comparison GEMBASSY-1.0.3/acd/gbaseentropy.acd @ 0:8300eb051bea draft

Initial upload
author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
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-1:000000000000 0:8300eb051bea
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