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comparison bowtie2_wrapper.xml @ 18:121110a12cc9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
author iuc
date Fri, 24 Nov 2017 07:44:07 -0500
parents 66f992977578
children 97d1923c8c4b
comparison
equal deleted inserted replaced
17:66f992977578 18:121110a12cc9
1 <tool id="bowtie2" name="Bowtie2" version="2.3.2.2" profile="17.01"> 1 <tool id="bowtie2" name="Bowtie2" version="2.3.3.1" profile="17.01">
2 <description>- map reads against reference genome</description> 2 <description>- map reads against reference genome</description>
3 <macros> 3 <macros>
4 <import>bowtie2_macros.xml</import> 4 <import>bowtie2_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="2.3.2">bowtie2</requirement> 7 <requirement type="package" version="2.3.3.1">bowtie2</requirement>
8 <requirement type="package" version="1.3.1">samtools</requirement> 8 <requirement type="package" version="1.6">samtools</requirement>
9 </requirements> 9 </requirements>
10 <version_command>bowtie2 --version</version_command> 10 <version_command>bowtie2 --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 ## prepare bowtie2 index 12 ## prepare bowtie2 index
13 #set index_path = '' 13 #set index_path = ''
14 #if str($reference_genome.source) == "history": 14 #if str($reference_genome.source) == "history":
15 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome && 15 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
16 ln -s -f '$reference_genome.own_file' genome.fa && 16 ln -s -f '$reference_genome.own_file' genome.fa &&
17 #set index_path = 'genome' 17 #set index_path = 'genome'
18 #else:
19 #set index_path = $reference_genome.index.fields.path
20 #end if
21
22 ## Link in the input files, so bowtie2 can tell their type
23
24 #set compressed="False"
25 #set reads_are_fastq = True
26 #if str($library.type) == 'paired':
27 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
28 #set read1 = "input_f.fastq.gz"
29 #set compressed = "GZ"
30 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
31 #set read1 = "input_f.fastq.bz2"
32 #set compressed = "BZ2"
33 #else if $library.input_1.is_of_type('fasta'):
34 #set reads_are_fastq = False
35 #set read1 = "input_f.fasta"
36 #else:
37 #set read1 = "input_f.fastq"
38 #end if
39 ln -f -s '${library.input_1}' ${read1} &&
40
41 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
42 #set read2 = "input_r.fastq.gz"
43 #set compressed = "GZ"
44 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
45 #set read2 = "input_r.fastq.bz2"
46 #set compressed = "BZ2"
47 #else if $library.input_2.is_of_type('fasta'):
48 #set read2 = "input_r.fasta"
49 #else:
50 #set read2 = "input_r.fastq"
51 #end if
52 ln -f -s '${library.input_2}' ${read2} &&
53 #else if str($library.type) == 'paired_collection':
54 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
55 #set read1 = "input_f.fastq.gz"
56 #set compressed = "GZ"
57 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
58 #set read1 = "input_f.fastq.bz2"
59 #set compressed = "BZ2"
60 #else if $library.input_1.forward.is_of_type('fasta'):
61 #set reads_are_fastq = False
62 #set read1 = "input_f.fasta"
63 #else:
64 #set read1 = "input_f.fastq"
65 #end if
66 ln -s '${library.input_1.forward}' ${read1} &&
67
68 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
69 #set read2 = "input_r.fastq.gz"
70 #set compressed = "GZ"
71 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
72 #set read2 = "input_r.fastq.bz2"
73 #set compressed = "BZ2"
74 #else if $library.input_1.reverse.is_of_type("fasta"):
75 #set read2 = "input_r.fasta"
76 #else:
77 #set read2 = "input_r.fastq"
78 #end if
79 ln -s '${library.input_1.reverse}' ${read2} &&
80
81 #else if str($library.type) == 'paired_interleaved':
82 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
83 #set read1 = "input_il.fastq.gz"
84 #set compressed = "GZ"
85 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
86 #set read1 = "input_il.fastq.bz2"
87 #set compressed = "BZ2"
88 #else if $library.input_1.is_of_type("fasta"):
89 #set reads_are_fastq = False
90 #set read1 = "input_il.fasta"
91 #else:
92 #set read1 = "input_il.fastq"
93 #end if
94 ln -s '${library.input_1}' ${read1} &&
95 #else:
96 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
97 #set read1 = "input_f.fastq.gz"
98 #set compressed = "GZ"
99 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
100 #set read1 = "input_f.fastq.bz2"
101 #set compressed = "BZ2"
102 #else if $library.input_1.is_of_type("fasta"):
103 #set reads_are_fastq = False
104 #set read1 = "input_f.fasta"
105 #else:
106 #set read1 = "input_f.fastq"
107 #end if
108 ln -s '${library.input_1}' ${read1} &&
109 #end if
110
111 ## execute bowtie2
112
113 bowtie2
114
115 ## number of threads
116 -p \${GALAXY_SLOTS:-4}
117
118 ## index file path
119 -x '$index_path'
120
121 ## Input reads are fasta?
