Mercurial > repos > devteam > bwa
comparison bwa.xml @ 18:48f306c57611 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
author | iuc |
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date | Fri, 24 Nov 2017 09:55:45 -0500 |
parents | 051eba708f43 |
children | 4f774c1e6049 |
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17:d1228ec6233f | 18:48f306c57611 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="bwa" name="Map with BWA" version="@VERSION@.2"> | 2 <tool id="bwa" name="Map with BWA" version="@VERSION@.3"> |
3 <description>- map short reads (< 100 bp) against reference genome</description> | 3 <description>- map short reads (< 100 bp) against reference genome</description> |
4 <macros> | 4 <macros> |
5 <import>read_group_macros.xml</import> | 5 <import>read_group_macros.xml</import> |
6 <import>bwa_macros.xml</import> | 6 <import>bwa_macros.xml</import> |
7 <token name="@command_options@"> | 7 <token name="@command_options@"> |
8 #if str( $analysis_type.analysis_type_selector ) == "full": | 8 #if str( $analysis_type.analysis_type_selector ) == "full": |
9 -n ${analysis_type.n} | 9 -n ${analysis_type.n} |
10 -o ${analysis_type.o} | 10 -o ${analysis_type.o} |
11 -e ${analysis_type.e} | 11 -e ${analysis_type.e} |
12 -i ${analysis_type.i} | 12 -i ${analysis_type.i} |
13 -d ${analysis_type.d} | 13 -d ${analysis_type.d} |
14 -l ${analysis_type.l} | 14 -l ${analysis_type.l} |
15 -k ${analysis_type.k} | 15 -k ${analysis_type.k} |
16 -m ${analysis_type.m} | 16 -m ${analysis_type.m} |
17 -M ${analysis_type.M} | 17 -M ${analysis_type.M} |
18 -O ${analysis_type.O} | 18 -O ${analysis_type.O} |
19 -E ${analysis_type.E} | 19 -E ${analysis_type.E} |
20 -R ${analysis_type.R} | 20 -R ${analysis_type.R} |
21 -q ${analysis_type.q} | 21 -q ${analysis_type.q} |
22 | 22 #if str( $analysis_type.B ): |
23 #if str( $analysis_type.B ): | |
24 -B ${analysis_type.B} | 23 -B ${analysis_type.B} |
25 #end if | 24 #end if |
26 | 25 #if str( $analysis_type.L ): |
27 #if str( $analysis_type.L ): | |
28 -L ${analysis_type.L} | 26 -L ${analysis_type.L} |
29 #end if | 27 #end if |
30 #end if | 28 #end if |
31 </token> | 29 </token> |
32 <token name="@read_group_options@"> | 30 <token name="@read_group_options@"> |
33 #if $use_rg: | 31 #if $use_rg: |
34 @set_rg_string@ | 32 @set_rg_string@ |
35 -r '$rg_string' | 33 -r '$rg_string' |
36 #end if | 34 #end if |
37 </token> | 35 </token> |
38 | 36 <xml name="advanced_pe_options"> |
39 <xml name="advanced_pe_options"> | 37 <param name="adv_pe_options_selector" type="select" label="Set advanced paired end options?" |
40 <param name="adv_pe_options_selector" type="select" label="Set advanced paired end options?" help="Provides additional controls"> | 38 help="Provides additional controls"> |
41 <option value="set">Set</option> | 39 <option value="set">Set</option> |
42 <option value="do_not_set" selected="True">Do not set</option> | 40 <option value="do_not_set" selected="True">Do not set</option> |
43 </param> | 41 </param> |
44 <when value="set"> | 42 <when value="set"> |
45 <param name="a" type="integer" value="500" label="Maximum insert size for a read pair to be considered being mapped properly." help="sampe -a; This option is only used when there are not enough good alignment to infer the distribution of insert sizes; default=500"/> | 43 <param name="a" type="integer" value="500" |
46 <param name="o" type="integer" value="100000" label="Maximum occurrences of a read for pairing. A read with more occurrences will be treated as a single-end read." help="sampe -o; Reducing this parameter helps faster pairing; default=100000"/> | 44 label="Maximum insert size for a read pair to be considered being mapped properly." |
47 <param name="n" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly." help="sampe -n; If a read has more than this many hits, the XA tag will not be written; default=3"/> | 45 help="sampe -a; This option is only used when there are not enough good alignment to infer the distribution of insert sizes; default=500"/> |
48 <param name="N" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)." help="sampe -N; If a read has more than this many hits, the XA tag will not be written; default=10"/> | 46 <param name="o" type="integer" value="100000" |
49 <param name="c" type="float" value="0.00005" label="Prior of chimeric rate (lower bound)" help="sampe -c"/> | 47 label="Maximum occurrences of a read for pairing. A read with more occurrences will be treated as a single-end read." |
50 </when> | 48 help="sampe -o; Reducing this parameter helps faster pairing; default=100000"/> |
