annotate bwa.xml @ 5:86c73f0eb389 draft default tip

Uploaded
author devteam
date Thu, 06 Nov 2014 14:52:29 -0500
parents 6bfb657c8fe1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
1 <?xml version="1.0"?>
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
2 <tool id="bwa_aln_0_7_10" name="BWA" version="bwa-0.7.10-r837-dirty_galaxy_0.2">
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
3
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
4 <requirements>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
5 <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
6 <requirement type="package" version="1.1">samtools</requirement>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
7 </requirements>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
8 <description>- map short reads (&lt; 100 bp) against referece genome</description>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
9 <command>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
10
5e72d136a39e Uploaded
devteam
parents:
diff changeset
11 #set $reference_fasta_filename = "localref.fa"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
12
5e72d136a39e Uploaded
devteam
parents:
diff changeset
13 #if str( $reference_source.reference_source_selector ) == "history":
5e72d136a39e Uploaded
devteam
parents:
diff changeset
14
5e72d136a39e Uploaded
devteam
parents:
diff changeset
15 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
5e72d136a39e Uploaded
devteam
parents:
diff changeset
16
5e72d136a39e Uploaded
devteam
parents:
diff changeset
17 ## The following shell commands decide with of the BWA indexing algorithms (IS or BWTSW) will be run
5e72d136a39e Uploaded
devteam
parents:
diff changeset
18 ## depending ob the size of the input FASTA dataset
5e72d136a39e Uploaded
devteam
parents:
diff changeset
19
5e72d136a39e Uploaded
devteam
parents:
diff changeset
20 (
5e72d136a39e Uploaded
devteam
parents:
diff changeset
21 size=`stat -c %s "${reference_fasta_filename}" 2&gt;/dev/null`; ## Linux
5e72d136a39e Uploaded
devteam
parents:
diff changeset
22 if [ $? -eq 0 ];
5e72d136a39e Uploaded
devteam
parents:
diff changeset
23 then
5e72d136a39e Uploaded
devteam
parents:
diff changeset
24 if [ \$size -lt 2000000000 ];
5e72d136a39e Uploaded
devteam
parents:
diff changeset
25 then
5e72d136a39e Uploaded
devteam
parents:
diff changeset
26 bwa index -a is "${reference_fasta_filename}";
5e72d136a39e Uploaded
devteam
parents:
diff changeset
27 else
5e72d136a39e Uploaded
devteam
parents:
diff changeset
28 bwa index -a bwtsw "${reference_fasta_filename}";
5e72d136a39e Uploaded
devteam
parents:
diff changeset
29 fi;
5e72d136a39e Uploaded
devteam
parents:
diff changeset
30 fi;
5e72d136a39e Uploaded
devteam
parents:
diff changeset
31
5e72d136a39e Uploaded
devteam
parents:
diff changeset
32 eval \$(stat -s "${reference_fasta_filename}"); ## OSX
5e72d136a39e Uploaded
devteam
parents:
diff changeset
33 if [ $? -eq 0 ];
5e72d136a39e Uploaded
devteam
parents:
diff changeset
34 then
5e72d136a39e Uploaded
devteam
parents:
diff changeset
35 if [ \$st_size -lt 2000000000 ];
5e72d136a39e Uploaded
devteam
parents:
diff changeset
36 then
5e72d136a39e Uploaded
devteam
parents:
diff changeset
37 bwa index -a is "${reference_fasta_filename}";
5e72d136a39e Uploaded
devteam
parents:
diff changeset
38 echo "Generating BWA index with is algorithm";
5e72d136a39e Uploaded
devteam
parents:
diff changeset
39 else
5e72d136a39e Uploaded
devteam
parents:
diff changeset
40 bwa index -a bwtsw "${reference_fasta_filename}";
5e72d136a39e Uploaded
devteam
parents:
diff changeset
41 echo "Generating BWA index with bwtsw algorithm";
5e72d136a39e Uploaded
devteam
parents:
diff changeset
42 fi;
5e72d136a39e Uploaded
devteam
parents:
diff changeset
43 fi;
5e72d136a39e Uploaded
devteam
parents:
diff changeset
44 ) &amp;&amp;
5e72d136a39e Uploaded
devteam
parents:
diff changeset
45
5e72d136a39e Uploaded
devteam
parents:
diff changeset
46 #else:
5e72d136a39e Uploaded
devteam
parents:
diff changeset
47 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
5e72d136a39e Uploaded
devteam
parents:
diff changeset
48 #end if
5e72d136a39e Uploaded
devteam
parents:
diff changeset
49
5e72d136a39e Uploaded
devteam
parents:
diff changeset
50 ## Begin bwa command line
5e72d136a39e Uploaded
devteam
parents:
diff changeset
51
5e72d136a39e Uploaded
devteam
parents:
diff changeset
52 ####### Fastq paired
5e72d136a39e Uploaded
devteam
parents:
diff changeset
53
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
54 #if str( $input_type.input_type_selector ) == "paired" or str( $input_type.input_type_selector ) == "paired_collection":
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
55
5e72d136a39e Uploaded
devteam
parents:
diff changeset
56 bwa aln
5e72d136a39e Uploaded
devteam
parents:
diff changeset
57 -t "\${GALAXY_SLOTS:-1}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
58
5e72d136a39e Uploaded
devteam
parents:
diff changeset
59 @command_options@
5e72d136a39e Uploaded
devteam
parents:
diff changeset
60
5e72d136a39e Uploaded
devteam
parents:
diff changeset
61 "${reference_fasta_filename}"
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
62
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
63 #if str( $input_type.input_type_selector ) == "paired_collection":
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
64 "${input_type.fastq_input1.forward}"
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
65 #else
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
66 "${input_type.fastq_input1}"
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
67 #end if
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
68
