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comparison flexbar_no_split.xml @ 12:55b539a509f0 draft

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add flexbar_no_split
author rnateam
date Mon, 23 Nov 2015 10:42:04 -0500
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11:f5bb83740999 12:55b539a509f0
1
2 <!-- Flexbar tool definition for Galaxy, version 2.5 -->
3 <!-- Author: Johannes Roehr -->
4 <!-- Modified by Daniel Maticzka -->
5 <!-- * Removed ability to split. This enables setting a fixed number of -->
6 <!-- outputs so that the tool can be used in workflows. -->
7
8
9 <tool id="flexbar_no_split" name="Flexbar" version="2.5">
10
11 <description>flexible adapter removal (no barcodes version)</description>
12
13 <requirements>
14 <requirement type="package" version="2.5">flexbar</requirement>
15 </requirements>
16
17 <version_command>flexbar --version</version_command>
18
19 <command>
20
21 flexbar
22
23 --threads \${GALAXY_SLOTS:-1}
24
25 --reads $reads
26
27 --reads2 $reads2
28
29 #if $reads.ext == "fastqsanger":
30 --format sanger
31 #end if
32 #if $reads.ext == "fastqsolexa":
33 --format solexa
34 #end if
35 #if $reads.ext == "fastqillumina":
36 --format i1.3
37 #end if
38 #if $reads.ext == "csfasta":
39 --color-space
40 #end if
41 #if $reads.ext == "fastqcssanger":
42 --color-space
43 #end if
44
45
46 --max-uncalled $maxUncalled
47 --min-read-length $minReadLen
48
49 #if $trimEnds.select == "on":
50 --pre-trim-left $trimEnds.trimLeft
51 --pre-trim-right $trimEnds.trimRight
52 #end if
53
54 #if $cTrimPhred.select == "on":
55 --pre-trim-phred $cTrimPhred.trimPhred
56 #end if
57
58 #if $cTrimLen.select == "on":
59 --post-trim-length $cTrimLen.trimLen
60 #end if
61
62
63 #if $cAdapters.select == "on":
64
65 #if $cAdapters.ccAdapters.select == "data":
66 --adapters $cAdapters.ccAdapters.adaptersData
67 #end if
68
69 #if $cAdapters.ccAdapters.select == "seq":
70 --adapter-seq $cAdapters.ccAdapters.adapterSeq
71 #end if
72
73 --adapter-trim-end $cAdapters.aTrimEnd
74
75 #if $cAdapters.caTailLen.select == "yes":
76 --adapter-tail-length $cAdapters.caTailLen.aTailLen
77 #end if
78
79 $cAdapters.aReadSet
80
81 --adapter-min-overlap $cAdapters.aMinOverlap
82 --adapter-threshold $cAdapters.aThresh
83
84 #if $cAdapters.caAlignScores.select == "yes":
85 --adapter-match $aMatch
86 --adapter-mismatch $aMismatch
87 --adapter-gap $aGap
88 #end if
89 #end if
90
91
92 #if $cOutput.select == "show":
93 $cOutput.fastaOutput
94 $cOutput.lenDist
95 $cOutput.singleReads
96 #end if
97
98 #if $cLogging.select == "show":
99 $cLogging.logLevel
100 $cLogging.numTags
101 $cLogging.remTags
102 $cLogging.rndTags
103 #end if
104
105 > $output;
106
107 mv flexbar_1.fastq $output_1;
108 mv flexbar_2.fastq $output_2;
109
110 </command>
111
112
113 <inputs>
114
115 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
116
117
118 <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"/>
119
120
121 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/>
122
123 <conditional name="trimEnds">
124 <param name="select" type="select" label="2) Trimming of ends">
125 <option value="off" selected="true">Off</option>
126 <option value="on">On</option>
127 </param>
128 <when value="off">
129 </when>
130 <when value="on">
131 <param name="trimLeft" size="4" type="integer" value="0" label="Left" optional="false"/>
132 <param name="trimRight" size="4" type="integer" value="0" label="Right" optional="false" help="trims specified number of bases from read ends"/>
133 </when>
134 </conditional>
135
136 <conditional name="cTrimPhred">
137 <param name="select" type="select" label="3) Phred-trimming">
138 <option value="off" selected="true">Off</option>
139 <option value="on">On</option>
140 </param>
141 <when value="off">
142 </when>
143 <when value="on">
144 <param name="trimPhred" size="4" type="integer" value="10" label="Threshold" optional="false" help="trim right end until specified or higher quality reached"/>
145 </when>
146 </conditional>
147
148
149 <conditional name="cAdapters">
150 <param name="select" type="select" label="5) Adapter removal">
151 <option value="off" selected="true">Off</option>
152 <option value="on">On</option>
153 </param>
154
155 <when value="off">
156 </when>
157 <when value="on">
158 <conditional name="ccAdapters">
159 <param name="select" type="select" label="Adapter source">
160 <option value="data" selected="true">Fasta</option>
161 <option value="seq">Sequence</option>
162 <!-- <option value="file">File</option> -->
163 </param>
164 <when value="data">
165 <param format="fasta" name="adaptersData" type="data" label="Adapters" optional="false"/>
166 </when>
167 <when value="seq">
168 <param name="adapterSeq" size="40" label="Adapter" type="text" value="AAAAAAAAAAAAAA" optional="false"/>
169 </when>
170 <!-- <when value="file">
171 <param name="adaptersFile" type="file" label="Adapters file" optional="false"/>
172 </when> -->
173 </conditional>
174
175 <param name="aTrimEnd" type="select" label="Trim-end mode" optional="false">
176 <option value="ANY">Any</option>
177 <option value="RIGHT" selected="true">Right</option>
178 <option value="RIGHT_TAIL">Right tail</option>
179 <option value="LEFT">Left</option>
180 <option value="LEFT_TAIL">Left tail</option>
181 </param>
182
183 <conditional name="caTailLen">
184 <param name="select" type="select" label="Change tail length">
