1application: polydot [
2  documentation: "Draw dotplots for all-against-all comparison of a
3                  sequence set"
4  groups: "Alignment:Dot plots"
5    relations: "EDAM_topic:0159 Sequence comparison"
6    relations: "EDAM_operation:0490 Dotplot plotting"
7]
8
9section: input [
10  information: "Input section"
11  type: "page"
12]
13
14  seqset: sequences [
15    parameter: "Y"
16    type: "any"
17    help: "File containing a sequence alignment"
18    aligned: "N"
19    relations: "EDAM_data:0849 Sequence record"
20  ]
21
22endsection: input
23
24section: required [
25  information: "Required section"
26  type: "page"
27]
28
29  integer: wordsize [
30    standard: "Y"
31    default: "6"
32    minimum: "2"
33    information: "Word size"
34    relations: "EDAM_data:1250 Word size"
35  ]
36
37endsection: required
38
39section: output [
40  information: "Output section"
41  type: "page"
42]
43
44  integer: gap [
45    default: "10"
46    minimum: "0"
47    information: "Gap (in residues) between dotplots"
48    help: "This specifies the size of the gap that is used to separate
49           the individual dotplots in the display. The size is measured in
50           residues, as displayed in the output."
51    relations: "EDAM_data:1249 Sequence length"
52  ]
53
54  boolean: boxit [
55    default: "Y"
56    additional: "Y"
57    information: "Draw a box around each dotplot"
58    relations: "EDAM_data:2527 Parameter"
59  ]
60
61  toggle: dumpfeat [
62    default: "N"
63    additional: "Y"
64    information: "Dump all matches as feature files"
65    relations: "EDAM_data:2527 Parameter"
66  ]
67
68  featout: outfeat [
69    standard: "$(dumpfeat)"
70    nullok: "@(!$(dumpfeat))"
71    nulldefault: "@(!$(dumpfeat))"
72    relations: "EDAM_data:1255 Feature record"
73  ]
74
75  graph: graph [
76    standard: "Y"
77    gdesc: "Poly dotplot"
78    relations: "EDAM_data:0862 Dotplot"
79  ]
80
81endsection: output
82