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
69 > first.sai &amp;&amp;
5e72d136a39e Uploaded
devteam
parents:
diff changeset
70
5e72d136a39e Uploaded
devteam
parents:
diff changeset
71 bwa aln
5e72d136a39e Uploaded
devteam
parents:
diff changeset
72 -t "\${GALAXY_SLOTS:-1}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
73
5e72d136a39e Uploaded
devteam
parents:
diff changeset
74 @command_options@
5e72d136a39e Uploaded
devteam
parents:
diff changeset
75
5e72d136a39e Uploaded
devteam
parents:
diff changeset
76 "${reference_fasta_filename}"
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
77
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
78 #if str( $input_type.input_type_selector ) == "paired_collection":
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
79 "${input_type.fastq_input1.reverse}"
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
80 #else
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
81 "${input_type.fastq_input2}"
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
82 #end if
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
83
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
84 > second.sai &amp;&amp;
5e72d136a39e Uploaded
devteam
parents:
diff changeset
85
5e72d136a39e Uploaded
devteam
parents:
diff changeset
86 bwa sampe
5e72d136a39e Uploaded
devteam
parents:
diff changeset
87
5e72d136a39e Uploaded
devteam
parents:
diff changeset
88 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True":
5e72d136a39e Uploaded
devteam
parents:
diff changeset
89
5e72d136a39e Uploaded
devteam
parents:
diff changeset
90 -a ${$input_type.adv_pe_options.a}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
91 -o ${$input_type.adv_pe_options.o}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
92 -n ${$input_type.adv_pe_options.n}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
93 -N ${$input_type.adv_pe_options.N}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
94
5e72d136a39e Uploaded
devteam
parents:
diff changeset
95 #end if
5e72d136a39e Uploaded
devteam
parents:
diff changeset
96
5e72d136a39e Uploaded
devteam
parents:
diff changeset
97 @read_group_options@
5e72d136a39e Uploaded
devteam
parents:
diff changeset
98
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
99 #if str( $input_type.input_type_selector ) == "paired_collection":
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
100
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
101 "${reference_fasta_filename}" first.sai second.sai "${input_type.fastq_input1.forward}" "${input_type.fastq_input1.reverse}"
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
102
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
103 #else:
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
104
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
105 "${reference_fasta_filename}" first.sai second.sai "${input_type.fastq_input1}" "${input_type.fastq_input2}"
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
106
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
107 #end if
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
108
5e72d136a39e Uploaded
devteam
parents:
diff changeset
109 ####### Fastq single
5e72d136a39e Uploaded
devteam
parents:
diff changeset
110
5e72d136a39e Uploaded
devteam
parents:
diff changeset
111 #elif str( $input_type.input_type_selector ) == "single":
5e72d136a39e Uploaded
devteam
parents:
diff changeset
112
5e72d136a39e Uploaded
devteam
parents:
diff changeset
113 bwa aln
5e72d136a39e Uploaded
devteam
parents:
diff changeset
114 -t "\${GALAXY_SLOTS:-1}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
115
5e72d136a39e Uploaded
devteam
parents:
diff changeset
116 @command_options@
5e72d136a39e Uploaded
devteam
parents:
diff changeset
117
5e72d136a39e Uploaded
devteam
parents:
diff changeset
118 "${reference_fasta_filename}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
119 "${input_type.fastq_input1}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
120 > first.sai &amp;&amp;
5e72d136a39e Uploaded
devteam
parents:
diff changeset
121
5e72d136a39e Uploaded
devteam
parents:
diff changeset
122 bwa samse
5e72d136a39e Uploaded
devteam
parents:
diff changeset
123
5e72d136a39e Uploaded
devteam
parents:
diff changeset
124 #if str( $input_type.adv_se_options.adv_se_options_selector) == "True":
5e72d136a39e Uploaded
devteam
parents:
diff changeset
125
5e72d136a39e Uploaded
devteam
parents:
diff changeset
126 -n ${$input_type.adv_se_options.n}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
127
5e72d136a39e Uploaded
devteam
parents:
diff changeset
128 #end if
5e72d136a39e Uploaded
devteam
parents:
diff changeset
129
5e72d136a39e Uploaded
devteam
parents:
diff changeset
130 @read_group_options@
5e72d136a39e Uploaded
devteam
parents:
diff changeset
131
5e72d136a39e Uploaded
devteam
parents:
diff changeset
132 "${reference_fasta_filename}" first.sai "${input_type.fastq_input1}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
133
5e72d136a39e Uploaded
devteam
parents:
diff changeset
134 ####### BAM paired
5e72d136a39e Uploaded
devteam
parents:
diff changeset
135
5e72d136a39e Uploaded
devteam
parents:
diff changeset
136 #elif str( $input_type.input_type_selector ) == "paired_bam":
5e72d136a39e Uploaded
devteam
parents:
diff changeset
137
5e72d136a39e Uploaded
devteam
parents:
diff changeset
138 bwa aln
5e72d136a39e Uploaded
devteam
parents:
diff changeset
139 -t "\${GALAXY_SLOTS:-1}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
140 -b
5e72d136a39e Uploaded
devteam
parents:
diff changeset
141 -1
5e72d136a39e Uploaded
devteam
parents:
diff changeset
142
5e72d136a39e Uploaded
devteam
parents:
diff changeset