122 #if not reads_are_fastq:
123 -f
124 #end if
125
126 ## Input reads
127 #if str( $library.type ) == "single":
128 -U '${read1}'
129 #if str( $library.unaligned_file ) == "true":
130 #if $compressed == "GZ":
131 --un-gz '${output_unaligned_reads_l}'
132 #else if $compressed == "BZ2":
133 --un-bz2 '${output_unaligned_reads_l}'
18 #else: 134 #else:
19 #set index_path = $reference_genome.index.fields.path 135 --un '${output_unaligned_reads_l}'
20 #end if 136 #end if
21 137 #end if
22 ## Link in the input files, so bowtie2 can tell their type 138 #if str( $library.aligned_file ) == "true":
23 139 #if $compressed == "GZ":
24 #set compressed="False" 140 --al-gz '${output_aligned_reads_l}'
25 #set reads_are_fastq = True 141 #else if $compressed == "BZ2":
26 #if str($library.type) == 'paired': 142 --al-bz2 '${output_aligned_reads_l}'
27 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
28 #set read1 = "input_f.fastq.gz"
29 #set compressed = "GZ"
30 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
31 #set read1 = "input_f.fastq.bz2"
32 #set compressed = "BZ2"
33 #else if $library.input_1.is_of_type('fasta'):
34 #set reads_are_fastq = False
35 #set read1 = "input_f.fasta"
36 #else:
37 #set read1 = "input_f.fastq"
38 #end if
39 ln -f -s '${library.input_1}' ${read1} &&
40
41 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
42 #set read2 = "input_r.fastq.gz"
43 #set compressed = "GZ"
44 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
45 #set read2 = "input_r.fastq.bz2"
46 #set compressed = "BZ2"
47 #else if $library.input_2.is_of_type('fasta'):
48 #set read2 = "input_r.fasta"
49 #else:
50 #set read2 = "input_r.fastq"
51 #end if
52 ln -f -s '${library.input_2}' ${read2} &&
53 #else if str($library.type) == 'paired_collection':
54 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
55 #set read1 = "input_f.fastq.gz"
56 #set compressed = "GZ"
57 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
58 #set read1 = "input_f.fastq.bz2"
59 #set compressed = "BZ2"
60 #else if $library.input_1.forward.is_of_type('fasta'):
61 #set reads_are_fastq = False
62 #set read1 = "input_f.fasta"
63 #else:
64 #set read1 = "input_f.fastq"
65 #end if
66 ln -s '${library.input_1.forward}' ${read1} &&
67
68 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
69 #set read2 = "input_r.fastq.gz"
70 #set compressed = "GZ"
71 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
72 #set read2 = "input_r.fastq.bz2"
73 #set compressed = "BZ2"
74 #else if $library.input_1.reverse.is_of_type("fasta"):
75 #set read2 = "input_r.fasta"
76 #else:
77 #set read2 = "input_r.fastq"
78 #end if
79 ln -s '${library.input_1.reverse}' ${read2} &&
80
81 #else if str($library.type) == 'paired_interleaved':
82 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
83 #set read1 = "input_il.fastq.gz"
84 #set compressed = "GZ"
85 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
86 #set read1 = "input_il.fastq.bz2"
87 #set compressed = "BZ2"
88 #else if $library.input_1.is_of_type("fasta"):
89 #set reads_are_fastq = False
90 #set read1 = "input_il.fasta"
91 #else:
92 #set read1 = "input_il.fastq"
93 #end if
94 ln -s '${library.input_1}' ${read1} &&
95 #else: 143 #else:
