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comparison GEMBASSY-1.0.3/acd/ggcsi.acd @ 0:8300eb051bea draft

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author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
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1 application: ggcsi [
2 documentation: "GC Skew Index: an index for strand-specific mutational bias"
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 selection: gcsi [
30 information: "GCSI version to use"
31 values: "1;2"
32 default: "2"
33 ]
34
35 integer: window [
36 information: "Number of windows. Must be a power of 2"
37 default: "4096"
38 ]
39
40 boolean: purine [
41 information: "Use purine skew for calculation"
42 default: "N"
43 ]
44
45 boolean: keto [
46 information: "Use keto skew for calculation"
47 default: "N"
48 ]
49
50 boolean: at [
51 information: "Use AT skew for calculation"
52 default: "N"
53 ]
54
55 boolean: pval [
56 information: "Calculate p-value when GCSI version 2 is selected"
57 default: "N"
58 ]
59
60 endsection: advanced
61
62 section: output [
63 information: "Output section"
64 type: "page"
65 ]
66
67 outfile: outfile [
68 parameter: "Y"
69 information: "Program compseq output file"
70 knowntype: "compseq output"
71 relations: "EDAM_data:3086 Nucleic acid sequence composition"
72 ]
73
74 endsection: output