143 @command_options@
5e72d136a39e Uploaded
devteam
parents:
diff changeset
144
5e72d136a39e Uploaded
devteam
parents:
diff changeset
145 "${reference_fasta_filename}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
146 "${input_type.bam_input}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
147 > first.sai &amp;&amp;
5e72d136a39e Uploaded
devteam
parents:
diff changeset
148
5e72d136a39e Uploaded
devteam
parents:
diff changeset
149 bwa aln
5e72d136a39e Uploaded
devteam
parents:
diff changeset
150 -t "\${GALAXY_SLOTS:-1}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
151 -b
5e72d136a39e Uploaded
devteam
parents:
diff changeset
152 -2
5e72d136a39e Uploaded
devteam
parents:
diff changeset
153 @command_options@
5e72d136a39e Uploaded
devteam
parents:
diff changeset
154 "${reference_fasta_filename}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
155 "${input_type.bam_input}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
156 > second.sai &amp;&amp;
5e72d136a39e Uploaded
devteam
parents:
diff changeset
157
5e72d136a39e Uploaded
devteam
parents:
diff changeset
158 bwa sampe
5e72d136a39e Uploaded
devteam
parents:
diff changeset
159
5e72d136a39e Uploaded
devteam
parents:
diff changeset
160 #if str( $input_type.adv_bam_pe_options.adv_pe_options_selector) == "True":
5e72d136a39e Uploaded
devteam
parents:
diff changeset
161
5e72d136a39e Uploaded
devteam
parents:
diff changeset
162 -a ${$input_type.adv_bam_pe_options.a}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
163 -o ${$input_type.adv_bam_pe_options.o}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
164 -n ${$input_type.adv_bam_pe_options.n}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
165 -N ${$input_type.adv_bam_pe_options.N}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
166
5e72d136a39e Uploaded
devteam
parents:
diff changeset
167 #end if
5e72d136a39e Uploaded
devteam
parents:
diff changeset
168
5e72d136a39e Uploaded
devteam
parents:
diff changeset
169 @read_group_options@
5e72d136a39e Uploaded
devteam
parents:
diff changeset
170
5e72d136a39e Uploaded
devteam
parents:
diff changeset
171 "${reference_fasta_filename}" first.sai second.sai "${input_type.bam_input}" "${input_type.bam_input}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
172
5e72d136a39e Uploaded
devteam
parents:
diff changeset
173 ####### Fastq single ------------ to do next
5e72d136a39e Uploaded
devteam
parents:
diff changeset
174
5e72d136a39e Uploaded
devteam
parents:
diff changeset
175 #elif str( $input_type.input_type_selector ) == "single_bam":
5e72d136a39e Uploaded
devteam
parents:
diff changeset
176
5e72d136a39e Uploaded
devteam
parents:
diff changeset
177 bwa aln
5e72d136a39e Uploaded
devteam
parents:
diff changeset
178 -t "\${GALAXY_SLOTS:-1}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
179 -b
5e72d136a39e Uploaded
devteam
parents:
diff changeset
180 -0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
181
5e72d136a39e Uploaded
devteam
parents:
diff changeset
182 @command_options@
5e72d136a39e Uploaded
devteam
parents:
diff changeset
183
5e72d136a39e Uploaded
devteam
parents:
diff changeset
184 "${reference_fasta_filename}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
185 "${input_type.bam_input}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
186 > first.sai &amp;&amp;
5e72d136a39e Uploaded
devteam
parents:
diff changeset
187
5e72d136a39e Uploaded
devteam
parents:
diff changeset
188 bwa samse
5e72d136a39e Uploaded
devteam
parents:
diff changeset
189
5e72d136a39e Uploaded
devteam
parents:
diff changeset
190 #if str( $input_type.adv_bam_se_options.adv_se_options_selector) == "True":
5e72d136a39e Uploaded
devteam
parents:
diff changeset
191
5e72d136a39e Uploaded
devteam
parents:
diff changeset
192 -n ${$input_type.adv_bam_se_options.n}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
193
5e72d136a39e Uploaded
devteam
parents:
diff changeset
194 #end if
5e72d136a39e Uploaded
devteam
parents:
diff changeset
195
5e72d136a39e Uploaded
devteam
parents:
diff changeset
196 @read_group_options@
5e72d136a39e Uploaded
devteam
parents:
diff changeset
197
5e72d136a39e Uploaded
devteam
parents:
diff changeset
198 "${reference_fasta_filename}" first.sai "${input_type.bam_input}"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
199
5e72d136a39e Uploaded
devteam
parents:
diff changeset
200 #end if
5e72d136a39e Uploaded
devteam
parents:
diff changeset
201
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
202 | samtools view -Sb - > temporary_bam_file.bam &amp;&amp;
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
203
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
204 samtools sort -f temporary_bam_file.bam ${bam_output}
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
205
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
206
5e72d136a39e Uploaded
devteam
parents:
diff changeset
207 </command>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
208
5e72d136a39e Uploaded
devteam
parents:
diff changeset
209 <macros>
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
210 <import>bwa_macros.xml</import>
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
211 <token name="@command_options@">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
212 #if str( $analysis_type.analysis_type_selector ) == "illumina":
5e72d136a39e Uploaded
devteam
parents:
diff changeset
213
5e72d136a39e Uploaded
devteam
parents:
diff changeset
214 ## do nothing -> just align with default parameters
5e72d136a39e Uploaded
devteam
parents:
diff changeset
215
5e72d136a39e Uploaded
devteam
parents:
diff changeset
216 #elif str( $analysis_type.analysis_type_selector ) == "full":
