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

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author ktnyt
date Fri, 26 Jun 2015 05:21:44 -0400
parents 84a17b3fad1f
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1:84a17b3fad1f 2:8947fca5f715
1 application: gwvalue [
2 documentation: "Calculates the 'relative adaptiveness of each codon' (W)"
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 string: include [
29 information: "Regular expression to include genes in a reference set a
30 reference set in several studies are in-built 1: Nakamura
31 and Tabata, 2: Sharp and Li, 3: Sakai et al."
32 knowntype: "regular expression"
33 default: "ribosomal.*protein"
34 ]
35
36 string: exclude [
37 information: "Regular expression to exclude genes from a reference set"
38 knowntype: "regular expression"
39 default: "[Mm]itochondrial"
40 ]
41
42 boolean: accid [
43 information: "Include to use sequence accession ID as query"
44 default: "N"
45 ]
46
47 endsection: advanced
48
49 section: output [
50 information: "Output section"
51 type: "page"
52 ]
53
54 outfile: outfile [
55 parameter: "Y"
56 information: "Codon usage output file"
57 knowntype: "codon usage"
58 relations: "EDAM_data:2865 Codon usage bias"
59 ]
60
61 endsection: output