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

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author ktnyt
date Fri, 26 Jun 2015 05:21:44 -0400
parents 84a17b3fad1f
children
comparison
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1:84a17b3fad1f 2:8947fca5f715
1 application: gdinuc [
2 documentation: "Calculates dinucleotide usage "
3 groups: "Nucleic:Codon Usage"
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 boolean: translate [
30 information: "Include when translates using standard codon table"
31 default: "N"
32 ]
33
34 list: position [
35 information: "Codon position or reading frame"
36 values: "all:Assess all codon positions;
37 12:Assess the reading frame 1-2;
38 23:Assess the reading frame 2-3;
39 31:Assess the reading frame 3-1"
40 default: "all"
41 ]
42
43 string: delkey [
44 information: "Regular expression to delete key (i.e. amino acids and nucleotides)"
45 knowntype: "regular expression"
46 default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
47 ]
48
49 boolean: accid [
50 information: "Include to use sequence accession ID as query"
51 default: "N"
52 ]
53
54 endsection: advanced
55
56 section: output [
57 information: "Output section"
58 type: "page"
59 ]
60
61 outfile: outfile [
62 parameter: "Y"
63 information: "Program compseq output file"
64 knowntype: "compseq output"
65 relations: "EDAM_data:3086 Nucleic acid sequence composition"
66 ]
67
68 endsection: output