5e72d136a39e Uploaded
devteam
parents:
diff changeset
217
5e72d136a39e Uploaded
devteam
parents:
diff changeset
218 -n ${analysis_type.n}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
219 -o ${analysis_type.o}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
220 -e ${analysis_type.e}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
221 -i ${analysis_type.i}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
222 -d ${analysis_type.d}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
223 -l ${analysis_type.l}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
224 -k ${analysis_type.k}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
225 -m ${analysis_type.m}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
226 -M ${analysis_type.M}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
227 -O ${analysis_type.O}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
228 -E ${analysis_type.E}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
229 -R ${analysis_type.R}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
230 -q ${analysis_type.q}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
231
5e72d136a39e Uploaded
devteam
parents:
diff changeset
232 #if str( $analysis_type.B ):
5e72d136a39e Uploaded
devteam
parents:
diff changeset
233 -B ${analysis_type.B}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
234 #end if
5e72d136a39e Uploaded
devteam
parents:
diff changeset
235
5e72d136a39e Uploaded
devteam
parents:
diff changeset
236 #if str( $analysis_type.L ):
5e72d136a39e Uploaded
devteam
parents:
diff changeset
237 -B ${analysis_type.L}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
238 #end if
5e72d136a39e Uploaded
devteam
parents:
diff changeset
239
5e72d136a39e Uploaded
devteam
parents:
diff changeset
240 #elif str( $analysis_type.analysis_type_selector ) == "cline":
5e72d136a39e Uploaded
devteam
parents:
diff changeset
241 ${analysis_type.cline}
5e72d136a39e Uploaded
devteam
parents:
diff changeset
242 #end if
5e72d136a39e Uploaded
devteam
parents:
diff changeset
243 </token>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
244 <token name="@read_group_options@">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
245
5e72d136a39e Uploaded
devteam
parents:
diff changeset
246 #if str( $rg.rg_selector ) == "True":
5e72d136a39e Uploaded
devteam
parents:
diff changeset
247
5e72d136a39e Uploaded
devteam
parents:
diff changeset
248 -r "@RG\tID:$rg.ID\tSM:$rg.SM"
5e72d136a39e Uploaded
devteam
parents:
diff changeset
249
5e72d136a39e Uploaded
devteam
parents:
diff changeset
250 #end if
5e72d136a39e Uploaded
devteam
parents:
diff changeset
251 </token>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
252
5e72d136a39e Uploaded
devteam
parents:
diff changeset
253 <xml name="advanced_pe_options">
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
254 <param name="adv_pe_options_selector" type="select" label="Set advanced paired end options?" help="Provides additional controls">
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
255 <option value="set">Set</option>
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
256 <option value="do_not_set" selected="True">Do not set</option>
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
257 </param>
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
258 <when value="set">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
259 <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"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
260 <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"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
261 <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"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
262 <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"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
263 <param name="c" type="float" value="0.00005" label="Prior of chimeric rate (lower bound)" help="sampe -c"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
264 </when>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
265 <when value="do_not_set">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
266 <!-- do nothing -->
5e72d136a39e Uploaded
devteam
parents:
diff changeset
267 </when>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
268 </xml>
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
269 <xml name="advanced_se_options">
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
270 <param name="adv_se_options_selector" type="select" label="Set advanced single end options?" help="Provides additional controls">
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
271 <option value="set">Set</option>
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
272 <option value="do_not_set" selected="True">Do not set</option>
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
273 </param>
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
274 <when value="set">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
275 <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"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
276 </when>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
277 <when value="do_not_set">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
278 <!-- do nothing -->
5e72d136a39e Uploaded
devteam
parents:
diff changeset
279 </when>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
280 </xml>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
281 </macros>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
282
5e72d136a39e Uploaded
devteam
parents:
diff changeset
283 <inputs>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
284
