annotate GEMBASSY-1.0.3/acd/ggcskew.acd @ 0:8300eb051bea draft

Initial upload
author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
1 application: ggcskew [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
2 documentation: "Calculates and plots the GC skew of the input sequence"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
3 groups: "Nucleic:Composition"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
4 embassy: "gembassy"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
5 relations: "EDAM_topic:0157 Sequence composition analysis"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
6 relations: "EDAM_operation:0377 Sequence composition calculation
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
7 (nucleic acid)"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
8 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
9
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
10 section: input [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
11 information: "Input section"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
12 type: "page"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
13 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
14
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
15 seqall: sequence [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
16 parameter: "Y"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
17 type: "nucleotide"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
18 features: "Y"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
19 relations: "EDAM_data:0849 Sequence record"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
20 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
21
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
22 endsection: input
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
23
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
24 section: advanced [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
25 information: "Advanced section"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
26 type: "page"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
27 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
28
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
29 integer: window [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
30 information: "Window size to observe"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
31 default: "10000"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
32 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
33
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
34 integer: slide [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
35 information: "Window slide size"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
36 default: "10000"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
37 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
38
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
39 boolean: cumulative [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
40 information: "Include to calculate cumulative skew"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
41 default: "N"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
42 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
43
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
44 boolean: at [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
45 information: "Include for observing AT skew instead of GC skew"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
46 default: "N"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
47 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
48
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
49 boolean: purine [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
50 information: "Include for observing purine (AG/TC) skew"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
51 default: "N"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
52 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
53
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
54 boolean: keto [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
55 information: "Include for observing keto (TG/AC) skew"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
56 default: "N"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
57 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
58
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
59 endsection: advanced
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
60
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
61 section: output [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
62 information: "Output section"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
63 type: "page"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
64 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
65
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
66 toggle: plot [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
67 information: "Include to plot result"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
68 default: "Y"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
69 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
70
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
71 xygraph: graph [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
72 standard: "$(plot)"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
73 gtitle: "ggcskew of $(sequence.name)"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
74 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
75
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
76 outfile: outfile [
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
77 standard: "@(!$(plot))"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
78 nullok: "Y"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
79 nulldefault: "$(plot)"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
80 information: "Program compseq output file (optional)"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
81 knowntype: "compseq output"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
82 relations: "EDAM_data:3086 Nucleic acid sequence composition"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
83 ]
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
84
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
85 endsection: output