-left $trimEnds.trimLeft 38 --pre-trim-left $trimEnds.trimLeft
35 --pre-trim-right $trimEnds.trimRight 39 --pre-trim-right $trimEnds.trimRight
36 #end if 40 #end if
37 41
38 #if $cTrimPhred.select == "on": 42
39 --qtrim TAIL --qtrim-threshold $cTrimPhred.trimPhred 43 #if $cTrimQual.select != "off":
40 44 #if $reads.mode == "se":
41 #if $reads.ext == "fastqsanger": 45 #if $reads.rs.ext == "fastqsanger":
42 --qtrim-format sanger 46 --qtrim-format sanger
43 #end if 47 #end if
44 #if $reads.ext == "fastqsolexa": 48 #if $reads.rs.ext == "fastqsolexa":
45 --qtrim-format solexa 49 --qtrim-format solexa
46 #end if 50 #end if
47 #if $reads.ext == "fastqillumina": 51 #if $reads.rs.ext == "fastqillumina":
48 --qtrim-format i1.3 52 --qtrim-format i1.3
49 #end if 53 #end if
50 #end if 54 #elif $reads.mode == "pe":
55 #if $reads.r1.ext == "fastqsanger":
56 --qtrim-format sanger
57 #end if
58 #if $reads.r1.ext == "fastqsolexa":
59 --qtrim-format solexa
60 #end if
61 #if $reads.r1.ext == "fastqillumina":
62 --qtrim-format i1.3
63 #end if
64 #else:
65 #if $reads.rc.forward.ext == "fastqsanger":
66 --qtrim-format sanger
67 #end if
68 #if $reads.rc.forward.ext == "fastqsolexa":
69 --qtrim-format solexa
70 #end if
71 #if $reads.rc.forward.ext == "fastqillumina":
72 --qtrim-format i1.3
73 #end if
74 #end if
75 #end if
76
77 #if $cTrimQual.select == "tail":
78 --qtrim TAIL
79 --qtrim-threshold $cTrimQual.trimQualTail
80 $cTrimQual.trimQualPostTail
81 #end if
82 #if $cTrimQual.select == "win":
83 --qtrim WIN
84 --qtrim-threshold $cTrimQual.trimQualWin
85 --qtrim-win-size $cTrimQual.trimQualWinSize
86 $cTrimQual.trimQualPostWin
87 #end if
88 #if $cTrimQual.select == "bwa":
89 --qtrim BWA
90 --qtrim-threshold $cTrimQual.trimQualBWA
91 $cTrimQual.trimQualPostBWA
92 #end if
93
51 94
52 #if $cTrimLen.select == "on": 95 #if $cTrimLen.select == "on":
53 --post-trim-length $cTrimLen.trimLen 96 --post-trim-length $cTrimLen.trimLen
54 #end if 97 #end if
55 98
56 99
57 #if $cBarcodes.select == "on":
58 --barcodes $cBarcodes.barcodes
59
60 #if $cBarcodes.cbReads.select == "yes":
61 --barcode-reads $cBarcodes.cbReads.bReads
62 #end if
63
64 #if $cBarcodes.cbReads.select == "no":
65 $cBarcodes.cbReads.bKeep
66 #end if
67
68 $cBarcodes.bUnassigned
69
70 --barcode-trim-end $cBarcodes.bTrimEnd
71
72 #if $cBarcodes.cbTailLen.select == "yes":
73 --barcode-tail-length $cBarcodes.cbTailLen.bTailLen
74 #end if
75
76 #if $cBarcodes.cbMinOverlap.select == "yes":
77 --barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap
78 #end if
79
80 --barcode-error-rate $cBarcodes.bThresh
81
82 #if $cBarcodes.cbAlignScores.select == "yes":
83 --barcode-match $bMatch
84 --barcode-mismatch $bMismatch
85 --barcode-gap $bGap
86 #end if
87 #end if
88
89
90 #if $cAdapters.select == "on": 100 #if $cAdapters.select == "on":
91 101
92 #if $cAdapters.ccAdapters.select == "data": 102 #if $cAdapters.ccAdapters.select == "file":
93 --adapters $cAdapters.ccAdapters.adaptersData 103 --adapters '$cAdapters.ccAdapters.adapterFile'
94 #end if 104 #end if
95 105 #if $cAdapters.ccAdapters.select == "files":
106 --adapters '$cAdapters.ccAdapters.adapterFile1'
107 --adapters2 '$cAdapters.ccAdapters.adapterFile2'
108 #end if
109 #if $cAdapters.ccAdapters.select == "preset":
110 --adapter-preset '$cAdapters.ccAdapters.adapterPreset'
111 #end if
96 #if $cAdapters.ccAdapters.select == "seq": 112 #if $cAdapters.ccAdapters.select == "seq":
97 --adapter-seq $cAdapters.ccAdapters.adapterSeq 113 --adapter-seq $cAdapters.ccAdapters.adapterSeq
98 #end if 114 #end if
99 115
100 --adapter-trim-end $cAdapters.aTrimEnd 116 --adapter-trim-end $cAdapters.aTrimEnd
101
102 #if $cAdapters.caTailLen.select == "yes":
103 --adapter-tail-length $cAdapters.caTailLen.aTailLen
104 #end if
105
106 $cAdapters.aReadSet
107