51 <when value="do_not_set"> | 49 <param name="n" type="integer" value="3" |
52 <!-- do nothing --> | 50 label="Maximum number of alignments to output in the XA tag for reads paired properly." |
53 </when> | 51 help="sampe -n; If a read has more than this many hits, the XA tag will not be written; default=3"/> |
54 </xml> | 52 <param name="N" type="integer" value="10" |
55 <xml name="advanced_se_options"> | 53 label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)." |
56 <param name="adv_se_options_selector" type="select" label="Set advanced single end options?" help="Provides additional controls"> | 54 help="sampe -N; If a read has more than this many hits, the XA tag will not be written; default=10"/> |
57 <option value="set">Set</option> | 55 <param name="c" type="float" value="0.00005" label="Prior of chimeric rate (lower bound)" |
58 <option value="do_not_set" selected="True">Do not set</option> | 56 help="sampe -c"/> |
59 </param> | 57 </when> |
60 <when value="set"> | 58 <when value="do_not_set"> |
61 <param name="n" type="integer" value="3" label="Maximum number of alignments to output in the XA tag." help="-n; If a read has more than this many hits, the XA tag will not be written; default=3"/> | 59 <!-- do nothing --> |
62 </when> | 60 </when> |
63 <when value="do_not_set"> | 61 </xml> |
64 <!-- do nothing --> | 62 <xml name="advanced_se_options"> |
65 </when> | 63 <param name="adv_se_options_selector" type="select" label="Set advanced single end options?" |
66 </xml> | 64 help="Provides additional controls"> |
67 </macros> | 65 <option value="set">Set</option> |
68 <expand macro="requirements" /> | 66 <option value="do_not_set" selected="True">Do not set</option> |
69 <expand macro="stdio" /> | 67 </param> |
70 <command> | 68 <when value="set"> |
71 <![CDATA[ | 69 <param name="n" type="integer" value="3" label="Maximum number of alignments to output in the XA tag." |
72 @set_reference_fasta_filename@ | 70 help="-n; If a read has more than this many hits, the XA tag will not be written; default=3"/> |
73 | 71 </when> |
74 ## setup vars for rg handling... | 72 <when value="do_not_set"> |
75 @define_read_group_helpers@ | 73 <!-- do nothing --> |
76 #if str( $input_type.input_type_selector ) == "paired": | 74 </when> |
77 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1, $input_type.fastq_input2) | 75 </xml> |
78 #elif str( $input_type.input_type_selector ) in ["single_bam", "paired_bam"]: | 76 </macros> |
79 #set $rg_auto_name = $read_group_name_default($input_type.bam_input) | 77 <expand macro="requirements"/> |
78 <expand macro="stdio"/> | |
79 <command> | |
80 <![CDATA[ | |
81 @set_reference_fasta_filename@ | |
82 | |
83 ## setup vars for rg handling... | |
84 @define_read_group_helpers@ | |
85 #if str( $input_type.input_type_selector ) == "paired": | |
86 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1, $input_type.fastq_input2) | |
87 #elif str( $input_type.input_type_selector ) in ["single_bam", "paired_bam"]: | |
88 #set $rg_auto_name = $read_group_name_default($input_type.bam_input) | |
89 #else | |
90 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1) | |
91 #end if | |
92 @set_use_rg_var@ | |
93 @set_read_group_vars@ | |
94 | |
95 ## Begin bwa command line | |
96 | |
97 ####### Fastq paired | |
98 | |
99 #if str( $input_type.input_type_selector ) == "paired" or str( $input_type.input_type_selector ) == "paired_collection": | |
100 bwa aln | |
101 -t "\${GALAXY_SLOTS:-1}" | |
102 @command_options@ | |
103 '$reference_fasta_filename' | |
104 #if str( $input_type.input_type_selector ) == "paired_collection": | |
105 '${input_type.fastq_input1.forward}' | |
80 #else | 106 #else |
81 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1) | 107 '${input_type.fastq_input1}' |
82 #end if | 108 #end if |
83 @set_use_rg_var@ | 109 > first.sai && |
84 @set_read_group_vars@ | 110 |
85 | 111 bwa aln |
86 ## Begin bwa command line | 112 -t "\${GALAXY_SLOTS:-1}" |
87 | 113 @command_options@ |
88 ####### Fastq paired | 114 '${reference_fasta_filename}' |
89 | 115 #if str( $input_type.input_type_selector ) == "paired_collection": |
90 #if str( $input_type.input_type_selector ) == "paired" or str( $input_type.input_type_selector ) == "paired_collection": | 116 '${input_type.fastq_input1.reverse}' |
91 bwa aln | 117 #else |
92 -t "\${GALAXY_SLOTS:-1}" | 118 '${input_type.fastq_input2}' |
93 | 119 #end if |
94 @command_options@ | 120 > second.sai && |
95 | 121 |
96 "${reference_fasta_filename}" | 122 bwa sampe |
97 | 123 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True": |
