Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/acd/gwvalue.acd @ 0:8300eb051bea draft
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author | ktnyt |
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date | Fri, 26 Jun 2015 05:19:29 -0400 |
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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 |