108 --adapter-min-overlap $cAdapters.aMinOverlap 117 --adapter-min-overlap $cAdapters.aMinOverlap
109 --adapter-error-rate $cAdapters.aThresh 118 --adapter-error-rate $cAdapters.aThresh
110 119
111 #if $cAdapters.caAlignScores.select == "yes": 120 #if $cAdapters.cPairOverlap.select == "on":
112 --adapter-match $aMatch 121 --adapter-pair-overlap $cAdapters.cPairOverlap.aPairOverlap
113 --adapter-mismatch $aMismatch 122 --adapter-min-poverlap $cAdapters.cPairOverlap.aMinPoverlap
114 --adapter-gap $aGap 123 #end if
115 #end if 124
116 #end if 125 #if $cAdapters.aAdvanced.caTailLen.select == "yes":
117 126 --adapter-tail-length $cAdapters.aAdvanced.caTailLen.aTailLen
118 127 #end if
119 #if $cOutput.select == "show": 128
120 $cOutput.fastaOutput 129 #if $cAdapters.aAdvanced.cRevComp.select == "on":
121 $cOutput.lenDist 130 --adapter-revcomp ON
122 $cOutput.singleReads 131 #if $cAdapters.aAdvanced.cRevComp.aRevCompEnd != "off":
123 #end if 132 --adapter-revcomp-end $cAdapters.aAdvanced.cRevComp.aRevCompEnd
124 133 #end if
125 #if $cLogging.select == "show": 134 #end if
126 $cLogging.logLevel 135 #if $cAdapters.aAdvanced.cRevComp.select == "only":
127 $cLogging.numTags 136 --adapter-revcomp ONLY
128 $cLogging.remTags 137 #end if
129 $cLogging.rndTags 138
130 #end if 139 $cAdapters.aAdvanced.aReadSet
131 140
132 141 --adapter-cycles $cAdapters.aAdvanced.aCycles
133 $output $output.id $__new_file_path__ $reads.ext 142
134 143 #if $cAdapters.aAdvanced.caAlignScores.select == "yes":
144 --adapter-match $cAdapters.aAdvanced.caAlignScores.aMatch
145 --adapter-mismatch $cAdapters.aAdvanced.caAlignScores.aMismatch
146 --adapter-gap $cAdapters.aAdvanced.caAlignScores.aGap
147 #end if
148 #end if
149
150
151 #if $cAddOptions.select == "show":
152 $cAddOptions.logLevel
153 $cAddOptions.numTags
154 $cAddOptions.remTags
155 $cAddOptions.rndTags
156 $cAddOptions.singleReadsP
157
158 #if $cAddOptions.cReadBundle.select == "show":
159 --bundle $cAddOptions.cReadBundle.bundle
160
161 #if $cAddOptions.cReadBundle.bundles != "":
162 --bundles $cAddOptions.cReadBundle.bundles
163 #end if
164 #end if
165 #end if
166
167
168 #if $reads.mode == "se":
169 --output-reads '$rsout'
170 #elif $reads.mode == "pe":
171 --output-reads '$r1out'
172 --output-reads2 '$r2out'
173 #else:
174 --output-reads '$rcout.forward'
175 --output-reads2 '$rcout.reverse'
176 #end if
177
178 --output-log '$outlog'
179
180 ]]>
135 </command> 181 </command>
136 182
137 183
138 <inputs> 184 <inputs>
139 185
140 <param format="fastq,fastqsanger,fastqsolexa,fastqillumina" name="reads" type="data" label="Reads fastq file" optional="false"/> 186 <conditional name="reads">
141 187 <param name="mode" type="select" label="Sequencing reads">
142 188 <option value="se">Single read file</option>
143 <conditional name="cReads2"> 189 <option value="pe" selected="true">Paired read files</option>
144 <param name="select" type="select" label="Paired reads file"> 190 <option value="pc">Paired read collection</option>
191 </param>
192 <when value="se">
193 <param name="rs" type="data" format="fastqsanger,fastqsolexa,fastqillumina" label="Fastq read file"/>
194 </when>
195 <when value="pe">
196 <param name="r1" type="data" format="fastqsanger,fastqsolexa,fastqillumina" label="Fastq read file 1"/>
197 <param name="r2" type="data" format="fastqsanger,fastqsolexa,fastqillumina" label="Fastq read file 2"/>
198 </when>
199 <when value="pc">
200 <param name="rc" format="fastqsanger,fastqsolexa,fastqillumina" type="data_collection" collection_type="paired" label="Fastq pair collection"/>
201 </when>
202 </conditional>
203
204 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Maximum uncalled bases"/>
205
206 <conditional name="trimEnds">
207 <param name="select" type="select" label="2) Trimming of read ends">