98 #if str( $input_type.input_type_selector ) == "paired_collection": | |
99 "${input_type.fastq_input1.forward}" | |
100 #else | |
101 "${input_type.fastq_input1}" | |
102 #end if | |
103 | |
104 > first.sai && | |
105 | |
106 bwa aln | |
107 -t "\${GALAXY_SLOTS:-1}" | |
108 | |
109 @command_options@ | |
110 | |
111 "${reference_fasta_filename}" | |
112 | |
113 #if str( $input_type.input_type_selector ) == "paired_collection": | |
114 "${input_type.fastq_input1.reverse}" | |
115 #else | |
116 "${input_type.fastq_input2}" | |
117 #end if | |
118 | |
119 > second.sai && | |
120 | |
121 bwa sampe | |
122 | |
123 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True": | |
124 -a ${$input_type.adv_pe_options.a} | 124 -a ${$input_type.adv_pe_options.a} |
125 -o ${$input_type.adv_pe_options.o} | 125 -o ${$input_type.adv_pe_options.o} |
126 -n ${$input_type.adv_pe_options.n} | 126 -n ${$input_type.adv_pe_options.n} |
127 -N ${$input_type.adv_pe_options.N} | 127 -N ${$input_type.adv_pe_options.N} |
128 #end if | 128 #end if |
129 | 129 @read_group_options@ |
130 @read_group_options@ | 130 #if str( $input_type.input_type_selector ) == "paired_collection": |
131 | 131 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1.forward}' '${input_type.fastq_input1.reverse}' |
132 #if str( $input_type.input_type_selector ) == "paired_collection": | 132 #else: |
133 "${reference_fasta_filename}" first.sai second.sai "${input_type.fastq_input1.forward}" "${input_type.fastq_input1.reverse}" | 133 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1}' '${input_type.fastq_input2}' |
134 #else: | 134 #end if |
135 "${reference_fasta_filename}" first.sai second.sai "${input_type.fastq_input1}" "${input_type.fastq_input2}" | 135 |
136 #end if | 136 ## Fastq single |
137 | 137 |
138 ####### Fastq single | 138 #elif str( $input_type.input_type_selector ) == "single": |
139 | 139 bwa aln |
140 #elif str( $input_type.input_type_selector ) == "single": | 140 -t "\${GALAXY_SLOTS:-1}" |
141 bwa aln | 141 |
142 -t "\${GALAXY_SLOTS:-1}" | 142 @command_options@ |
143 | 143 |
144 @command_options@ | 144 '${reference_fasta_filename}' |
145 | 145 '${input_type.fastq_input1}' |
146 "${reference_fasta_filename}" | 146 > first.sai && |
147 "${input_type.fastq_input1}" | 147 |
148 > first.sai && | 148 bwa samse |
149 | 149 |
150 bwa samse | 150 #if str( $input_type.adv_se_options.adv_se_options_selector) == "True": |
151 | 151 -n ${$input_type.adv_se_options.n} |
152 #if str( $input_type.adv_se_options.adv_se_options_selector) == "True": | 152 #end if |
153 -n ${$input_type.adv_se_options.n} | 153 @read_group_options@ |
154 #end if | 154 '${reference_fasta_filename}' first.sai '${input_type.fastq_input1}' |
155 | |
156 @read_group_options@ | |
157 | |
158 "${reference_fasta_filename}" first.sai "${input_type.fastq_input1}" | |
159 | 155 |
160 ####### BAM paired | 156 ####### BAM paired |
161 | 157 |
162 #elif str( $input_type.input_type_selector ) == "paired_bam": | 158 #elif str( $input_type.input_type_selector ) == "paired_bam": |
163 bwa aln | 159 bwa aln |
164 -t "\${GALAXY_SLOTS:-1}" | 160 -t "\${GALAXY_SLOTS:-1}" |
165 -b | 161 -b |
166 -1 | 162 -1 |
167 | 163 @command_options@ |
168 @command_options@ | 164 '${reference_fasta_filename}' |
169 | 165 '${input_type.bam_input}' |
170 "${reference_fasta_filename}" | 166 > first.sai && |
171 "${input_type.bam_input}" | 167 |
172 > first.sai && | 168 bwa aln |
173 | 169 -t "\${GALAXY_SLOTS:-1}" |
174 bwa aln | 170 -b |
175 -t "\${GALAXY_SLOTS:-1}" | 171 -2 |
176 -b | 172 @command_options@ |
177 -2 | 173 '${reference_fasta_filename}' |
178 @command_options@ | 174 '${input_type.bam_input}' |
179 "${reference_fasta_filename}" | 175 > second.sai && |
180 "${input_type.bam_input}" | 176 |
181 > second.sai && | 177 bwa sampe |
182 | 178 |
183 bwa sampe | 179 #if str( $input_type.adv_bam_pe_options.adv_pe_options_selector) == "True": |
184 | |
185 #if str( $input_type.adv_bam_pe_options.adv_pe_options_selector) == "True": | |
186 -a ${$input_type.adv_bam_pe_options.a} | 180 -a ${$input_type.adv_bam_pe_options.a} |
187 -o ${$input_type.adv_bam_pe_options.o} | 181 -o ${$input_type.adv_bam_pe_options.o} |
188 -n ${$input_type.adv_bam_pe_options.n} | 182 -n ${$input_type.adv_bam_pe_options.n} |
189 -N ${$input_type.adv_bam_pe_options.N} | 183 -N ${$input_type.adv_bam_pe_options.N} |
190 #end if | 184 #end if |
191 | 185 @read_group_options@ |
192 @read_group_options@ | 186 '${reference_fasta_filename}' first.sai second.sai '${input_type.bam_input}' '${input_type.bam_input}' |