5e72d136a39e Uploaded
devteam
parents:
diff changeset
285 <conditional name="reference_source">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
286 <param name="reference_source_selector" type="select" label="Load reference genome from">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
287 <option value="cached">Local cache</option>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
288 <option value="history">History</option>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
289 </param>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
290 <when value="cached">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
291 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
292 <options from_data_table="bwa_mem_indexes">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
293 <filter type="sort_by" column="2" />
5e72d136a39e Uploaded
devteam
parents:
diff changeset
294 <validator type="no_options" message="No indexes are available" />
5e72d136a39e Uploaded
devteam
parents:
diff changeset
295 </options>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
296 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
297 </param>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
298 </when>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
299 <when value="history">
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
300 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
301 </when>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
302 </conditional>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
303 <conditional name="input_type">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
304 <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">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
305 <option value="paired">Paired fastq</option>
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
306 <option value="paired_collection">Paired fastq collection</option>
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
307 <option value="single">Single fastq</option>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
308 <option value="paired_bam">Paired BAM</option>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
309 <option value="single_bam">Single BAM</option>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
310 </param>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
311 <when value="paired">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
312 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
313 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
314 <conditional name="adv_pe_options">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
315
5e72d136a39e Uploaded
devteam
parents:
diff changeset
316 <expand macro="advanced_pe_options" />
5e72d136a39e Uploaded
devteam
parents:
diff changeset
317
5e72d136a39e Uploaded
devteam
parents:
diff changeset
318 </conditional>
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
319 </when>
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
320
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
321 <when value="paired_collection">
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
322 <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
323 <conditional name="adv_pe_options">
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
324
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
325 <expand macro="advanced_pe_options" />
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
326
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
327 </conditional>
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
328 </when>
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
329
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
330
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
331 <when value="single">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
332 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
333 <conditional name="adv_se_options">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
334
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
335 <expand macro="advanced_se_options" />
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
336
5e72d136a39e Uploaded
devteam
parents:
diff changeset
337 </conditional>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
338 </when>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
339
5e72d136a39e Uploaded
devteam
parents:
diff changeset
340 <!-- the difference between single and paired bams is in the <command> tag portion and realated to -0, -1, and -2 options -->
5e72d136a39e Uploaded
devteam
parents:
diff changeset
341
5e72d136a39e Uploaded
devteam
parents:
diff changeset
342 <when value="paired_bam">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
343 <param name="bam_input" type="data" format="bam" label="Select BAM dataset" help="Specify BAM dataset with paired reads"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
344 <conditional name="adv_bam_pe_options">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
345
5e72d136a39e Uploaded
devteam
parents:
diff changeset
346 <expand macro="advanced_pe_options" />
5e72d136a39e Uploaded
devteam
parents:
diff changeset
347
5e72d136a39e Uploaded
devteam
parents:
diff changeset
348 </conditional>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
349 </when>
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
350
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
351 <when value="single_bam">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
352 <param name="bam_input" type="data" format="bam" label="Select BAM dataset" help="Specify BAM dataset with single reads"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