96 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): 144 --al '${output_aligned_reads_l}'
97 #set read1 = "input_f.fastq.gz"
98 #set compressed = "GZ"
99 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
100 #set read1 = "input_f.fastq.bz2"
101 #set compressed = "BZ2"
102 #else if $library.input_1.is_of_type("fasta"):
103 #set reads_are_fastq = False
104 #set read1 = "input_f.fasta"
105 #else:
106 #set read1 = "input_f.fastq"
107 #end if
108 ln -s '${library.input_1}' ${read1} &&
109 #end if 145 #end if
110 146 #end if
111 ## execute bowtie2 147
112 148 #elif str( $library.type ) == "paired_interleaved":
113 bowtie2 149 --interleaved '${read1}'
114 150 #if str( $library.unaligned_file ) == "true":
115 ## number of threads 151 #if $compressed == "GZ":
116 -p \${GALAXY_SLOTS:-4} 152 --un-gz '${output_unaligned_reads_l}'
117 153 #else if $compressed == "BZ2":
118 ## index file path 154 --un-bz2 '${output_unaligned_reads_l}'
119 -x '$index_path' 155 #else:
120 156 --un '${output_unaligned_reads_l}'
121 ## Input reads are fasta?
122 #if not reads_are_fastq:
123 -f
124 #end if 157 #end if
125 158 #end if
126 ## Input reads 159 #if str( $library.aligned_file ) == "true":
127 #if str( $library.type ) == "single": 160 #if $compressed == "GZ":
128 -U '${read1}' 161 --al-gz '${output_aligned_reads_l}'
129 #if str( $library.unaligned_file ) == "true": 162 #else if $compressed == "BZ2":
130 #if $compressed == "GZ": 163 --al-bz2 '${output_aligned_reads_l}'
131 --un-gz '${output_unaligned_reads_l}'
132 #else if $compressed == "BZ2":
133 --un-bz2 '${output_unaligned_reads_l}'
134 #else:
135 --un '${output_unaligned_reads_l}'
136 #end if
137 #end if
138 #if str( $library.aligned_file ) == "true":
139 #if $compressed == "GZ":
140 --al-gz '${output_aligned_reads_l}'
141 #else if $compressed == "BZ2":
142 --al-bz2 '${output_aligned_reads_l}'
143 #else:
144 --al '${output_aligned_reads_l}'
145 #end if
146 #end if
147
148 #elif str( $library.type ) == "paired_interleaved":
149 --interleaved '${read1}'
150 #if str( $library.unaligned_file ) == "true":
151 #if $compressed == "GZ":
152 --un-gz '${output_unaligned_reads_l}'
153 #else if $compressed == "BZ2":
154 --un-bz2 '${output_unaligned_reads_l}'
155 #else:
156 --un '${output_unaligned_reads_l}'
157 #end if
158 #end if
159 #if str( $library.aligned_file ) == "true":
160 #if $compressed == "GZ":
161 --al-gz '${output_aligned_reads_l}'
162 #else if $compressed == "BZ2":
163 --al-bz2 '${output_aligned_reads_l}'
164 #else:
165 --al '${output_aligned_reads_l}'
166 #end if
167 #end if
168 #else: 164 #else:
169 -1 '${read1}' 165 --al '${output_aligned_reads_l}'
170 -2 '${read2}'
171 #if str( $library.unaligned_file ) == "true":
172 #if $compressed == "GZ":
173 --un-conc-gz '${output_unaligned_reads_l}'
174 #else if $compressed == "BZ2":
175 --un-conc-bz2 '${output_unaligned_reads_l}'
176 #else:
177 --un-conc '${output_unaligned_reads_l}'
178 #end if
179 #end if
180 #if str( $library.aligned_file ) == "true":
181 #if $compressed == "GZ":
182 --al-conc-gz '${output_aligned_reads_l}'
183 #else if $compressed == "BZ2":
184 --al-conc-bz2 '${output_aligned_reads_l}'
185 #else:
186 --al-conc '${output_aligned_reads_l}'
187 #end if
188 #end if
