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author devteam
date Mon, 27 Jan 2014 09:25:15 -0500
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1 <tool id="bowtie2" name="Bowtie2" version="0.2">
2 <!-- Wrapper compatible with Bowtie version 2.0.0 -->
3 <description>is a short-read aligner</description>
4 <version_command>bowtie2 --version</version_command>
5 <requirements>
6 <requirement type="package" version="2.1.0">bowtie2</requirement>
7 <requirement type="package" version="0.1.18">samtools</requirement>
8 </requirements>
9
10 <command>
11 ## prepare bowtie2 index
12 #set index_path = ''
13 #if str($reference_genome.source) == "history":
14 bowtie2-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
15 #set index_path = 'genome'
16 #else:
17 #set index_path = $reference_genome.index.fields.path
18 #end if
19
20 ## execute bowtie2
21 bowtie2
22
23 ## number of threads
24 -p \${GALAXY_SLOTS:-4}
25
26 ## index file path
27 -x $index_path
28
29 ## check for single/pair-end
30 #if str( $library.type ) == "single"
31 ## prepare inputs
32 -U $library.input_1
33
34 #if $output_unaligned_reads_l
35 --un $output_unaligned_reads_l
36 #end if
37 #else
38 ## prepare inputs
39 -1 $library.input_1
40 -2 $library.input_2
41 -I $library.min_insert
42 -X $library.max_insert
43
44 #if $output_unaligned_reads_l
45 --un-conc $output_unaligned_reads_l
46 #end if
47 #end if
48
49 ## configure settings
50 #if str($params.full) == "yes":
51 ## add alignment type
52 $params.align_type
53
54 ## add performance
55 $params.performance
56
57 ## add time flag
58 $params.time
59
60 ## add nofw/norc
61 $params.nofw_norc
62
63 ## set gbar
64 --gbar $params.gbar
65
66 ## check skip
67 #if str($params.skip) != "0":
68 -s $params.skip
69 #end if
70
71 ## check upto
72 #if str($params.upto) != "0":
73 -u $params.upto
74 #end if
75
76 ## check trim5
77 #if str($params.trim5) != "0":
78 -5 $params.trim5
79 #end if
80
81 ## check trim3
82 #if str($params.trim3) != "0":
83 -3 $params.trim3
84 #end if
85 #end if
86
87 ## read group information
88 #if str($read_group.selection) == "yes":
89 #if $read_group.rgid and $read_group.rglb and $read_group.rgpl and $read_group.rgsm:
90 --rg-id "$read_group.rgid"
91 --rg "LB:$read_group.rglb"
92 --rg "PL:$read_group.rgpl"
93 --rg "SM:$read_group.rgsm"
94 #end if
95 #end if
96
97 ## view/sort and output file
98 | samtools view -Su - | samtools sort -o - - > $output
99
100 ## rename unaligned sequence files
101 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
102 #set left = str($output_unaligned_reads_l).replace( '.dat', '.1.dat' )
103 #set right = str($output_unaligned_reads_l).replace( '.dat', '.2.dat' )
104
105 ; mv $left $output_unaligned_reads_l;
106 mv $right $output_unaligned_reads_r
107 #end if
108 </command>
109
110 <!-- basic error handling -->
111 <stdio>
112 <exit_code range="1:" level="fatal" description="Tool exception" />
113 </stdio>
114
115 <inputs>
116 <!-- single/paired -->
117 <conditional name="library">
118 <param name="type" type="select" label="Is this library mate-paired?">
119 <option value="single">Single-end</option>
120 <option value="paired">Paired-end</option>
121 </param>
122 <when value="single">
123 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
124 </when>
125 <when value="paired">
126 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
127 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
128 <param name="min_insert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
129 <param name="max_insert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" />
130 </when>
131 </conditional>
132
133 <!-- unaligned file -->
134 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads to separate file(s)" />
135
136 <!-- reference genome -->
137 <conditional name="reference_genome">
138 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
139 <option value="indexed">Use a built-in index</option>
140 <option value="history">Use one from the history</option>
141 </param>
142 <when value="indexed">
143 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
144 <options from_data_table="bowtie2_indexes">
145 <filter type="sort_by" column="2"/>
146 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
147 </options>
148 </param>
149 </when>
150 <when value="history">
151 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
152 </when>
153 </conditional>
154
155 <!-- group settings -->
