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comparison GEMBASSY-1.0.3/acd/ggcskew.acd @ 2:8947fca5f715 draft default tip

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author ktnyt
date Fri, 26 Jun 2015 05:21:44 -0400
parents 84a17b3fad1f
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1:84a17b3fad1f 2:8947fca5f715
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