189 #if str( $library.paired_options.paired_options_selector ) == "yes":
190 -I "${library.paired_options.I}"
191 -X "${library.paired_options.X}"
192 ${library.paired_options.fr_rf_ff}
193 ${library.paired_options.no_mixed}
194 ${library.paired_options.no_discordant}
195 ${library.paired_options.dovetail}
196 ${library.paired_options.no_contain}
197 ${library.paired_options.no_overlap}
198 #end if
199 #end if 166 #end if
200 167 #end if
201 ## Read group information. 168 #else:
202 @define_read_group_helpers@ 169 -1 '${read1}'
203 #if str( $library.type ) == "single": 170 -2 '${read2}'
204 #set $rg_auto_name = $read_group_name_default($library.input_1) 171 #if str( $library.unaligned_file ) == "true":
205 #elif str( $library.type ) == "paired": 172 #if $compressed == "GZ":
206 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2) 173 --un-conc-gz '${output_unaligned_reads_l}'
207 #else 174 #else if $compressed == "BZ2":
208 #set $rg_auto_name = $read_group_name_default($library.input_1) 175 --un-conc-bz2 '${output_unaligned_reads_l}'
176 #else:
177 --un-conc '${output_unaligned_reads_l}'
209 #end if 178 #end if
210 @set_use_rg_var@ 179 #end if
211 @set_read_group_vars@ 180 #if str( $library.aligned_file ) == "true":
212 #if $use_rg 181 #if $compressed == "GZ":
213 $format_read_group("", $rg_id, '"', arg='--rg-id ') 182 --al-conc-gz '${output_aligned_reads_l}'
214 $format_read_group("SM:", $rg_sm, '"', arg='--rg ') 183 #else if $compressed == "BZ2":
215 $format_read_group("PL:", $rg_pl, '"', arg='--rg ') 184 --al-conc-bz2 '${output_aligned_reads_l}'
216 $format_read_group("LB:", $rg_lb, '"', arg='--rg ') 185 #else:
217 $format_read_group("CN:", $rg_cn, '"', arg='--rg ') 186 --al-conc '${output_aligned_reads_l}'
218 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
219 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
220 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
221 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
222 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
223 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
224 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
225 #end if 187 #end if
226 188 #end if
227 ## Analysis type 189 #if str( $library.paired_options.paired_options_selector ) == "yes":
228 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ): 190 -I ${library.paired_options.I}
229 $analysis_type.presets 191 -X ${library.paired_options.X}
230 #elif str( $analysis_type.analysis_type_selector ) == "full": 192 ${library.paired_options.fr_rf_ff}
231 #if str( $analysis_type.input_options.input_options_selector ) == "yes": 193 ${library.paired_options.no_mixed}
232 --skip "${analysis_type.input_options.skip}" 194 ${library.paired_options.no_discordant}
233 --qupto "${analysis_type.input_options.qupto}" 195 ${library.paired_options.dovetail}
234 --trim5 "${analysis_type.input_options.trim5}" 196 ${library.paired_options.no_contain}
235 --trim3 "${analysis_type.input_options.trim3}" 197 ${library.paired_options.no_overlap}
236 ${analysis_type.input_options.qv_encoding} 198 #end if
237 ${analysis_type.input_options.solexa_quals} 199 #end if
238 ${analysis_type.input_options.int_quals} 200
239 #end if 201 ## Read group information.