145 <option value="off" selected="true">Off</option> 208 <option value="off" selected="true">Off</option>
146 <option value="on">On</option> 209 <option value="on">On</option>
147 </param> 210 </param>
148 <when value="off"> 211 <when value="off">
149 </when> 212 </when>
150 <when value="on"> 213 <when value="on">
151 <param format="fastq,fastqsanger,fastqsolexa,fastqillumina" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/> 214 <param name="trimLeft" size="4" type="integer" value="0" label="Left"/>
215 <param name="trimRight" size="4" type="integer" value="0" label="Right" help="trims specified number of bases at ends"/>
152 </when> 216 </when>
153 </conditional> 217 </conditional>
154 218
155 219 <conditional name="cTrimQual">
156 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/> 220 <param name="select" type="select" label="3) Quality-based trimming">
157 221 <option value="off" selected="true">Off</option>
158 <conditional name="trimEnds"> 222 <option value="tail">Tail</option>
159 <param name="select" type="select" label="2) Trimming of ends"> 223 <option value="win">Window</option>
224 <option value="bwa">BWA</option>
225 </param>
226 <when value="off">
227 </when>
228 <when value="tail">
229 <param name="trimQualTail" size="4" type="integer" value="20" label="Quality threshold" help="trim right end until specified quality or higher"/>
230
231 <param name="trimQualPostTail" type="select" label="After adapter removal">
232 <option value="" selected="true">No</option>
233 <option value="--qtrim-post-removal">Yes</option>
234 </param>
235 </when>
236 <when value="win">
237 <param name="trimQualWin" size="4" type="integer" value="20" label="Quality threshold"/>
238 <param name="trimQualWinSize" size="4" type="integer" value="5" label="Window length" help="sliding window average quality approach from left end"/>
239
240 <param name="trimQualPostWin" type="select" label="After adapter removal">
241 <option value="" selected="true">No</option>
242 <option value="--qtrim-post-removal">Yes</option>
243 </param>
244 </when>
245 <when value="bwa">
246 <param name="trimQualBWA" size="4" type="integer" value="20" label="Quality threshold" help="trimming approach used by BWA"/>
247
248 <param name="trimQualPostBWA" type="select" label="After adapter removal">
249 <option value="" selected="true">No</option>
250 <option value="--qtrim-post-removal">Yes</option>
251 </param>
252 </when>
253 </conditional>
254
255
256 <conditional name="cAdapters">
257 <param name="select" type="select" label="4) Adapter removal">
160 <option value="off" selected="true">Off</option> 258 <option value="off" selected="true">Off</option>
161 <option value="on">On</option> 259 <option value="on">On</option>
162 </param> 260 </param>
163 <when value="off"> 261 <when value="off">
164 </when> 262 </when>
165 <when value="on"> 263 <when value="on">
166 <param name="trimLeft" size="4" type="integer" value="0" label="Left" optional="false"/> 264 <conditional name="ccAdapters">
167 <param name="trimRight" size="4" type="integer" value="0" label="Right" optional="false" help="trims specified number of bases from read ends"/> 265 <param name="select" type="select" label="Adapter source">
266 <option value="file" selected="true">Adapter file</option>
267 <option value="files">Two adapter files</option>
268 <option value="preset">Illumina preset</option>
269 <option value="seq">Single sequence</option>
270 </param>
271 <when value="file">
272 <param format="fasta" name="adapterFile" type="data" label="Fasta adapter file"/>
273 </when>
274 <when value="files">
275 <param format="fasta" name="adapterFile1" type="data" label="Fasta adapter file for reads 1"/>
276 <param format="fasta" name="adapterFile2" type="data" label="Fasta adapter file for reads 2"/>