193 | |
194 "${reference_fasta_filename}" first.sai second.sai "${input_type.bam_input}" "${input_type.bam_input}" | |
195 | 187 |
196 ####### Fastq single ------------ to do next | 188 ####### Fastq single ------------ to do next |
197 | 189 |
198 #elif str( $input_type.input_type_selector ) == "single_bam": | 190 #elif str( $input_type.input_type_selector ) == "single_bam": |
199 bwa aln | 191 bwa aln |
200 -t "\${GALAXY_SLOTS:-1}" | 192 -t "\${GALAXY_SLOTS:-1}" |
201 -b | 193 -b |
202 -0 | 194 -0 |
203 | 195 |
204 @command_options@ | 196 @command_options@ |
205 | 197 |
206 "${reference_fasta_filename}" | 198 '${reference_fasta_filename}' |
207 "${input_type.bam_input}" | 199 '${input_type.bam_input}' |
208 > first.sai && | 200 > first.sai && |
209 | 201 |
210 bwa samse | 202 bwa samse |
211 | 203 |
212 #if str( $input_type.adv_bam_se_options.adv_se_options_selector) == "True": | 204 #if str( $input_type.adv_bam_se_options.adv_se_options_selector) == "True": |
213 -n ${$input_type.adv_bam_se_options.n} | 205 -n ${$input_type.adv_bam_se_options.n} |
214 #end if | 206 #end if |
215 | 207 @read_group_options@ |
216 @read_group_options@ | 208 '${reference_fasta_filename}' first.sai '${input_type.bam_input}' |
217 | 209 #end if |
218 "${reference_fasta_filename}" first.sai "${input_type.bam_input}" | 210 |
219 #end if | 211 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$bam_output' |
220 | |
221 | samtools sort -O bam -o '$bam_output' | |
222 ]]> | 212 ]]> |
223 </command> | 213 </command> |
224 | 214 |
225 <inputs> | 215 <inputs> |
226 <expand macro="reference_source_conditional" /> | 216 <expand macro="reference_source_conditional"/> |
227 <conditional name="input_type"> | 217 <conditional name="input_type"> |
228 <param name="input_type_selector" type="select" label="Select input type" help="Select between fastq and bam datasets and between paired and single end data"> | 218 <param name="input_type_selector" type="select" label="Select input type" |
229 <option value="paired">Paired fastq</option> | 219 help="Select between fastq and bam datasets and between paired and single end data"> |
230 <option value="paired_collection">Paired fastq collection</option> | 220 <option value="paired">Paired fastq</option> |
231 <option value="single">Single fastq</option> | 221 <option value="paired_collection">Paired fastq collection</option> |
232 <option value="paired_bam">Paired BAM</option> | 222 <option value="single">Single fastq</option> |
233 <option value="single_bam">Single BAM</option> | 223 <option value="paired_bam">Paired BAM</option> |
234 </param> | 224 <option value="single_bam">Single BAM</option> |
235 <when value="paired"> | 225 </param> |
236 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/> | 226 <when value="paired"> |
237 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/> | 227 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" |
238 <conditional name="adv_pe_options"> | 228 label="Select first set of reads" help="Specify dataset with forward reads"/> |
239 | 229 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" |
240 <expand macro="advanced_pe_options" /> | 230 label="Select second set of reads" help="Specify dataset with reverse reads"/> |
241 | 231 <conditional name="adv_pe_options"> |
232 <expand macro="advanced_pe_options"/> | |
233 </conditional> | |
234 </when> | |
235 <when value="paired_collection"> | |
236 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" | |
237 help="See help section for an explanation of dataset collections"/> | |
238 <conditional name="adv_pe_options"> | |
239 <expand macro="advanced_pe_options"/> | |
240 </conditional> | |
241 </when> | |
242 <when value="single"> | |
243 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" | |
244 label="Select fastq dataset" help="Specify dataset with single reads"/> | |
245 <conditional name="adv_se_options"> | |
246 <expand macro="advanced_se_options"/> | |
247 </conditional> | |
248 </when> | |
249 <!-- the difference between single and paired bams is in the <command> tag portion and realated to -0, -1, and -2 options --> | |
250 <when value="paired_bam"> | |
251 <param name="bam_input" type="data" format="bam" label="Select BAM dataset" | |
252 help="Specify BAM dataset with paired reads"/> | |
253 <conditional name="adv_bam_pe_options"> | |
254 <expand macro="advanced_pe_options"/> | |
255 </conditional> | |
256 </when> | |
257 <when value="single_bam"> | |
258 <param name="bam_input" type="data" format="bam" label="Select BAM dataset" | |