240 202 @define_read_group_helpers@
241 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes": 203 #if str( $library.type ) == "single":
242 -N "${analysis_type.alignment_options.N}" 204 #set $rg_auto_name = $read_group_name_default($library.input_1)
243 -L "${analysis_type.alignment_options.L}" 205 #elif str( $library.type ) == "paired":
244 -i "${analysis_type.alignment_options.i}" 206 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
245 --n-ceil "${analysis_type.alignment_options.n_ceil}" 207 #else
246 --dpad "${analysis_type.alignment_options.dpad}" 208 #set $rg_auto_name = $read_group_name_default($library.input_1)
247 --gbar "${analysis_type.alignment_options.gbar}" 209 #end if
248 ${analysis_type.alignment_options.ignore_quals} 210 @set_use_rg_var@
249 ${analysis_type.alignment_options.nofw} 211 @set_read_group_vars@
250 ${analysis_type.alignment_options.norc} 212 #if $use_rg
251 ${analysis_type.alignment_options.no_1mm_upfront} 213 $format_read_group("", $rg_id, '"', arg='--rg-id ')
252 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end": 214 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
253 --end-to-end 215 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
254 --score-min "${analysis_type.alignment_options.align_mode.score_min_ete}" 216 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
255 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local": 217 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
256 --local 218 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
257 --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}" 219 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
258 #end if 220 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
259 #end if 221 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
260 222 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
261 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes": 223 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
262 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ): 224 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
263 --ma "${analysis_type.scoring_options.ma}" 225 #end if
264 #end if 226
265 --mp "${analysis_type.scoring_options.mp}" 227 ## Analysis type
266 --np "${analysis_type.scoring_options.np}" 228 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
267 --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}" 229 $analysis_type.presets
268 --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}" 230 #elif str( $analysis_type.analysis_type_selector ) == "full":
269 #end if 231 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
270 232 --skip ${analysis_type.input_options.skip}
271 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k": 233 --qupto ${analysis_type.input_options.qupto}
272 -k "${analysis_type.reporting_options.k}" 234 --trim5 ${analysis_type.input_options.trim5}
273 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a": 235 --trim3 ${analysis_type.input_options.trim3}
274 -a 236 ${analysis_type.input_options.qv_encoding}
275 #end if 237 ${analysis_type.input_options.solexa_quals}
276 238 ${analysis_type.input_options.int_quals}
277 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes": 239 #end if
278 -D "${analysis_type.effort_options.D}" 240
279 -R "${analysis_type.effort_options.R}" 241 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
280 #end if 242 -N ${analysis_type.alignment_options.N}
281 243 -L ${analysis_type.alignment_options.L}
282 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes": 244 -i '${analysis_type.alignment_options.i}'
283 ${analysis_type.sam_options.no_unal} 245 --n-ceil '${analysis_type.alignment_options.n_ceil}'
284 ${analysis_type.sam_options.omit_sec_seq} 246 --dpad ${analysis_type.alignment_options.dpad}
285 #end if 247 --gbar ${analysis_type.alignment_options.gbar}
286 248 ${analysis_type.alignment_options.ignore_quals}
287 #if str( $analysis_type.other_options.other_options_selector ) == "yes": 249 ${analysis_type.alignment_options.nofw}
288 ${analysis_type.other_options.reorder} 250 ${analysis_type.alignment_options.norc}
289 ${analysis_type.other_options.non_deterministic} 251 ${analysis_type.alignment_options.no_1mm_upfront}
290 --seed "${analysis_type.other_options.seed}" 252 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
291 #end if 253 --end-to-end
292 254 --score-min '${analysis_type.alignment_options.align_mode.score_min_ete}'
293 #elif str( $analysis_type.analysis_type_selector ) == "cline": 255 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
294 ${analysis_type.cline} 256 --local
257 --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}'
295 #end if 258 #end if
296 259 #end if
297 ## mapping stats (i.e. stderr from bowtie2) 260
298 #if $save_mapping_stats 261 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
299 2> '$mapping_stats' 262 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
263 --ma ${analysis_type.scoring_options.ma}
300 #end if 264 #end if
301 265 --mp '${analysis_type.scoring_options.mp}'
302 ## output file 266 --np ${analysis_type.scoring_options.np}
303 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ): 267 --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}
304 | samtools sort -O bam -o '$output' 268 --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}
305 #else 269 #end if
306 > '$output_sam' 270