277 </when>
278 <when value="preset">
279 <param name="adapterPreset" type="select" label="Adapter preset">
280 <option value="TruSeq" selected="true">TruSeq LT and HT-based kits</option>
281 <option value="SmallRNA">TruSeq Small RNA</option>
282 <option value="Methyl">TruSeq DNA Methylation and ScriptSeq</option>
283 <option value="Ribo">TruSeq Ribo Profile</option>
284 <option value="Nextera">Nextera, AmpliSeq, and TruSight</option>
285 <option value="NexteraMP">Nextera Mate Pair</option>
286 </param>
287 </when>
288 <when value="seq">
289 <param name="adapterSeq" size="40" label="Adapter sequence" type="text" value=""/>
290 </when>
291 </conditional>
292
293 <param name="aMinOverlap" size="4" type="integer" value="3" label="Minimum overlap"/>
294 <param name="aThresh" size="4" type="float" value="0.1" label="Error rate" help="allowed fraction of mismatches and indels"/>
295
296 <param name="aTrimEnd" type="select" label="Trim-end mode">
297 <option value="RIGHT" selected="true">Right</option>
298 <option value="LEFT">Left</option>
299 <option value="RTAIL">Right tail</option>
300 <option value="LTAIL">Left tail</option>
301 <option value="ANY">Any</option>
302 </param>
303
304 <conditional name="cPairOverlap">
305 <param name="select" type="select" label="Pair overlap detection">
306 <option value="off" selected="true">Off</option>
307 <option value="on">On</option>
308 </param>
309 <when value="off">
310 </when>
311 <when value="on">
312 <param name="aPairOverlap" type="select" label="Detection mode">
313 <option value="ON" selected="true">Standard</option>
314 <option value="SHORT">Trim short</option>
315 </param>
316 <param name="aMinPoverlap" size="4" type="integer" value="40" label="Minimum pair overlap"/>
317 </when>
318 </conditional>
319
320 <section name="aAdvanced" title="Advanced options" expanded="false">
321
322 <conditional name="caTailLen">
323 <param name="select" type="select" label="Change tail length">
324 <option value="no" selected="true">No</option>
325 <option value="yes">Yes</option>
326 </param>
327 <when value="no">
328 </when>
329 <when value="yes">
330 <param name="aTailLen" size="4" type="integer" value="" label="Tail length"/>
331 </when>
332 </conditional>
333
334 <conditional name="cRevComp">
335 <param name="select" type="select" label="Reverse complements of adapters">
336 <option value="off" selected="true">Off</option>
337 <option value="on">On</option>
338 <option value="only">Only</option>
339 </param>
340 <when value="off">
341 </when>
342 <when value="on">
343 <param name="aRevCompEnd" type="select" label="Different trim-end for reverse complements">
344 <option value="off" selected="true">Off</option>
345 <option value="RIGHT">Right</option>
346 <option value="LEFT">Left</option>
347 <option value="RTAIL">Right tail</option>
348 <option value="LTAIL">Left tail</option>
349 <option value="ANY">Any</option>
350 </param>
351 </when>
352 </conditional>
353
354
355 <param name="aReadSet" type="select" label="Removal for single read set">
356 <option value="" selected="true">No</option>
357 <option value="--adapter-read-set 1">1st</option>
358 <option value="--adapter-read-set 2">2nd</option>
359 </param>
360
361 <param name="aCycles" size="4" type="integer" value="1" label="Number of removal cycles"/>
362
363 <conditional name="caAlignScores">
364 <param name="select" type="select" label="Modify alignment scores">
365 <option value="no" selected="true">No</option>
366 <option value="yes">Yes</option>
367 </param>
368 <when value="no">
369 </when>
370 <when value="yes">
371 <param name="aMatch" size="3" type="integer" value="1" label="Match"/>
372 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch"/>
373 <param name="aGap" size="3" type="integer" value="-6" label="Gap"/>