353 <conditional name="adv_bam_se_options">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
354
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
355 <expand macro="advanced_se_options" />
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
356
5e72d136a39e Uploaded
devteam
parents:
diff changeset
357 </conditional>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
358 </when>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
359
5e72d136a39e Uploaded
devteam
parents:
diff changeset
360 </conditional>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
361
5e72d136a39e Uploaded
devteam
parents:
diff changeset
362 <conditional name="rg">
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
363 <param name="rg_selector" type="select" label="Set readgroups information?" help="Specifying readgroup information can greatly simplify your downstream analyses by allowing combining multiple datasets. See help below for more details">
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
364 <option value="set">Set</option>
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
365 <option value="do_not_set" selected="True">Do not set</option>
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
366 </param>
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
367 <when value="set">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
368 <param name="ID" type="text" value="readgroup1" size="20" label="Specify readgroup ID" help="This value must be unique among multiple samples in your experiment">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
369 <sanitizer invalid_char="">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
370 <valid initial="string.printable"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
371 </sanitizer>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
372 </param>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
373 <param name="SM" type="text" value="blood" size="20" label="Specify readgroup sample name (SM)" help="This value should be descriptive">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
374 <sanitizer invalid_char="">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
375 <valid initial="string.printable"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
376 </sanitizer>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
377 </param>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
378 </when>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
379 <when value="do_not_set">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
380 <!-- do nothing -->
5e72d136a39e Uploaded
devteam
parents:
diff changeset
381 </when>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
382 </conditional>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
383
5e72d136a39e Uploaded
devteam
parents:
diff changeset
384 <conditional name="analysis_type">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
385 <param name="analysis_type_selector" type="select" label="Select analysis mode">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
386 <option value="illumina">1.Simple Illumina mode</option>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
387 <option value="full">2.Full list of options</option>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
388 <option value="cline">3.Input parameters on the command line</option>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
389 </param>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
390 <when value="illumina">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
391 <!-- do nothing -->
5e72d136a39e Uploaded
devteam
parents:
diff changeset
392 </when>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
393 <when value="full">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
394 <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"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
395 <param name="o" type="integer" value="1" label="maximum number or gap openings" help="aln -o; default=1"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
396 <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"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
397 <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"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
398 <param name="d" type="integer" value="10" label="maximum occurrences for extending a long deletion" help="aln -d; default=10"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
399 <param name="l" type="integer" value="32" label="seed length" help="aln -l; default=32"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
400 <param name="k" type="integer" value="2" label="maximum differences in the seed" help="aln -k; default=2"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
401 <param name="m" type="integer" value="2000000" label="maximum entries in the queue" help="aln -m; default=2000000"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
402 <param name="M" type="integer" value="3" label="mismatch penalty" help="aln -M; default=3"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
403 <param name="O" type="integer" value="11" label="gap open penalty" help="aln -O; default=11"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
404 <param name="E" type="integer" value="4" label="gap extension penalty" help="aln -E; default=4"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
405 <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"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
406 <param name="q" type="integer" value="0" label="quality threshold for read trimming down to 35bp" help="aln -q; default=0"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
