|
0
|
1 application: ggcskew [
|
|
|
2 documentation: "Calculates and plots the GC skew of the input sequence"
|
|
|
3 groups: "Nucleic:Composition"
|
|
|
4 embassy: "gembassy"
|
|
|
5 relations: "EDAM_topic:0157 Sequence composition analysis"
|
|
|
6 relations: "EDAM_operation:0377 Sequence composition calculation
|
|
|
7 (nucleic acid)"
|
|
|
8 ]
|
|
|
9
|
|
|
10 section: input [
|
|
|
11 information: "Input section"
|
|
|
12 type: "page"
|
|
|
13 ]
|
|
|
14
|
|
|
15 seqall: sequence [
|
|
|
16 parameter: "Y"
|
|
|
17 type: "nucleotide"
|
|
|
18 features: "Y"
|
|
|
19 relations: "EDAM_data:0849 Sequence record"
|
|
|
20 ]
|
|
|
21
|
|
|
22 endsection: input
|
|
|
23
|
|
|
24 section: advanced [
|
|
|
25 information: "Advanced section"
|
|
|
26 type: "page"
|
|
|
27 ]
|
|
|
28
|
|
|
29 integer: window [
|
|
|
30 information: "Window size to observe"
|
|
|
31 default: "10000"
|
|
|
32 ]
|
|
|
33
|
|
|
34 integer: slide [
|
|
|
35 information: "Window slide size"
|
|
|
36 default: "10000"
|
|
|
37 ]
|
|
|
38
|
|
|
39 boolean: cumulative [
|
|
|
40 information: "Include to calculate cumulative skew"
|
|
|
41 default: "N"
|
|
|
42 ]
|
|
|
43
|
|
|
44 boolean: at [
|
|
|
45 information: "Include for observing AT skew instead of GC skew"
|
|
|
46 default: "N"
|
|
|
47 ]
|
|
|
48
|
|
|
49 boolean: purine [
|
|
|
50 information: "Include for observing purine (AG/TC) skew"
|
|
|
51 default: "N"
|
|
|
52 ]
|
|
|
53
|
|
|
54 boolean: keto [
|
|
|
55 information: "Include for observing keto (TG/AC) skew"
|
|
|
56 default: "N"
|
|
|
57 ]
|
|
|
58
|
|
|
59 endsection: advanced
|
|
|
60
|
|
|
61 section: output [
|
|
|
62 information: "Output section"
|
|
|
63 type: "page"
|
|
|
64 ]
|
|
|
65
|
|
|
66 toggle: plot [
|
|
|
67 information: "Include to plot result"
|
|
|
68 default: "Y"
|
|
|
69 ]
|
|
|
70
|
|
|
71 xygraph: graph [
|
|
|
72 standard: "$(plot)"
|
|
|
73 gtitle: "ggcskew of $(sequence.name)"
|
|
|
74 ]
|
|
|
75
|
|
|
76 outfile: outfile [
|
|
|
77 standard: "@(!$(plot))"
|
|
|
78 nullok: "Y"
|
|
|
79 nulldefault: "$(plot)"
|
|
|
80 information: "Program compseq output file (optional)"
|
|
|
81 knowntype: "compseq output"
|
|
|
82 relations: "EDAM_data:3086 Nucleic acid sequence composition"
|
|
|
83 ]
|
|
|
84
|
|
|
85 endsection: output
|