374 </when>
375 </conditional>
376 </section>
168 </when> 377 </when>
169 </conditional> 378 </conditional>
170 379
171 <conditional name="cTrimPhred"> 380
172 <param name="select" type="select" label="3) Quality-based trimming"> 381 <conditional name="cTrimLen">
382 <param name="select" type="select" label="5) Trimming to length">
173 <option value="off" selected="true">Off</option> 383 <option value="off" selected="true">Off</option>
174 <option value="on">On</option> 384 <option value="on">On</option>
175 </param> 385 </param>
176 <when value="off"> 386 <when value="off">
177 </when> 387 </when>
178 <when value="on"> 388 <when value="on">
179 <param name="trimPhred" size="4" type="integer" value="10" label="Threshold" optional="false" help="trim right end until specified or higher quality reached"/> 389 <param name="trimLen" size="4" type="integer" value="" label="Length" help="trim reads to certain length from right"/>
180 </when> 390 </when>
181 </conditional> 391 </conditional>
182 392
183 393 <param name="minReadLen" size="4" type="integer" value="20" label="6) Minimum read length"/>
184 <conditional name="cBarcodes"> 394
185 <param name="select" type="select" label="4) Barcode detection"> 395 <conditional name="cAddOptions">
186 <option value="off" selected="true">Off</option> 396 <param name="select" type="select" label="Additional options">
187 <option value="on">On</option> 397 <option value="hide" selected="true">Hide</option>
188 </param>
189 <when value="off">
190 </when>
191 <when value="on">
192 <param format="fasta" name="barcodes" type="data" label="Barcodes" optional="false"/>
193
194 <conditional name="cbReads">
195 <param name="select" type="select" label="Separate barcode reads">
196 <option value="no" selected="true">No</option>
197 <option value="yes">Yes</option>
198 </param>
199 <when value="yes">
200 <param format="fastq,fastqsanger,fastqsolexa,fastqillumina" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
201 </when>
202 <when value="no">
203 <param name="bKeep" type="select" label="Remove barcodes within reads">
204 <option value="" selected="true">Yes</option>
205 <option value="--barcode-keep">No</option>
206 </param>
207 </when>
208 </conditional>
209
210 <param name="bUnassigned" type="select" label="Include unassigned reads">
211 <option value="" selected="true">No</option>
212 <option value="--barcode-unassigned">Yes</option>
213 </param>
214
215 <param name="bTrimEnd" type="select" label="Trim-end mode" optional="false">
216 <option value="ANY" selected="true">Any</option>
217 <option value="RIGHT">Right</option>
218 <option value="RTAIL">Right tail</option>
219 <option value="LEFT">Left</option>
220 <option value="LTAIL">Left tail</option>
221 </param>
222
223 <conditional name="cbTailLen">
224 <param name="select" type="select" label="Change tail length">
225 <option value="no" selected="true">No</option>
226 <option value="yes">Yes</option>
227 </param>
228 <when value="no">
229 </when>
230 <when value="yes">
231 <param name="bTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
232 </when>
233 </conditional>
234
235 <conditional name="cbMinOverlap">
236 <param name="select" type="select" label="Change min-overlap" help="default: barcode length">
237 <option value="no" selected="true">No</option>
238 <option value="yes">Yes</option>
239 </param>
240 <when value="no">
241 </when>
242 <when value="yes">
243 <param name="bMinOverlap" size="4" type="integer" value="8" label="Min-overlap" optional="false"/>
244 </when>
245 </conditional>
246
247 <param name="bThresh" size="4" type="integer" value="1" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
248
249 <conditional name="cbAlignScores">
250 <param name="select" type="select" label="Modify alignment scores">
