Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/acd/gbasecounter.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: gbasecounter [ | |
2 documentation: "Creates a position weight matrix of oligomers around start | |
3 codon" | |
4 groups: "Nucleic:Composition" | |
5 embassy: "gembassy" | |
6 relations: "EDAM_topic:0157 Sequence composition analysis" | |
7 relations: "EDAM_operation:0377 Sequence composition calculation | |
8 (nucleic acid)" | |
9 ] | |
10 | |
11 section: input [ | |
12 information: "Input section" | |
13 type: "page" | |
14 ] | |
15 | |
16 seqall: sequence [ | |
17 parameter: "Y" | |
18 type: "nucleotide" | |
19 features: "Y" | |
20 relations: "EDAM_data:0849 Sequence record" | |
21 ] | |
22 | |
23 endsection: input | |
24 | |
25 section: advanced [ | |
26 information: "Advanced section" | |
27 type: "page" | |
28 ] | |
29 | |
30 selection: position [ | |
31 information: "Either 'start' (around start codon) or 'end' | |
32 (around stop codon) to create the PWM" | |
33 values: "start;end" | |
34 default: "start" | |
35 ] | |
36 | |
37 integer: patlen [ | |
38 information: "Length of oligomer to count" | |
39 default: "3" | |
40 ] | |
41 | |
42 integer: upstream [ | |
43 information: "Length upstream of specified position to create PWM" | |
44 default: "30" | |
45 ] | |
46 | |
47 integer: downstream [ | |
48 information: "Length downstream of specified position to create PWM" | |
49 default: "30" | |
50 ] | |
51 | |
52 boolean: accid [ | |
53 information: "Include to use sequence accession ID as query" | |
54 default: "N" | |
55 ] | |
56 | |
57 endsection: advanced | |
58 | |
59 section: output [ | |
60 information: "Output section" | |
61 type: "page" | |
62 ] | |
63 | |
64 outfile: outfile [ | |
65 parameter: "Y" | |
66 information: "Weight matrix output file" | |
67 knowntype: "matrix" | |
68 relations: "EDAM_data:1362 Position weight matrix" | |
69 ] | |
70 | |
71 endsection: output |