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

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author ktnyt
date Fri, 26 Jun 2015 05:21:44 -0400
parents 84a17b3fad1f
children
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1:84a17b3fad1f 2:8947fca5f715
1 application: gbasezvalue [
2 documentation: "Extracts conserved oligomers per position using Z-score"
3 groups: "Nucleic:Composition"
4 embassy: "gembassy"
5 relations: "EDAM_topic:0157 Sequence composition analysis"
6 relations: "EDAM_operation:0377 Sequence composition calculation
7 (nucleic acid)"
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 integer: limit [
30 information: "Rank threshold for showing the conserved oligomer"
31 default: "5"
32 ]
33
34 selection: position [
35 information: "Either 'start' (around start codon) or 'end'
36 (around stop codon) to create the PWM"
37 values: "start;end"
38 default: "start"
39 ]
40
41 integer: patlen [
42 information: "Length of oligomer to count"
43 default: "3"
44 ]
45
46 integer: upstream [
47 information: "Length upstream of specified position to create PWM"
48 default: "30"
49 ]
50
51 integer: downstream [
52 information: "Length downstream of specified position to create PWM"
53 default: "30"
54 ]
55
56 boolean: accid [
57 information: "Include to use sequence accession ID as query"
58 default: "N"
59 ]
60
61 endsection: advanced
62
63 section: output [
64 information: "Output section"
65 type: "page"
66 ]
67
68 outfile: outfile [
69 parameter: "Y"
70 information: "Program compseq output file (optional)"
71 knowntype: "compseq output"
72 relations: "EDAM_data:3086 Nucleic acid sequence composition"
73 ]
74
75 endsection: output