185 <option value="no" selected="true">No</option>
186 <option value="yes">Yes</option>
187 </param>
188 <when value="no">
189 </when>
190 <when value="yes">
191 <param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/>
192 </when>
193 </conditional>
194
195 <param name="aReadSet" type="select" label="Removal for single read set">
196 <option value="" selected="true">No</option>
197 <option value="--adapter-read-set 1">1st</option>
198 <option value="--adapter-read-set 2">2nd</option>
199 </param>
200
201 <param name="aMinOverlap" size="4" type="integer" value="1" label="Min-overlap" optional="false"/>
202 <param name="aThresh" size="4" type="integer" value="3" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
203
204 <conditional name="caAlignScores">
205 <param name="select" type="select" label="Modify alignment scores">
206 <option value="no" selected="true">No</option>
207 <option value="yes">Yes</option>
208 </param>
209 <when value="no">
210 </when>
211 <when value="yes">
212 <param name="aMatch" size="3" type="integer" value="1" label="Match" optional="false"/>
213 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
214 <param name="aGap" size="3" type="integer" value="-7" label="Gap" optional="false"/>
215 </when>
216 </conditional>
217 </when>
218 </conditional>
219
220
221 <conditional name="cTrimLen">
222 <param name="select" type="select" label="6) Trimming to length">
223 <option value="off" selected="true">Off</option>
224 <option value="on">On</option>
225 </param>
226 <when value="off">
227 </when>
228 <when value="on">
229 <param name="trimLen" size="4" type="integer" value="30" label="Length" optional="false" help="trim reads to certain length from right"/>
230 </when>
231 </conditional>
232
233 <param name="minReadLen" size="4" type="integer" value="18" label="7) Minimum read length" optional="false" help="shorter reads are discarded"/>
234
235 <conditional name="cOutput">
236 <param name="select" type="select" label="Output selection">
237 <option value="off" selected="true">Off</option>
238 <option value="show">Show</option>
239 </param>
240 <when value="off">
241 </when>
242 <when value="show">
243 <param name="fastaOutput" type="select" label="Fasta output">
244 <option value="" selected="true">Off</option>
245 <option value="--fasta-output">Always</option>
246 </param>
247
248 <param name="lenDist" type="select" label="Read length distribution">
249 <option value="" selected="true">Off</option>
250 <option value="--length-dist">On</option>
251 </param>
252
253 <param name="singleReads" type="select" label="Single reads">
254 <option value="" selected="true">Off</option>
255 <option value="--single-reads">On</option>
256 </param>
257 </when>
258 </conditional>
259
260 <conditional name="cLogging">
261 <param name="select" type="select" label="Logging and tagging options">
262 <option value="off" selected="true">Off</option>
263 <option value="show">Show</option>
264 </param>
265 <when value="off">
266 </when>
267 <when value="show">
268 <param name="logLevel" type="select" label="Alignment logging">
269 <option value="" selected="true">Off</option>
270 <option value="--log-level ALL">All</option>
271 <option value="--log-level MOD">Modified</option>
272 <option value="--log-level TAB">Tabular</option>
273 </param>
274
275 <param name="numTags" type="select" label="Number tags">
276 <option value="" selected="true">Off</option>
277 <option value="--number-tags">On</option>
278 </param>
279
280 <param name="remTags" type="select" label="Removal tags">
281 <option value="" selected="true">Off</option>
282 <option value="--removal-tags">On</option>
283 </param>
284
285 <param name="rndTags" type="select" label="Random tags">
286 <option value="" selected="true">Off</option>
287 <option value="--random-tags">On</option>
288 </param>
289 </when>
290 </conditional>
291
292 </inputs>
293
294 <stdio>
295 <exit_code range="1:" level="fatal" description="Error!" />
296 </stdio>
297
298 <outputs>
299 <data format="txt" name="output" metadata_source="reads"/>
300 <data format="fastq" name="output_1"/>
301 <data format="fastq" name="output_2"/>
302 </outputs>
303
304
305 <help>
306
307 **Description**
308
309 A restricted version of the flexbar tool for use in workflows. This version is missing the ability to demultiplex barcoded runs. It is restricted to handling paired-end reads. For that reason there is always two fastq outputs, allowing the tool to be incorporated into workflows.
310
311 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.
312
313 .. _project: https://github.com/seqan/flexbar
314
315 ------
316
317 **Trim-end modes**
318
319 **Any:** longer side of read remains after overlap removal
320
321 **Left:** right side remains after removal, align before or at read end
322
323 **Right:** left part remains after removal, align after or at read start
324
325 **Left tail:** consider first n bases of reads in alignment
326
327 **Right tail:** use only last n bases, see tail-length options
328
329 ------
330
331 **Documentation**
332
333 Further documentation is available on the `manual`__ wiki page and via the command line help screen.
334
335 .. __: https://github.com/seqan/flexbar/wiki
336
337 ------
338
339 **Reference**
340
341 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.
342
343 </help>
344
345 </tool>