1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
|
% Using a function from the command line
To make a Haskell function accessible from the command line, you must add a JSON file to the directory `bindings/` that registers the Haskell function.
For example, the file `bindings/models/hky85.json` allows the user to specify (for example) `-S hky85(kappa=2)` as a substitution model.
The JSON looks like this:
``` json
{
"name": "hky85",
"title": "The Hasegawa-Kishino-Yano (1985) nucleotide rate matrix",
"deprecated-synonyms": ["HKY","hky","HKY85"],
"result_type": "RevCTMC<a>",
"constraints": ["Nucleotides<a>"],
"citation":{"type": "article",
"title": "Dating of the human-ape splitting by a molecular clock of mitochondrial DNA",
"year": "1985",
"author": [{"name": "Hasegawa, Masami"}, {"name": "Kishino, Hirohisa"}, {"name": "Yano, Taka-aki"}],
"journal": {"name": "Journal of molecular evolution", "volume": "22", "number": "2", "pages": "160--174"},
"identifier": [{"type":"doi","id":"10.1007/BF02101694"}]
},
"call": "hky85'(@a,@kappa,@pi)",
"import": ["SModel"],
"args": [
{
"arg_name": "kappa",
"arg_type": "Double",
"default_value": "~logNormal(log(2),0.25)",
"description": "Transition\/transversion ratio"
},
{
"arg_name": "pi",
"arg_type": "List<(String,Double)>",
"default_value": "~symmetric_dirichlet_on(letters(@a),1)",
"description": "Letter frequencies"
},
{
"arg_name": "a",
"arg_type": "a",
"default_value": "get_state(alphabet)",
"description": "The alphabet"
}
],
"description":"The HKY85 model",
"extract": "all"
}
```
The fields are defined as follows:
`name`
: The name of this function on the command line.
`call`
: The Haskell function to call, and the order of the arguments to pass.
`import`
: The Haskell modules to import so that the function `hky85` is in scope.
`result_type`
: The result type of the function.
`args`
: The list of named arguments
`arg_name`
: The name of each argument
`arg_type`
: The type of each argument
`default_value`
: A value for the argument if not specified (optional).
`description`
: A short phrase describing the argument (optional).
`title`
: A title for the function (optional).
`description`
: A longer description of the function (optional).
|