259 help="Specify BAM dataset with single reads"/> | |
260 <conditional name="adv_bam_se_options"> | |
261 <expand macro="advanced_se_options"/> | |
262 </conditional> | |
263 </when> | |
242 </conditional> | 264 </conditional> |
243 </when> | 265 <expand macro="read_group_conditional"/> |
244 | 266 <conditional name="analysis_type"> |
245 <when value="paired_collection"> | 267 <param name="analysis_type_selector" type="select" label="Select analysis mode"> |
246 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> | 268 <option value="illumina">1.Simple Illumina mode</option> |
247 <conditional name="adv_pe_options"> | 269 <option value="full">2.Full list of options</option> |
248 | 270 </param> |
249 <expand macro="advanced_pe_options" /> | 271 <when value="illumina"> |
250 | 272 <!-- do nothing --> |
273 </when> | |
274 <when value="full"> | |
275 <param name="n" type="text" value="0.04" | |
276 label="maximum edit distance if the value is integer, or the fraction of missing alignments given 2% uniform base error rate if float. In the latter case, the maximum edit distance is automatically chosen for different read lengths." | |
277 help="aln -n; default=0.04"/> | |
278 <param name="o" type="integer" value="1" label="maximum number or gap openings" | |
279 help="aln -o; default=1"/> | |
280 <param name="e" type="integer" value="-1" label="maximum number of gap extensions" | |
281 help="aln -e; -1 disables long gaps and invokes k-difference mode; default=-1"/> | |
282 <param name="i" type="integer" value="5" | |
283 label="do not put an indel within this many bp towards the ends" help="aln -i; default=5"/> | |
284 <param name="d" type="integer" value="10" label="maximum occurrences for extending a long deletion" | |
285 help="aln -d; default=10"/> | |
286 <param name="l" type="integer" value="32" label="seed length" help="aln -l; default=32"/> | |
287 <param name="k" type="integer" value="2" label="maximum differences in the seed" | |
288 help="aln -k; default=2"/> | |
289 <param name="m" type="integer" value="2000000" label="maximum entries in the queue" | |
290 help="aln -m; default=2000000"/> | |
291 <param name="M" type="integer" value="3" label="mismatch penalty" help="aln -M; default=3"/> | |
292 <param name="O" type="integer" value="11" label="gap open penalty" help="aln -O; default=11"/> | |
293 <param name="E" type="integer" value="4" label="gap extension penalty" help="aln -E; default=4"/> | |
294 <param name="R" type="integer" value="30" | |
295 label="stop searching when there are more than this value of equally best hits" | |
296 help="aln -R; default=30"/> | |
297 <param name="q" type="integer" value="0" label="quality threshold for read trimming down to 35bp" | |
298 help="aln -q; default=0"/> | |
299 <param name="B" type="integer" optional="True" label="length of barcode" | |
300 help="aln -B; optional parameter"/> | |
301 <param name="L" type="float" optional="True" label="log-scaled gap penalty for long deletions" | |
302 help="aln -L; optional parameter"/> | |
303 </when> | |
251 </conditional> | 304 </conditional> |
252 </when> | 305 </inputs> |
253 | 306 <outputs> |
254 <when value="single"> | 307 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"> |
255 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/> | 308 <expand macro="dbKeyActionsBwa"/> |
256 <conditional name="adv_se_options"> | 309 </data> |
257 | 310 </outputs> |
258 <expand macro="advanced_se_options" /> | 311 <tests> |
259 | 312 <test> |
260 </conditional> | 313 <param name="reference_source_selector" value="history"/> |
261 </when> | 314 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
262 | 315 <param name="input_type_selector" value="single"/> |
263 <!-- the difference between single and paired bams is in the <command> tag portion and realated to -0, -1, and -2 options --> | 316 <param name="fastq_input1" ftype="fasta" value="bwa-mem-fasta1.fa"/> |
264 | 317 <param name="analysis_type_selector" value="illumina"/> |
265 <when value="paired_bam"> | 318 <output name="bam_output" ftype="bam" file="bwa-aln-test1-fasta.bam" lines_diff="2"/> |
266 <param name="bam_input" type="data" format="bam" label="Select BAM dataset" help="Specify BAM dataset with paired reads"/> | 319 </test> |
267 <conditional name="adv_bam_pe_options"> | 320 <test> |
268 | 321 <param name="reference_source_selector" value="history"/> |
269 <expand macro="advanced_pe_options" /> | 322 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
270 | 323 <param name="input_type_selector" value="paired"/> |
271 </conditional> | 324 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> |
