-
Notifications
You must be signed in to change notification settings - Fork 0
/
spec.json
149 lines (149 loc) · 4.53 KB
/
spec.json
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
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
{
"ver": "1.0.0",
"authors": [
"dylan", "jmc", "caozhichongchong"
],
"contact": "http://www.kbase.us/support/",
"categories": ["active", "communities"],
"widgets": {
"input": null,
"output": "no-display"
},
"parameters": [
{
"id": "in_genome_ref",
"optional": false,
"advanced": false,
"allow_multiple": false,
"default_values": [ "" ],
"field_type": "text",
"text_options": {
"valid_ws_types": [
"KBaseGenomes.Genome"
]
}
},
{
"id": "in_readslib_refs",
"optional": false,
"advanced": false,
"allow_multiple": true,
"default_values": null,
"field_type": "text",
"text_options": {
"valid_ws_types": [
"KBaseFile.PairedEndLibrary",
"KBaseFile.SingleEndLibrary",
"KBaseAssembly.PairedEndLibrary",
"KBaseAssembly.SingleEndLibrary",
"KBaseSets.ReadsSet"
]
}
},
{
"id": "min_mapping_quality",
"optional": false,
"advanced": true,
"allow_multiple": false,
"default_values": [ "30" ],
"field_type": "text",
"text_options": {
"validate_as": "int"
}
},
{
"id": "min_depth",
"optional": false,
"advanced": true,
"allow_multiple": false,
"default_values": [ "3" ],
"field_type": "text",
"text_options": {
"validate_as": "int"
}
},
{
"id": "max_depth",
"optional": false,
"advanced": true,
"allow_multiple": false,
"default_values": [ "10000" ],
"field_type": "text",
"text_options": {
"validate_as": "int"
}
},
{
"id": "out_genomeSet_obj_name",
"optional": false,
"advanced": false,
"allow_multiple": false,
"default_values": null,
"field_type": "text",
"text_options": {
"is_output_name": true,
"valid_ws_types": [
"KBaseSearch.GenomeSet",
"KBaseSets.AssemblySet"
]
}
}
],
"behavior": {
"service-mapping": {
"url": "",
"name": "kb_StrainFinder",
"method": "run_StrainFinder_v1",
"input_mapping": [
{
"narrative_system_variable": "workspace",
"target_property": "workspace_name",
"target_argument_position": 0
},
{
"input_parameter": "in_genome_ref",
"target_property": "in_genome_ref",
"target_type_transform": "resolved-ref",
"target_argument_position": 0
},
{
"input_parameter": "in_readslib_refs",
"target_property": "in_readslib_refs",
"target_type_transform": "list<resolved-ref>",
"target_argument_position": 0
},
{
"input_parameter": "min_mapping_quality",
"target_property": "min_mapping_quality",
"target_argument_position": 0
},
{
"input_parameter": "min_depth",
"target_property": "min_depth",
"target_argument_position": 0
},
{
"input_parameter": "max_depth",
"target_property": "max_depth",
"target_argument_position": 0
},
{
"input_parameter": "out_genomeSet_obj_name",
"target_property": "out_genomeSet_obj_name",
"target_argument_position": 0
}
],
"output_mapping": [
{
"service_method_output_path": [0, "report_name"],
"target_property": "report_name"
},
{
"service_method_output_path": [0, "report_ref"],
"target_property": "report_ref"
}
]
}
},
"job_id_output_field": "docker"
}