251 <option value="no" selected="true">No</option>
252 <option value="yes">Yes</option>
253 </param>
254 <when value="no">
255 </when>
256 <when value="yes">
257 <param name="bMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
258 <param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
259 <param name="bGap" size="3" type="integer" value="-9" label="Gap" optional="false"/>
260 </when>
261 </conditional>
262 </when>
263 </conditional>
264
265
266 <conditional name="cAdapters">
267 <param name="select" type="select" label="5) Adapter removal">
268 <option value="off" selected="true">Off</option>
269 <option value="on">On</option>
270 </param>
271
272 <when value="off">
273 </when>
274 <when value="on">
275 <conditional name="ccAdapters">
276 <param name="select" type="select" label="Adapter source">
277 <option value="data" selected="true">Fasta</option>
278 <option value="seq">Sequence</option>
279 <!-- <option value="file">File</option> -->
280 </param>
281 <when value="data">
282 <param format="fasta" name="adaptersData" type="data" label="Adapters" optional="false"/>
283 </when>
284 <when value="seq">
285 <param name="adapterSeq" size="40" label="Adapter" type="text" value="AAAAAAAAAAAAAA" optional="false"/>
286 </when>
287 <!-- <when value="file">
288 <param name="adaptersFile" type="file" label="Adapters file" optional="false"/>
289 </when> -->
290 </conditional>
291
292 <param name="aTrimEnd" type="select" label="Trim-end mode" optional="false">
293 <option value="ANY">Any</option>
294 <option value="RIGHT" selected="true">Right</option>
295 <option value="RTAIL">Right tail</option>
296 <option value="LEFT">Left</option>
297 <option value="LTAIL">Left tail</option>
298 </param>
299
300 <conditional name="caTailLen">
301 <param name="select" type="select" label="Change tail length">
302 <option value="no" selected="true">No</option>
303 <option value="yes">Yes</option>
304 </param>
305 <when value="no">
306 </when>
307 <when value="yes">
308 <param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
309 </when>
310 </conditional>
311
312 <param name="aReadSet" type="select" label="Removal for single read set">
313 <option value="" selected="true">No</option>
314 <option value="--adapter-read-set 1">1st</option>
315 <option value="--adapter-read-set 2">2nd</option>
316 </param>
317
318 <param name="aMinOverlap" size="4" type="integer" value="1" label="Min-overlap" optional="false"/>
319 <param name="aThresh" size="4" type="integer" value="3" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
320
321 <conditional name="caAlignScores">
322 <param name="select" type="select" label="Modify alignment scores">
323 <option value="no" selected="true">No</option>
324 <option value="yes">Yes</option>
325 </param>
326 <when value="no">
327 </when>
328 <when value="yes">
329 <param name="aMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
330 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
331 <param name="aGap" size="3" type="integer" value="-6" label="Gap" optional="false"/>
332 </when>
333 </conditional>
334 </when>
335 </conditional>
336
337
338 <conditional name="cTrimLen">
339 <param name="select" type="select" label="6) Trimming to length">
340 <option value="off" selected="true">Off</option>
341 <option value="on">On</option>
342 </param>
343 <when value="off">
344 </when>
345 <when value="on">
346 <param name="trimLen" size="4" type="integer" value="30" label="Length" optional="false" help="trim reads to certain length from right"/>
347 </when>
348 </conditional>
349
350 <param name="minReadLen" size="4" type="integer" value="18" label="7) Minimum read length" optional="false" help="shorter reads are discarded"/>
351
352 <conditional name="cOutput">
353 <param name="select" type="select" label="Output selection">