272 </when> | 325 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> |
273 | 326 <param name="analysis_type_selector" value="illumina"/> |
274 <when value="single_bam"> | 327 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/> |
275 <param name="bam_input" type="data" format="bam" label="Select BAM dataset" help="Specify BAM dataset with single reads"/> | 328 </test> |
276 <conditional name="adv_bam_se_options"> | 329 <test> |
277 | 330 <param name="reference_source_selector" value="history"/> |
278 <expand macro="advanced_se_options" /> | 331 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
279 | 332 <param name="input_type_selector" value="paired"/> |
280 </conditional> | 333 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/> |
281 </when> | 334 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> |
282 | 335 <param name="analysis_type_selector" value="illumina"/> |
283 </conditional> | 336 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/> |
284 | 337 </test> |
285 <expand macro="read_group_conditional" /> | 338 <test> |
286 | 339 <param name="reference_source_selector" value="history"/> |
287 <conditional name="analysis_type"> | 340 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
288 <param name="analysis_type_selector" type="select" label="Select analysis mode"> | 341 <param name="input_type_selector" value="paired_bam"/> |
289 <option value="illumina">1.Simple Illumina mode</option> | 342 <param name="bam_input" ftype="bam" value="bwa-aln-bam-input.bam"/> |
290 <option value="full">2.Full list of options</option> | 343 <param name="analysis_type_selector" value="illumina"/> |
291 </param> | 344 <output name="bam_output" ftype="bam" file="bwa-aln-test2.bam" lines_diff="2"/> |
292 <when value="illumina"> | 345 </test> |
293 <!-- do nothing --> | 346 <test> |
294 </when> | 347 <param name="reference_source_selector" value="history"/> |
295 <when value="full"> | 348 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
296 <param name="n" type="text" value="0.04" label="maximum edit distance if the value is integer, or the fraction of missing alignments given 2% uniform base error rate if float. In the latter case, the maximum edit distance is automatically chosen for different read lengths." help="aln -n; default=0.04"/> | 349 <param name="input_type_selector" value="paired"/> |
297 <param name="o" type="integer" value="1" label="maximum number or gap openings" help="aln -o; default=1"/> | 350 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> |
298 <param name="e" type="integer" value="-1" label="maximum number of gap extensions" help="aln -e; -1 disables long gaps and invokes k-difference mode; default=-1"/> | 351 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> |
299 <param name="i" type="integer" value="5" label="do not put an indel within this many bp towards the ends" help="aln -i; default=5"/> | 352 <param name="rg_selector" value="set"/> |
300 <param name="d" type="integer" value="10" label="maximum occurrences for extending a long deletion" help="aln -d; default=10"/> | 353 <param name="ID" value="rg1"/> |
301 <param name="l" type="integer" value="32" label="seed length" help="aln -l; default=32"/> | 354 <param name="PL" value="CAPILLARY"/> |
302 <param name="k" type="integer" value="2" label="maximum differences in the seed" help="aln -k; default=2"/> | 355 <param name="analysis_type_selector" value="illumina"/> |
303 <param name="m" type="integer" value="2000000" label="maximum entries in the queue" help="aln -m; default=2000000"/> | 356 <output name="bam_output" ftype="bam" file="bwa-aln-test3.bam" lines_diff="2"/> |
304 <param name="M" type="integer" value="3" label="mismatch penalty" help="aln -M; default=3"/> | 357 </test> |
305 <param name="O" type="integer" value="11" label="gap open penalty" help="aln -O; default=11"/> | 358 </tests> |
306 <param name="E" type="integer" value="4" label="gap extension penalty" help="aln -E; default=4"/> | 359 <help><![CDATA[ |
307 <param name="R" type="integer" value="30" label="stop searching when there are more than this value of equally best hits" help="aln -R; default=30"/> | |
308 <param name="q" type="integer" value="0" label="quality threshold for read trimming down to 35bp" help="aln -q; default=0"/> | |
309 <param name="B" type="integer" optional="True" label="length of barcode" help="aln -B; optional parameter"/> | |
310 <param name="L" type="float" optional="True" label="log-scaled gap penalty for long deletions" help="aln -L; optional parameter"/> | |
