|
0
|
1 application: gbaseentropy [
|
|
|
2 documentation: "Calculates and graphs the sequence conservation
|
|
|
3 using Shanon uncertainty (entropy)"
|
|
|
4 groups: "Nucleic:Composition"
|
|
|
5 embassy: "gembassy"
|
|
|
6 relations: "EDAM_topic:0160 Sequence sites and features"
|
|
|
7 relations: "EDAM_operation:0253 Feature prediction"
|
|
|
8 ]
|
|
|
9
|
|
|
10 section: input [
|
|
|
11 information: "Input section"
|
|
|
12 type: "page"
|
|
|
13 ]
|
|
|
14
|
|
|
15 seqall: sequence [
|
|
|
16 parameter: "Y"
|
|
|
17 type: "nucleotide"
|
|
|
18 features: "Y"
|
|
|
19 relations: "EDAM_data:0849 Sequence record"
|
|
|
20 ]
|
|
|
21
|
|
|
22 endsection: input
|
|
|
23
|
|
|
24 section: advanced [
|
|
|
25 information: "Advanced section"
|
|
|
26 type: "page"
|
|
|
27 ]
|
|
|
28
|
|
|
29 selection: position [
|
|
|
30 information: "Either 'start' (around start codon) or 'end'
|
|
|
31 (around stop codon) to create the PWM"
|
|
|
32 values: "start;end"
|
|
|
33 default: "start"
|
|
|
34 ]
|
|
|
35
|
|
|
36 integer: patlen [
|
|
|
37 information: "Length of oligomer to count"
|
|
|
38 default: "3"
|
|
|
39 ]
|
|
|
40
|
|
|
41 integer: upstream [
|
|
|
42 information: "Length upstream of specified position to create PWM"
|
|
|
43 default: "30"
|
|
|
44 ]
|
|
|
45
|
|
|
46 integer: downstream [
|
|
|
47 information: "Length downstream of specified position to create PWM"
|
|
|
48 default: "30"
|
|
|
49 ]
|
|
|
50
|
|
|
51 boolean: accid [
|
|
|
52 information: "Include to use sequence accession ID as query"
|
|
|
53 default: "N"
|
|
|
54 ]
|
|
|
55
|
|
|
56 endsection: advanced
|
|
|
57
|
|
|
58 section: output [
|
|
|
59 information: "Output section"
|
|
|
60 type: "page"
|
|
|
61 ]
|
|
|
62
|
|
|
63 toggle: plot [
|
|
|
64 information: "Include to plot result"
|
|
|
65 default: "Y"
|
|
|
66 ]
|
|
|
67
|
|
|
68 xygraph: graph [
|
|
|
69 standard: "$(plot)"
|
|
|
70 gtitle: "gbaseentropy of $(sequence.name)"
|
|
|
71 relations: "EDAM_data:2166 Sequence compisition plot"
|
|
|
72 ]
|
|
|
73
|
|
|
74 outfile: outfile [
|
|
|
75 standard: "@(!$(plot))"
|
|
|
76 nullok: "Y"
|
|
|
77 nulldefault: "$(plot)"
|
|
|
78 information: "Program compseq output file (optional)"
|
|
|
79 knowntype: "compseq output"
|
|
|
80 relations: "EDAM_data:3086 Nucleic acid sequence composition"
|
|
|
81 ]
|
|
|
82
|
|
|
83 endsection: output
|