354 <option value="off" selected="true">Off</option>
355 <option value="show">Show</option> 398 <option value="show">Show</option>
356 </param> 399 </param>
357 <when value="off"> 400 <when value="hide">
358 </when>
359 <when value="show">
360 <param name="fastaOutput" type="select" label="Fasta output">
361 <option value="" selected="true">Off</option>
362 <option value="--fasta-output">Always</option>
363 </param>
364
365 <param name="lenDist" type="select" label="Read length distribution">
366 <option value="" selected="true">Off</option>
367 <option value="--length-dist">On</option>
368 </param>
369
370 <param name="singleReads" type="select" label="Single reads">
371 <option value="" selected="true">Off</option>
372 <option value="--single-reads">On</option>
373 </param>
374 </when>
375 </conditional>
376
377 <conditional name="cLogging">
378 <param name="select" type="select" label="Logging and tagging options">
379 <option value="off" selected="true">Off</option>
380 <option value="show">Show</option>
381 </param>
382 <when value="off">
383 </when> 401 </when>
384 <when value="show"> 402 <when value="show">
385 <param name="logLevel" type="select" label="Alignment logging"> 403 <param name="logLevel" type="select" label="Alignment logging">
386 <option value="" selected="true">Off</option> 404 <option value="" selected="true">Off</option>
387 <option value="--align-log ALL">All</option> 405 <option value="--align-log ALL">All</option>
401 419
402 <param name="rndTags" type="select" label="UMI tags"> 420 <param name="rndTags" type="select" label="UMI tags">
403 <option value="" selected="true">Off</option> 421 <option value="" selected="true">Off</option>
404 <option value="--umi-tags">On</option> 422 <option value="--umi-tags">On</option>
405 </param> 423 </param>
424
425 <param name="singleReadsP" type="select" label="Single reads as paired">
426 <option value="" selected="true">Off</option>
427 <option value="--single-reads-paired">On</option>
428 </param>
429
430 <conditional name="cReadBundle">
431 <param name="select" type="select" label="Read bundle options">
432 <option value="hide" selected="true">Hide</option>
433 <option value="show">Show</option>
434 </param>
435 <when value="hide">
436 </when>
437 <when value="show">
438 <param name="bundle" size="4" type="integer" value="256" label="Number of paired reads per bundle"/>
439 <param name="bundles" size="4" type="integer" value="" optional="true" label="Only certain number of bundles for testing"/>
440 </when>
441 </conditional>
406 </when> 442 </when>
407 </conditional> 443 </conditional>
408 444
409 </inputs> 445 </inputs>
410 446
411 <stdio>
412 <exit_code range="1:" level="fatal" description="Error!" />
413 </stdio>
414
415 <outputs> 447 <outputs>
416 <data format="txt" name="output" metadata_source="reads"/> 448 <data name="outlog" format="txt" label="Flexbar log for ${on_string}"/>
449
450 <data name="rsout" label="Flexbar on ${reads.rs.name}" format_source="rs">
451 <filter>reads['mode'] == 'se'</filter>
452 </data>
453
454 <data name="r1out" label="Flexbar on ${reads.r1.name}" format_source="r1">
455 <filter>reads['mode'] == "pe"</filter>
456 </data>
457 <data name="r2out" label="Flexbar on ${reads.r2.name}" format_source="r2">
458 <filter>reads['mode'] == "pe"</filter>
459 </data>
460
461 <collection name="rcout" type="paired" label="Flexbar on ${on_string}">
462 <filter>reads['mode'] == "pc"</filter>
463 <data name="forward" label="Flexbar on ${reads.rc.forward.name}" format_source="rc['forward']"/>
464 <data name="reverse" label="Flexbar on ${reads.rc.reverse.name}" format_source="rc['reverse']"/>
465 </collection>
417 </outputs> 466 </outputs>
418
419 467
420 <help> 468 <help>
421 469
422 **Description** 470 **Description**
423 471