156 <conditional name="read_group">
157 <param name="selection" type="select" label="Specify the read group for this file?">
158 <option value="yes">Yes</option>
159 <option value="no" selected="True">No</option>
160 </param>
161 <when value="yes">
162 <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions." />
163 <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" />
164 <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO" />
165 <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" />
166 </when>
167 <when value="no" />
168 </conditional>
169
170 <!-- full/advanced params. -->
171 <conditional name="params">
172 <param name="full" type="select" label="Parameter Settings" help="You can use the default settings or set custom values for any of Bowtie's parameters.">
173 <option value="no">Use defaults</option>
174 <option value="yes">Full parameter list</option>
175 </param>
176 <when value="yes">
177 <param name="align_type" type="select" label="Type of alignment">
178 <option value="" selected="true">End to end</option>
179 <option value="--local">Local</option>
180 </param>
181
182 <param name="performance" type="select" label="Preset option">
183 <option value="">Default</option>
184 <option value="--very-fast">Very fast</option>
185 <option value="--fast">Fast</option>
186 <option value="--sensitive" selected="true">Sensitive</option>
187 <option value="--very-sensitive">Very sensitive</option>
188 </param>
189
190 <param name="gbar" type="integer" value="4" label="Disallow gaps within n-positions of read" />
191
192 <param name="trim5" type="integer" value="0" label="Trim n-bases from 5' of each read" />
193
194 <param name="trim3" type="integer" value="0" label="Trim n-bases from 3' of each read" />
195
196 <param name="skip" type="integer" value="0" label="Skip the first n-reads" />
197
198 <param name="upto" type="integer" value="0" label="Number of reads to be aligned (0 = unlimited)" />
199
200 <param name="nofw_norc" type="select" label="Strand directions">
201 <option value="">Both</option>
202 <option value="--nofw">Disable forward</option>
203 <option value="--norc">Disable reverse</option>
204 </param>
205
206 <param name="time" type="select" label="Log mapping time">
207 <option value="">No</option>
208 <option value="--time">Yes</option>
209 </param>
210
211 </when>
212 <when value="no" />
213 </conditional>
214
215 </inputs>
216
217 <!-- define outputs -->
218 <outputs>
219 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
220 <filter>unaligned_file is True</filter>
221 <actions>
222 <action type="format">
223 <option type="from_param" name="library.input_1" param_attribute="ext" />
224 </action>
225 </actions>
226 </data>
227 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
228 <filter>library['type'] == "paired" and unaligned_file is True</filter>
229 <actions>
230 <action type="format">
231 <option type="from_param" name="library.input_1" param_attribute="ext" />
232 </action>
233 </actions>
234 </data>
235 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads">
236 <actions>
237 <conditional name="reference_genome.source">
238 <when value="indexed">
239 <action type="metadata" name="dbkey">
240 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
241 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
242 <filter type="param_value" ref="reference_genome.index" column="0"/>
243 </option>
244 </action>
245 </when>
246 <when value="history">
247 <action type="metadata" name="dbkey">
248 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
249 </action>
250 </when>
251 </conditional>
252 </actions>
253 </data>
254 </outputs>
255
256 <tests>
257 <test>
258 <!-- basic test on single paired default run -->
259 <param name="type" value="single"/>
260 <param name="selection" value="no"/>
261 <param name="full" value="no"/>
262 <param name="unaligned_file" value="false"/>
263 <param name="source" value="history" />
264 <param name="input_1" value="bowtie2/phix_reads.fastq" ftype="fastqsanger"/>
265 <param name="own_file" value="bowtie2/phix_genome.fasta" />
266 <output name="output" file="bowtie2/phix_mapped.bam" />
267 </test>
268 </tests>
269
270 <help>
271 **Bowtie2 Overview**
272
273 Bowtie_ is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 supports gapped, local, and paired-end alignment modes. Bowtie 2 outputs alignments in SAM format, enabling interoperation with a large number of other tools.
