|
0
|
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
|