407 <param name="B" type="integer" optional="True" label="length of barcode" help="aln -B; optional parameter"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
408 <param name="L" type="float" optional="True" label="log-scaled gap penalty for long deletions" help="aln -L; optional parameter"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
409 </when>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
410
5e72d136a39e Uploaded
devteam
parents:
diff changeset
411 <when value="cline">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
412 <param name="cline" size="60" type="text" value="-n 0.04 -R 10" label="Type command line options here" help="All paremeters that DO NOT involve filenames can be typed here.">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
413 <sanitizer>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
414 <valid initial="string.printable">
5e72d136a39e Uploaded
devteam
parents:
diff changeset
415 <remove value="&apos;"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
416 </valid>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
417 </sanitizer>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
418 </param>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
419 </when>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
420 </conditional>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
421 </inputs>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
422
5e72d136a39e Uploaded
devteam
parents:
diff changeset
423 <outputs>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
424 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
425 </outputs>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
426
5e72d136a39e Uploaded
devteam
parents:
diff changeset
427 <tests>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
428 <test>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
429 <param name="reference_source_selector" value="history" />
5e72d136a39e Uploaded
devteam
parents:
diff changeset
430 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
431 <param name="input_type_selector" value="paired"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
432 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
433 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
434 <param name="analysis_type_selector" value="illumina"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
435 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2" />
5e72d136a39e Uploaded
devteam
parents:
diff changeset
436 </test>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
437 <test>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
438 <param name="reference_source_selector" value="history" />
5e72d136a39e Uploaded
devteam
parents:
diff changeset
439 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
440 <param name="input_type_selector" value="paired_bam"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
441 <param name="bam_input" ftype="bam" value="bwa-aln-bam-input.bam"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
442 <param name="analysis_type_selector" value="illumina"/>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
443 <output name="bam_output" ftype="bam" file="bwa-aln-test2.bam" lines_diff="2" />
5e72d136a39e Uploaded
devteam
parents:
diff changeset
444 </test>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
445 </tests>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
446 <stdio>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
447 <exit_code range="1:" />
5e72d136a39e Uploaded
devteam
parents:
diff changeset
448 </stdio>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
449 <help>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
450
5e72d136a39e Uploaded
devteam
parents:
diff changeset
451 **What is does**
5e72d136a39e Uploaded
devteam
parents:
diff changeset
452
5e72d136a39e Uploaded
devteam
parents:
diff changeset
453 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 separate Galaxy tool.
5e72d136a39e Uploaded
devteam
parents:
diff changeset
454
5e72d136a39e Uploaded
devteam
parents:
diff changeset
455 This Galaxy tool wraps bwa-aln, bwa-samse and -sampe modules of bwa read mapping tool:
5e72d136a39e Uploaded
devteam
parents:
diff changeset
456
5e72d136a39e Uploaded
devteam
parents:
diff changeset
457 - bwa aln - actual mapper placing reads onto the reference sequence
5e72d136a39e Uploaded
devteam
parents:
diff changeset
458 - bwa samse - post-processor converting suffix array coordinates into genome coordinates in SAM format for single reads
5e72d136a39e Uploaded
devteam
parents:
diff changeset
459 - bam sampe - post-processor for paired reads
5e72d136a39e Uploaded
devteam
parents:
diff changeset
460
5e72d136a39e Uploaded
devteam
parents:
diff changeset
461 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).
5e72d136a39e Uploaded
devteam
parents:
diff changeset
462
5e72d136a39e Uploaded
devteam
parents:
diff changeset
463 -----
5e72d136a39e Uploaded
devteam
parents:
diff changeset
464
5e72d136a39e Uploaded
devteam
parents:
diff changeset
465 **Galaxy-specific option**
5e72d136a39e Uploaded
devteam
parents:
diff changeset
466
5e72d136a39e Uploaded
devteam
parents:
diff changeset
467 Galaxy allows three levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are:
5e72d136a39e Uploaded
devteam
parents:
diff changeset
468
5e72d136a39e Uploaded
devteam
parents:
diff changeset
469 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 &lt;reference index&gt; &lt;fastq dataset1&gt; [fastq dataset2]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
470 2. *Full list of options*: Allows access to all options through Galaxy interface.
