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
|
#@UGENE_WORKFLOW
# The workflow takes two sets of annotations as input (denoted as A and B).
# It intersects the sets and outputs the result annotations.
#
#There are three options for the output:
# - Shared intervals between overlapped annotations from A and B;
# - Annotations from A that overlap annotations from B;
# - Annotations from A that DO NOT overlap annotations from B.
#
#It is also possible to tweak the percentage of the minimum overlap between A and B annotations.
workflow "Intersect annotations"{
intersect-annotations {
type:intersect-annotations;
name:"Intersect Annotations";
}
read-annotations {
type:read-annotations;
name:"Read Annotations A";
url-in {
dataset:"Dataset 1";
}
}
read-annotations-1 {
type:read-annotations;
name:"Read Annotations B";
url-in {
dataset:"Dataset 1";
}
}
write-annotations {
type:write-annotations;
name:"Write Annotations";
url-out:intersect.gb;
}
.actor-bindings {
intersect-annotations.output-intersect-annotations->write-annotations.in-annotations
read-annotations-1.out-annotations->intersect-annotations.input-annotations-b
read-annotations.out-annotations->intersect-annotations.input-annotations-a
}
read-annotations.annotations->intersect-annotations.input-annotations-a.input-annotations-a
read-annotations-1.annotations->intersect-annotations.input-annotations-b.input-annotations-b
intersect-annotations.output-intersect-annotations->write-annotations.in-annotations.annotations
read-annotations-1.annotations->write-annotations.in-annotations.annotations
read-annotations.annotations->write-annotations.in-annotations.annotations
.meta {
parameter-aliases {
intersect-annotations.minimum-overlap {
alias:min-overlap;
}
intersect-annotations.report {
alias:report;
}
intersect-annotations.unique {
alias:unique;
}
read-annotations.url-in {
alias:in-A;
}
read-annotations-1.url-in {
alias:in-B;
}
write-annotations.document-format {
alias:out-format;
}
write-annotations.url-out {
alias:out-file;
}
}
visual {
intersect-annotations {
pos:"-477 -583";
style:ext;
bg-color-ext:"207 74 41 64";
input-annotations-a.angle:150;
input-annotations-b.angle:210;
output-intersect-annotations.angle:360;
}
read-annotations {
pos:"-810 -693";
style:ext;
bg-color-ext:"0 141 212 64";
bounds:"-30 -30 148.875 87";
out-annotations.angle:360;
}
read-annotations-1 {
pos:"-813 -485";
style:ext;
bg-color-ext:"0 141 212 64";
bounds:"-30 -30 157.5 82";
out-annotations.angle:360;
}
write-annotations {
pos:"-122 -583";
style:ext;
bg-color-ext:"117 86 175 64";
in-annotations.angle:180;
}
intersect-annotations.output-intersect-annotations->write-annotations.in-annotations {
text-pos:"-45 -62";
}
read-annotations-1.out-annotations->intersect-annotations.input-annotations-b {
text-pos:"-44.9609 -28";
}
read-annotations.out-annotations->intersect-annotations.input-annotations-a {
text-pos:"-44.9609 -28";
}
}
wizard {
name:"Intersect Annotations Wizard";
help-page-id:16123490;
auto-run: true;
page {
id:1;
title:"Intersect annotations parameters";
parameters-area {
group {
title:"Input data";
label-size:120;
read-annotations.url-in {
label:"Annotations A";
}
read-annotations-1.url-in {
label:"Annotations B";
}
}
group {
title:"Output data";
label-size:120;
intersect-annotations.report {
label:Report;
}
write-annotations.url-out {
label:"Output file";
}
}
}
}
}
}
}
|
