1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
|
#@UGENE_WORKFLOW
#This simple workflow finds patterns in you sequences and save them as annotations.
#
#You can use the workflow to map primers, regulatory signals, genes, etc.
#
#It loads any set of sequences from your files or folders and finds patterns in them. Just specify a dataset for the algorithm in the "Read sequence" element.
#
#Patterns are entered in comma-delimited format in the corresponding field of the "Find Pattern" element. Also you can load patterns from a file. In that case names of patterns can be saved as names of annotations. Files with patterns can be in any sequence format or in newline-delimited format.
workflow "Find patterns"{
read-sequence {
type:read-sequence;
name:"Read Sequence";
url-in {
dataset:Dataset;
}
}
search {
type:search;
name:"Find Pattern";
result-name:misc_feature;
use-names:true;
}
write-sequence {
type:write-sequence;
name:"Write Sequence";
document-format:genbank;
write-mode:0;
url-out:annotations.gb;
}
.actor-bindings {
search.out-annotations->write-sequence.in-sequence
read-sequence.out-sequence->search.in-sequence
}
read-sequence.sequence->search.in-sequence.sequence
read-sequence.annotations->write-sequence.in-sequence.annotations
search.annotations->write-sequence.in-sequence.annotations
read-sequence.sequence->write-sequence.in-sequence.sequence
.meta {
visual {
read-sequence {
pos:"-855 -645";
style:ext;
bg-color-ext:"0 128 128 64";
out-sequence.angle:360;
}
search {
pos:"-660 -645";
style:ext;
bg-color-ext:"0 128 128 64";
in-sequence.angle:180;
out-annotations.angle:360;
}
write-sequence {
pos:"-375 -645";
style:ext;
bg-color-ext:"0 128 128 64";
in-sequence.angle:180;
}
read-sequence.out-sequence->search.in-sequence {
text-pos:"-27.5 -24";
}
search.out-annotations->write-sequence.in-sequence {
text-pos:"-45 -37";
}
}
wizard {
name:"Find patterns Wizard";
help-page-id:16122733;
auto-run: true;
page {
id:1;
next:2;
title:"Input sequence(s)";
parameters-area {
read-sequence.url-in {
type:datasets;
}
}
}
page {
id:2;
next:3;
title:"Find Pattern";
parameters-area {
group {
title:"Find Pattern parameters";
label-size:150;
search.pattern_file {
label:"Pattern";
}
search.result-name {
}
search.use-names {
}
search.max-mismatches-num {
}
search.allow-ins-del {
}
search.amino {
}
search.ambiguous {
}
search.pattern-name-qual {
label:"Qualifier name";
}
}
}
}
page {
id:3;
title:"Output data";
parameters-area {
group {
title:"Output data";
label-size:120;
write-sequence.url-out {
label:"Result file";
}
write-sequence.accumulate {
label:"Accumulate results";
}
}
}
}
}
}
}
|