307 #end if 271 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
308 272 -k ${analysis_type.reporting_options.k}
309 ## rename unaligned sequence files 273 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
310 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: 274 -a
311 #from os.path import splitext 275 #end if
312 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) ) 276
313 && mv "${ _unaligned_root }.1${_unaligned_ext}" '$output_unaligned_reads_l' 277 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
314 && mv "${ _unaligned_root }.2${_unaligned_ext}" '$output_unaligned_reads_r' 278 -D ${analysis_type.effort_options.D}
315 #end if 279 -R ${analysis_type.effort_options.R}
316 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r: 280 #end if
317 #from os.path import splitext 281
318 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) ) 282 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
319 && mv "${ _aligned_root }.1${_aligned_ext}" '$output_aligned_reads_l' 283 ${analysis_type.sam_options.no_unal}
320 && mv "${ _aligned_root }.2${_aligned_ext}" '$output_aligned_reads_r' 284 ${analysis_type.sam_options.omit_sec_seq}
321 #end if 285 ${analysis_type.sam_options.sam-no-qname-trunc}
286 ${analysis_type.sam_options.xeq}
287 ${analysis_type.sam_options.soft-clipped-unmapped-tlen}
288 #end if
289
290 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
291 ${analysis_type.other_options.reorder}
292 ${analysis_type.other_options.non_deterministic}
293 --seed ${analysis_type.other_options.seed}
294 #end if
295
296 #elif str( $analysis_type.analysis_type_selector ) == "cline":
297 ${analysis_type.cline}
298 #end if
299
300 ## mapping stats (i.e. stderr from bowtie2)
301 #if $save_mapping_stats
302 2> '$mapping_stats'
303 #end if
304
305 ## output file
306 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
307 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
308 #else
309 > '$output_sam'
310 #end if
311
312 ## rename unaligned sequence files
313 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
314 #from os.path import splitext
315 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
316 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
317 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
318 #end if
319 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
320 #from os.path import splitext
321 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
322 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
323 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
324 #end if
322 325
323 ]]></command> 326 ]]></command>
324 <inputs> 327 <inputs>
325 <!-- single/paired --> 328 <!-- single/paired -->
326 <conditional name="library"> 329 <conditional name="library">
331 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option> 334 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
332 </param> 335 </param>
333 336
334 <when value="single"> 337 <when value="single">
335 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" /> 338 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
336
337 <expand macro="align_unalign" /> 339 <expand macro="align_unalign" />
338
339 </when> 340 </when>
340 <when value="paired"> 341 <when value="paired">
341 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" /> 342 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
342 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" /> 343 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
343
344 <expand macro="align_unalign" /> 344 <expand macro="align_unalign" />
345 <expand macro="paired_end_options" /> 345 <expand macro="paired_end_options" />
346
347 </when> 346 </when>
348 <when value="paired_collection"> 347 <when value="paired_collection">
349 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" /> 348 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
350
351 <expand macro="align_unalign" /> 349 <expand macro="align_unalign" />
352 <expand macro="paired_end_options" /> 350 <expand macro="paired_end_options" />
353
354 </when> 351 </when>
355 <when value="paired_interleaved"> 352 <when value="paired_interleaved">
356 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/> 353 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
357
358 <expand macro="align_unalign" /> 354 <expand macro="align_unalign" />
359 <expand macro="paired_end_options" /> 355 <expand macro="paired_end_options" />
360
361 </when> 356 </when>
362 </conditional> 357 </conditional>
363
364 <!-- reference genome --> 358 <!-- reference genome -->
365 <conditional name="reference_genome"> 359 <conditional name="reference_genome">
366 <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. See `Indexes` section of help below"> 360 <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. See `Indexes` section of help below">
367 <option value="indexed">Use a built-in genome index</option> 361 <option value="indexed">Use a built-in genome index</option>
368 <option value="history">Use a genome from the history and build index</option> 362 <option value="history">Use a genome from the history and build index</option>
377 </when> 371 </when>
378 <when value="history"> 372 <when value="history">
379 <param name="own_file" type="data" format="fasta" label="Select reference genome" /> 373 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
380 </when> 374 </when>
381 </conditional> 375 </conditional>
382
