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

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author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
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-1:000000000000 0:8300eb051bea
1 application: gcai [
2 documentation: "Calculates codon adaptation index for each gene"
3 groups: "Nucleic:Codon usage"
4 embassy: "gembassy"
5 relations: "EDAM_operation:0286 Codon usage analysis"
6 relations: "EDAM_topic:0107 Codon usage analysis"
7 ]
8
9 section: input [
10 information: "Input section"
11 type: "page"
12 ]
13
14 seqall: sequence [
15 parameter: "Y"
16 type: "nucleotide"
17 features: "Y"
18 relations: "EDAM_data:0849 Sequence record"
19 ]
20
21 endsection: input
22
23 section: advanced [
24 information: "Advanced section"
25 type: "page"
26 ]
27
28 boolean: translate [
29 information: "Include when translating using standard codon table"
30 default: "N"
31 ]
32
33 string: wabsent [
34 information: "W value of codons absent from a reference set to negative
35 when excludes such codons from the calculation"
36
37 default: "-1"
38 ]
39
40 boolean: tai [
41 information: "Include when calculating tRNA adaptation index (TAI)"
42 default: "N"
43 ]
44
45 boolean: accid [
46 information: "Include to use sequence accession ID as query"
47 default: "N"
48 ]
49
50 endsection: advanced
51
52 section: output [
53 information: "Output section"
54 type: "page"
55 ]
56
57 outfile: outfile [
58 parameter: "Y"
59 information: "Codon usage output file"
60 knowntype: "codon usage"
61 relations: "EDAM_data:2865 Codon usage bias"
62 ]
63
64 endsection: output