Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/acd/ggeneskew.acd @ 2:8947fca5f715 draft default tip
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author | ktnyt |
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date | Fri, 26 Jun 2015 05:21:44 -0400 |
parents | 84a17b3fad1f |
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1:84a17b3fad1f | 2:8947fca5f715 |
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1 application: ggeneskew [ | |
2 documentation: "Calculates and plots the gene strand bias of the given genome" | |
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: "Input 1 to calculate cumulative skew" | |
41 default: "N" | |
42 ] | |
43 | |
44 selection: base [ | |
45 information: "Input 'gc', 'at', 'purine', or 'keto' for observing | |
46 GC/AT/Purine/Keto skews" | |
47 values: "none;gc;at;purine;keto" | |
48 default: "none" | |
49 ] | |
50 | |
51 boolean: gctri [ | |
52 information: "Include to use only the third codon positions" | |
53 default: "N" | |
54 ] | |
55 | |
56 boolean: accid [ | |
57 information: "Include to use sequence accession ID as query" | |
58 default: "N" | |
59 ] | |
60 | |
61 endsection: advanced | |
62 | |
63 section: output [ | |
64 information: "Output section" | |
65 type: "page" | |
66 ] | |
67 | |
68 toggle: plot [ | |
69 information: "Include to plot result" | |
70 default: "Y" | |
71 ] | |
72 | |
73 xygraph: graph [ | |
74 standard: "$(plot)" | |
75 gtitle: "ggeneskew of $(sequence.name)" | |
76 ] | |
77 | |
78 outfile: outfile [ | |
79 standard: "@(!$(plot))" | |
80 nullok: "Y" | |
81 nulldefault: "$(plot)" | |
82 information: "Program compseq output file (optional)" | |
83 knowntype: "compseq output" | |
84 relations: "EDAM_data:3086 Nucleic acid sequence composition" | |
85 ] | |
86 | |
87 endsection: output |