383 <!-- read group settings --> 376 <!-- read group settings -->
384 <expand macro="read_group_conditional" /> 377 <expand macro="read_group_conditional" />
385 <conditional name="analysis_type"> 378 <conditional name="analysis_type">
386 <param name="analysis_type_selector" type="select" label="Select analysis mode"> 379 <param name="analysis_type_selector" type="select" label="Select analysis mode">
387 <option value="simple">1: Default setting only</option> 380 <option value="simple">1: Default setting only</option>
500 </when> 493 </when>
501 <when value="no"> 494 <when value="no">
502 <!-- do nothing --> 495 <!-- do nothing -->
503 </when> 496 </when>
504 </conditional> 497 </conditional>
505
506 <conditional name="sam_options"> 498 <conditional name="sam_options">
507 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information"> 499 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information">
508 <option value="yes">Yes</option> 500 <option value="yes">Yes</option>
509 <option value="no" selected="true">No</option> 501 <option value="no" selected="true">No</option>
510 </param> 502 </param>
511 <when value="yes"> 503 <when value="yes">
512 <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/> 504 <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
513 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/> 505 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
506 <param argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
507 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
508 <param argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
514 </when> 509 </when>
515 <when value="no"> 510 <when value="no">
516 <!-- do nothing --> 511 <!-- do nothing -->
517 </when> 512 </when>
518 </conditional> 513 </conditional>
533 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/> 528 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
534 </when> 529 </when>
535 </conditional> 530 </conditional>
536 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" /> 531 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
537 </inputs> 532 </inputs>
538
539 <!-- define outputs --> 533 <!-- define outputs -->
540
541 <outputs> 534 <outputs>
542
543 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > 535 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
544 <filter>library['unaligned_file'] is True</filter> 536 <filter>library['unaligned_file'] is True</filter>
545 <actions> 537 <actions>
546 <conditional name="library.type"> 538 <conditional name="library.type">
547 <when value="single"> 539 <when value="single">
616 </action> 608 </action>
617 </when> 609 </when>
618 </conditional> 610 </conditional>
619 </actions> 611 </actions>
620 </data> 612 </data>
621
622 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)"> 613 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
623 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter> 614 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
624 <actions> 615 <actions>
625 <conditional name="reference_genome.source"> 616 <conditional name="reference_genome.source">
626 <when value="indexed"> 617 <when value="indexed">
637 </action> 628 </action>
638 </when> 629 </when>
639 </conditional> 630 </conditional>
640 </actions> 631 </actions>
641 </data> 632 </data>
642
643 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)"> 633 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
644 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter> 634 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
645 <actions> 635 <actions>
646 <conditional name="reference_genome.source"> 636 <conditional name="reference_genome.source">
647 <when value="indexed"> 637 <when value="indexed">
661 </actions> 651 </actions>
662 </data> 652 </data>
663 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats"> 653 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
664 <filter>save_mapping_stats is True</filter> 654 <filter>save_mapping_stats is True</filter>
665 </data> 655 </data>
666
667 </outputs> 656 </outputs>
668
669 <tests> 657 <tests>
670 <test> 658 <test>
671 <!-- test on paired-end datasets --> 659 <!-- test on paired-end datasets -->
672 <param name="type" value="paired"/> 660 <param name="type" value="paired"/>
673 <param name="paired_options_selector" value="no"/> 661 <param name="paired_options_selector" value="no"/>
777 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> 765 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
778 <param name="own_file" value="bowtie2-ref.fasta" /> 766 <param name="own_file" value="bowtie2-ref.fasta" />
779 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/> 767 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
780 </test> 768 </test>
781 </tests> 769 </tests>
782
783 <help><![CDATA[ 770 <help><![CDATA[
784 **Bowtie2 Overview** 771 **Bowtie2 Overview**
785 772
786 Bowtie2_ 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. Galaxy wrapper for Bowtie 2 outputs alignments in `BAM format`_, enabling interoperation with a large number of other tools available at this site. 773 Bowtie2_ 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. Galaxy wrapper for Bowtie 2 outputs alignments in `BAM format`_, enabling interoperation with a large number of other tools available at this site.
787 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead. 774 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.