311 </when> | |
312 </conditional> | |
313 </inputs> | |
314 | |
315 <outputs> | |
316 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"> | |
317 <expand macro="dbKeyActionsBwa" /> | |
318 </data> | |
319 </outputs> | |
320 | |
321 <tests> | |
322 <test> | |
323 <param name="reference_source_selector" value="history" /> | |
324 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | |
325 <param name="input_type_selector" value="single"/> | |
326 <param name="fastq_input1" ftype="fasta" value="bwa-mem-fasta1.fa"/> | |
327 <param name="analysis_type_selector" value="illumina"/> | |
328 <output name="bam_output" ftype="bam" file="bwa-aln-test1-fasta.bam" lines_diff="2" /> | |
329 </test> | |
330 <test> | |
331 <param name="reference_source_selector" value="history" /> | |
332 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | |
333 <param name="input_type_selector" value="paired"/> | |
334 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> | |
335 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> | |
336 <param name="analysis_type_selector" value="illumina"/> | |
337 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2" /> | |
338 </test> | |
339 <test> | |
340 <param name="reference_source_selector" value="history" /> | |
341 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | |
342 <param name="input_type_selector" value="paired"/> | |
343 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/> | |
344 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> | |
345 <param name="analysis_type_selector" value="illumina"/> | |
346 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2" /> | |
347 </test> | |
348 <test> | |
349 <param name="reference_source_selector" value="history" /> | |
350 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | |
351 <param name="input_type_selector" value="paired_bam"/> | |
352 <param name="bam_input" ftype="bam" value="bwa-aln-bam-input.bam"/> | |
353 <param name="analysis_type_selector" value="illumina"/> | |
354 <output name="bam_output" ftype="bam" file="bwa-aln-test2.bam" lines_diff="2" /> | |
355 </test> | |
356 <test> | |
357 <param name="reference_source_selector" value="history" /> | |
358 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | |
359 <param name="input_type_selector" value="paired"/> | |
360 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> | |
361 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> | |
362 <param name="rg_selector" value="set"/> | |
363 <param name="ID" value="rg1"/> | |
364 <param name="PL" value="CAPILLARY"/> | |
365 <param name="analysis_type_selector" value="illumina"/> | |
366 <output name="bam_output" ftype="bam" file="bwa-aln-test3.bam" lines_diff="2" /> | |
367 </test> | |
368 </tests> | |
369 <help> | |
370 **What is does** | 360 **What is does** |
371 | 361 |
372 BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. The bwa-aln algorithm is designed for Illumina sequence reads up to 100bp. For longer reads use BWA-MEM algorithm distributed as a separate Galaxy tool. | 362 BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the |
363 human genome. The bwa-aln algorithm is designed for Illumina sequence reads up to 100bp. For longer reads use | |
364 the separate BWA-MEM Galaxy tool. | |
373 | 365 |
374 This Galaxy tool wraps bwa-aln, bwa-samse and -sampe modules of bwa read mapping tool: | 366 This Galaxy tool wraps bwa-aln, bwa-samse and -sampe modules of bwa read mapping tool: |
375 | 367 |
376 - **bwa aln** - actual mapper placing reads onto the reference sequence | 368 - **bwa aln** - actual mapper placing reads onto the reference sequence |
377 - **bwa samse** - post-processor converting suffix array coordinates into genome coordinates in SAM format for single reads | 369 - **bwa samse** - post-processor converting suffix array coordinates into genome coordinates in SAM format for |
378 - **bam sampe** - post-processor for paired reads | 370 single reads |
379 | 371 - **bam sampe** - post-processor for paired reads |
380 Galaxy implementation takes fastq or BAM (unaligned BAM) datasets as input and produces output in BAM (not SAM; in reality SAM produced by the bwa is converted to BAM on the fly by samtools view command) format, which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard). | 372 |
373 | |
374 The Galaxy implementation takes fastq or BAM (unaligned BAM) datasets as input and produces output in BAM format, | |
375 which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard). | |
381 | 376 |
382 ----- | 377 ----- |
383 | 378 |