5e72d136a39e Uploaded
devteam
parents:
diff changeset
471 3. *Input parameters on the command line*: Similar to the choice above but for those who does not like clicking. Here options can be directly typed into a text box.
5e72d136a39e Uploaded
devteam
parents:
diff changeset
472
5e72d136a39e Uploaded
devteam
parents:
diff changeset
473 ------
5e72d136a39e Uploaded
devteam
parents:
diff changeset
474
5e72d136a39e Uploaded
devteam
parents:
diff changeset
475 **bwa-aln options**
5e72d136a39e Uploaded
devteam
parents:
diff changeset
476
5e72d136a39e Uploaded
devteam
parents:
diff changeset
477 Each Galaxy parameter widget corresponds to command line flags listed below::
5e72d136a39e Uploaded
devteam
parents:
diff changeset
478
5e72d136a39e Uploaded
devteam
parents:
diff changeset
479 -n NUM max #diff (int) or missing prob under 0.02 err rate (float) [0.04]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
480 -o INT maximum number or fraction of gap opens [1]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
481 -e INT maximum number of gap extensions, -1 for disabling long gaps [-1]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
482 -i INT do not put an indel within INT bp towards the ends [5]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
483 -d INT maximum occurrences for extending a long deletion [10]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
484 -l INT seed length [32]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
485 -k INT maximum differences in the seed [2]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
486 -m INT maximum entries in the queue [2000000]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
487 -M INT mismatch penalty [3]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
488 -O INT gap open penalty [11]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
489 -E INT gap extension penalty [4]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
490 -R INT stop searching when there are >INT equally best hits [30]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
491 -q INT quality threshold for read trimming down to 35bp [0]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
492 -B INT length of barcode
5e72d136a39e Uploaded
devteam
parents:
diff changeset
493 -L log-scaled gap penalty for long deletions
5e72d136a39e Uploaded
devteam
parents:
diff changeset
494 -N non-iterative mode: search for all n-difference hits (slooow)
5e72d136a39e Uploaded
devteam
parents:
diff changeset
495 -I the input is in the Illumina 1.3+ FASTQ-like format
5e72d136a39e Uploaded
devteam
parents:
diff changeset
496 -b the input read file is in the BAM format
5e72d136a39e Uploaded
devteam
parents:
diff changeset
497 -0 use single-end reads only (effective with -b)
5e72d136a39e Uploaded
devteam
parents:
diff changeset
498 -1 use the 1st read in a pair (effective with -b)
5e72d136a39e Uploaded
devteam
parents:
diff changeset
499 -2 use the 2nd read in a pair (effective with -b)
5e72d136a39e Uploaded
devteam
parents:
diff changeset
500
5e72d136a39e Uploaded
devteam
parents:
diff changeset
501 **bwa-samse options**::
5e72d136a39e Uploaded
devteam
parents:
diff changeset
502
5e72d136a39e Uploaded
devteam
parents:
diff changeset
503 -a INT maximum insert size [500]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
504 -o INT maximum occurrences for one end [100000]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
505 -n INT maximum hits to output for paired reads [3]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
506 -N INT maximum hits to output for discordant pairs [10]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
507 -c FLOAT prior of chimeric rate (lower bound) [1.0e-05]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
508 -r STR read group header line [null]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
509
5e72d136a39e Uploaded
devteam
parents:
diff changeset
510 **bwa-sampe options**::
5e72d136a39e Uploaded
devteam
parents:
diff changeset
511
5e72d136a39e Uploaded
devteam
parents:
diff changeset
512 -n INT maximum hits to output for paired reads [3]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
513 -r STR read group header line [null]
5e72d136a39e Uploaded
devteam
parents:
diff changeset
514
5e72d136a39e Uploaded
devteam
parents:
diff changeset
515
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
516 @dataset_collections@
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
517
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
518 @RG@
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
519
3
6bfb657c8fe1 Uploaded
devteam
parents: 0
diff changeset
520 @info@
0
5e72d136a39e Uploaded
devteam
parents:
diff changeset
521
5e72d136a39e Uploaded
devteam
parents:
diff changeset
522 </help>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
523 <citations>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
524 <citation type="doi">10.1093/bioinformatics/btp324</citation>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
525 <citation type="doi">10.1093/bioinformatics/btp698</citation>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
526 </citations>
5e72d136a39e Uploaded
devteam
parents:
diff changeset
527 </tool>