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
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
|
#@UGENE_WORKFLOW
#For each input sequence the workflow performs a search of inverted repeats. Then it saves the repeats found on the direct strand to the "direct_strand_repeat_units.fa" file and the complement ones to the "compl_strand_repeat_units.fa" file.
include "Get the first half of sequence.usa" as "Script-Get the first half of sequence"
include "Get the second half of sequence.usa" as "Script-Get the second half of sequence"
workflow "Search for inverted repeats"{
read-sequence {
type:read-sequence;
name:"Read Sequence";
url-in {
dataset:"Dataset 1";
}
}
repeats-search {
type:repeats-search;
name:"Find Inverted Repeats";
algorithm:0;
exclude-tandems:false;
filter-algorithm:0;
identity:90;
inverted:true;
max-distance:5000;
min-distance:100;
min-length:10;
threads:0;
}
extract-annotated-sequence {
type:extract-annotated-sequence;
name:"Get Sequences by Annotations";
}
reverse-complement {
type:reverse-complement;
name:"Reverse Complement";
}
write-sequence {
type:write-sequence;
name:"Write the Direct Strand Repeat Unit";
url-out:direct_strand_repeat_units.fa;
}
write-sequence-1 {
type:write-sequence;
name:"Write the Direct Strand Repeat Unit";
url-out:compl_strand_repeat_units.fa;
}
Script-Get-the-first-half-of-sequence {
type:"Script-Get the first half of sequence";
name:"Get the First Half of Sequence";
script {
out_sequence = subsequence(in_sequence, 0, size(in_sequence) / 2 - 1);
};
}
Script-Get-the-second-half-of-sequence {
type:"Script-Get the second half of sequence";
name:"Get the Second Half of Sequence";
script {
out_sequence = subsequence(in_sequence, size(in_sequence) / 2, size(in_sequence) - 1);
};
}
.actor-bindings {
read-sequence.out-sequence->repeats-search.in-sequence
repeats-search.out-annotations->extract-annotated-sequence.in-sequence
extract-annotated-sequence.out-sequence->Script-Get-the-second-half-of-sequence.in
extract-annotated-sequence.out-sequence->Script-Get-the-first-half-of-sequence.in
reverse-complement.out-sequence->write-sequence-1.in-sequence
Script-Get-the-first-half-of-sequence.out->write-sequence.in-sequence
Script-Get-the-second-half-of-sequence.out->reverse-complement.in-sequence
}
read-sequence.sequence->repeats-search.in-sequence.sequence
repeats-search.annotations->extract-annotated-sequence.in-sequence.annotations
read-sequence.sequence->extract-annotated-sequence.in-sequence.sequence
Script-Get-the-second-half-of-sequence.sequence->reverse-complement.in-sequence.sequence
Script-Get-the-first-half-of-sequence.sequence->write-sequence.in-sequence.sequence
reverse-complement.sequence->write-sequence-1.in-sequence.sequence
extract-annotated-sequence.sequence->Script-Get-the-first-half-of-sequence.in.sequence
extract-annotated-sequence.sequence->Script-Get-the-second-half-of-sequence.in.sequence
.meta {
visual {
Script-Get-the-first-half-of-sequence {
pos:"-491 -642";
style:ext;
bg-color-ext:"85 170 255 64";
in.angle:58.5704;
out.angle:290.298;
}
Script-Get-the-second-half-of-sequence {
pos:"-217 -651";
style:ext;
bg-color-ext:"85 170 255 64";
bounds:"-30 -30 81.625 81";
in.angle:47.0454;
out.angle:288.06;
}
extract-annotated-sequence {
pos:"-386 -822";
style:ext;
bg-color-ext:"0 128 128 64";
in-sequence.angle:180;
out-sequence.angle:294.605;
}
read-sequence {
pos:"-932 -828";
style:ext;
bg-color-ext:"255 170 127 64";
out-sequence.angle:360;
}
repeats-search {
pos:"-735 -828";
style:ext;
bg-color-ext:"0 128 128 64";
in-sequence.angle:180;
out-annotations.angle:358.946;
}
reverse-complement {
pos:"-221 -487";
style:ext;
bg-color-ext:"0 128 128 64";
bounds:"-30 -30 114.5 81";
in-sequence.angle:44.1931;
out-sequence.angle:292.714;
}
write-sequence {
pos:"-486 -471";
style:ext;
bg-color-ext:"170 170 0 64";
bounds:"-30 -30 87 112";
in-sequence.angle:49.844;
}
write-sequence-1 {
pos:"-209 -297";
style:ext;
bg-color-ext:"170 170 0 64";
bounds:"-30 -30 97.25 102";
in-sequence.angle:50.5275;
}
Script-Get-the-first-half-of-sequence.out->write-sequence.in-sequence {
text-pos:"-30.5 -12";
}
Script-Get-the-second-half-of-sequence.out->reverse-complement.in-sequence {
text-pos:"-32.5 -13";
}
extract-annotated-sequence.out-sequence->Script-Get-the-first-half-of-sequence.in {
text-pos:"-38 -15";
}
extract-annotated-sequence.out-sequence->Script-Get-the-second-half-of-sequence.in {
text-pos:"-52 -19";
}
read-sequence.out-sequence->repeats-search.in-sequence {
text-pos:"-27.5 -24";
}
repeats-search.out-annotations->extract-annotated-sequence.in-sequence {
text-pos:"-45 -37";
}
reverse-complement.out-sequence->write-sequence-1.in-sequence {
text-pos:"-37 -21";
}
}
wizard {
name:"Search for Inverted Repeats Wizard";
help-page-id:16122737;
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:"Search for inverted repeats parameters";
parameters-area {
group {
title:"Find Inverted Repeats parameters";
label-size:150;
repeats-search.result-name {
}
repeats-search.min-length {
}
repeats-search.identity {
}
repeats-search.min-distance {
}
repeats-search.max-distance {
}
repeats-search.filter-algorithm {
}
repeats-search.algorithm {
}
repeats-search.threads {
}
}
}
}
page {
id:3;
title:"Output sequences";
parameters-area {
group {
title:"Result files";
label-size:150;
write-sequence.url-out {
label:"Direct strand repeat units";
}
write-sequence-1.url-out {
label:"Compl. strand repeat units";
}
}
}
}
}
}
}
|