384 **Indices: Selecting reference genomes for BWA** | 379 **Indices: Selecting reference genomes for BWA** |
385 | 380 |
386 Galaxy wrapper for BWA allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options: | 381 The Galaxy wrapper for BWA allows you to select between precomputed and user-defined indices for reference genomes |
387 | 382 using the **Will you select a reference genome from your history or use a built-in index?** select box. |
388 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility and are ready to be mapped against. | 383 |
389 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run mapping with `bwa aln`. | 384 This select box has two options: |
390 | 385 |
386 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select | |
387 reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility | |
388 and are ready to be mapped against. | |
389 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select | |
390 reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your | |
391 current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome | |
392 from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run | |
393 mapping with `bwa aln`. | |
394 | |
395 | |
391 If your genome of interest is not listed here you have two choices: | 396 If your genome of interest is not listed here you have two choices: |
392 | 397 |
393 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added | 398 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index |
394 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option. | 399 needs to be added |
395 | 400 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history |
396 ----- | 401 and build index** option. |
397 | 402 |
398 **Galaxy-specific option** | |
399 | |
400 Galaxy allows three levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are: | |
401 | |
402 1. *Simple Illumina mode*: The simplest possible bwa mem application in which it alignes single or paired-end data to reference using default parameters. It is equivalent to the following command: bwa mem <reference index> <fastq dataset1> [fastq dataset2] | |
403 2. *Full list of options*: Allows access to all options through Galaxy interface. | |
404 | |
405 ------ | |
406 | |
407 **bwa-aln options** | |
408 | |
409 Each Galaxy parameter widget corresponds to command line flags listed below:: | |
410 | |
411 -n NUM max #diff (int) or missing prob under 0.02 err rate (float) [0.04] | |
412 -o INT maximum number or fraction of gap opens [1] | |
413 -e INT maximum number of gap extensions, -1 for disabling long gaps [-1] | |
414 -i INT do not put an indel within INT bp towards the ends [5] | |
415 -d INT maximum occurrences for extending a long deletion [10] | |
416 -l INT seed length [32] | |
417 -k INT maximum differences in the seed [2] | |
418 -m INT maximum entries in the queue [2000000] | |
419 -M INT mismatch penalty [3] | |
420 -O INT gap open penalty [11] | |
421 -E INT gap extension penalty [4] | |
422 -R INT stop searching when there are >INT equally best hits [30] | |
423 -q INT quality threshold for read trimming down to 35bp [0] | |
424 -B INT length of barcode | |
425 -L log-scaled gap penalty for long deletions | |
426 -N non-iterative mode: search for all n-difference hits (slooow) | |
427 -I the input is in the Illumina 1.3+ FASTQ-like format | |
428 -b the input read file is in the BAM format | |
429 -0 use single-end reads only (effective with -b) | |
430 -1 use the 1st read in a pair (effective with -b) | |
431 -2 use the 2nd read in a pair (effective with -b) | |
432 | |
433 **bwa-samse options**:: | |
434 | |
435 -a INT maximum insert size [500] | |
436 -o INT maximum occurrences for one end [100000] | |
437 -n INT maximum hits to output for paired reads [3] | |
438 -N INT maximum hits to output for discordant pairs [10] | |
439 -c FLOAT prior of chimeric rate (lower bound) [1.0e-05] | |
440 -r STR read group header line [null] | |
441 | |
442 **bwa-sampe options**:: | |
443 | |
444 -n INT maximum hits to output for paired reads [3] | |
445 -r STR read group header line [null] | |
446 | |
447 @dataset_collections@ | |
448 | 403 |
449 @RG@ | 404 @RG@ |
450 | 405 |
451 @info@ | 406 @info@ |
452 </help> | 407 ]]></help> |
453 <citations> | 408 <citations> |
454 <citation type="doi">10.1093/bioinformatics/btp324</citation> | 409 <citation type="doi">10.1093/bioinformatics/btp324</citation> |
455 <citation type="doi">10.1093/bioinformatics/btp698</citation> | 410 <citation type="doi">10.1093/bioinformatics/btp698</citation> |
456 </citations> | 411 </citations> |
457 </tool> | 412 </tool> |