274
275 *Please cite:* Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25 (2009)
276
277 .. _Bowtie: http://bowtie-bio.sourceforge.net/bowtie2/
278
279 ------
280
281 **Inputs**
282
283 Bowtie 2 accepts files in Sanger FASTQ format (single or pair-end). Use the FASTQ Groomer to prepare your files.
284
285 ------
286
287 **Outputs**
288
289 The mapped sequence reads are provided as BAM file, while unmapped reads are optionally available as SAM records. When Bowtie 2 finishes running, it prints messages summarizing what happened. These messages are printed to the "standard error" ("stderr") filehandle. For datasets consisting of unpaired reads, the summary might look like this::
290
291 20000 reads; of these:
292 20000 (100.00%) were unpaired; of these:
293 1247 (6.24%) aligned 0 times
294 18739 (93.69%) aligned exactly 1 time
295 14 (0.07%) aligned >1 times
296 93.77% overall alignment rate
297
298 ------
299
300 **Alignment options**
301
302 *--end-to-end/--local*
303
304 By default, Bowtie 2 performs end-to-end read alignment. That is, it searches for alignments involving all of the read characters. This is also called an "untrimmed" or "unclipped" alignment. When the --local option is specified, Bowtie 2 performs local read alignment. In this mode, Bowtie 2 might "trim" or "clip" some read characters from one or both ends of the alignment if doing so maximizes the alignment score.
305
306 End-to-end alignment example::
307
308 Read GACTGGGCGATCTCGACTTCG
309 ||||| ||||||||||||||
310 Reference GACTG--CGATCTCGACATCG
311
312 Local alignment example::
313
314 Read ACGGTTGCGTTAA-TCCGCCACG
315 ||||||||| ||||||
316 Reference TAACTTGCGTTAAATCCGCCTGG
317
318 *-s/--skip (default: 0)*
319
320 Skip (i.e. do not align) the first n-reads or pairs in the input.
321
322 *-u/--qupto (default: no limit)*
323
324 Align the first n-reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop.
325
326 *-5/--trim5 (default: 0)*
327
328 Trim n-bases from 5' (left) end of each read before alignment.
329
330 *-3/--trim3 (default: 0)*
331
332 Trim n-bases from 3' (right) end of each read before alignment.
333
334 *--nofw/--norc (default: both strands enabled)*
335
336 If --nofw is specified, Bowtie 2 will not attempt to align unpaired reads to the forward (Watson) reference strand. If --norc is specified, bowtie2 will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes Bowtie 2 to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default: both strands enabled.
337
338 *--gbar (default: 4)*
339
340 Disallow gaps within n-positions of the beginning or end of the read.
341
342 ------
343
344 **Paired-end options**
345
346 *-I/--minins (default: 0)*
347
348 The minimum fragment length for valid paired-end alignments. E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates.
349
350 The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences bewteen -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient.
351
352 *-X/--maxins (default: 0)*
353
354 The maximum fragment length for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates.
355
356 The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences bewteen -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient.
357
358 ------
359
360 **SAM options**
361
362 *--rg-id [text]*
363
364 Set the read group ID to [text]. This causes the SAM @RG header line to be printed, with [text] as the value associated with the ID: tag. It also causes the RG:Z: extra field to be attached to each SAM output record, with value set to [text].
365
366 *--rg [text]*
367
368 Add [text] as a field on the @RG header line. Note: in order for the @RG line to appear, --rg-id must also be specified. This is because the ID tag is required by the SAM Spec. Specify --rg multiple times to set multiple fields. See the SAM Spec for details about what fields are legal.
369
370 ------
371
372 **Output options**
373
374 *--un/--un-conc*
375
376 Write reads that fail to align concordantly to file(s). These reads correspond to the SAM records.
377
378 *-t/--time (default: off)*
379
380 Print the wall-clock time required to load the index files and align the reads. This is printed to the "standard error" ("stderr") filehandle.
381
382 </help>
383 </tool>