Commit 73f7434e authored by Bollen's avatar Bollen
Browse files

add stub for settings schema for primer3

parent d228cd87
{
"$schema": "http://json-schema.org/draft-04/schema#",
"description": "JSON schema for settings for primer3 for prinia",
"type": "object",
"properties": {
"primer_min_gc": {
"description": "Minimum GC-percentage of primers",
"type": "number",
"default": 20
},
"primer_internal_min_gc": {
"description": "Equivalent parameter of primer_min_gc for the internal oligo.",
"type": "number",
"default": 20
},
"primer_opt_gc_percent": {
"description": "Optimum GC-percentage of primers",
"type": "number",
"default": 50
},
"primer_max_gc": {
"description": "Maximum GC-percentage of primers.",
"type": "number",
"default": 80
},
"primer_internal_mac_gc": {
"description": "Equivalent parameter of primer_max_gc for the internal oligo.",
"type": "number",
"default": 80
},
"primer_wt_gc_percent_lt": {
"description": "Penalty weight for primers with GC-percentage lower than primer_opt_gc_percent",
"type": "number",
"default": 0
},
"primer_internal_wt_gc_percent_lt": {
"description": "Equivalent parameter of primer_wt_gc_percent_lt for the interal oligo.",
"type": "number",
"default": 0
},
"primer_wt_gc_percent_gt": {
"description": "Penality weight for primers with GC-percentage higher than primer_opt_gc_percent",
"type": "number",
"default": 0
},
"primer_internal_wt_gc_percent_gt": {
"description": "Equivalent parameter of primer_wt_gc_percent_gt for the internal oligo.",
"type": "number",
"default": 0
},
"primer_gc_clamp": {
"description": "Require the specified number of consecutive Gs and Cs at the 3' end of both the left and right primer.",
"type": "integer",
"default": 0
},
"primer_max_end_gc": {
"description": "The maximum number of Gs or Cs allowed in the last five 3' bases of a left or right primer.",
"type": "integer",
"default": 5
},
"primer_opt_size": {
"description": "Optimum size of primers in bases.",
"type": "integer",
"default": 25
},
"primer_min_size": {
"description": "Minimum size of primers in bases.",
"type": "integer",
"default": 20
},
"primer_max_size": {
"description": "Maximum size of primers in bases.",
"type": "integer",
"default": 30
},
"primer_max_ns_accepted": {
"description": "Maximum number of unknown bases (N) accepted in a primer",
"type": "integer",
"default:": 0
},
"primer_product_size_range": {
"description": "Accepted size range of the product size.",
"type": "string",
"default": "200-450",
"pattern": "^\d+\-\d+$"
},
"primer_product_opt_size": {
"description": "Optimum size of product. Will default to the midpoint in primer_product_size_range unless specified",
"type": "integer",
"default": 325
},
"primer_pair_wt_product_size_gt": {
"description": "Penalty weight for products larger than primer_product_opt_size",
"type": "number",
"default": 0.1
},
"primer_pair_wt_product_size_lt": {
"description": "Penalty weight for products smaller than primer_product_opt_size",
"type": "number",
"default": 0.1
},
"primer_min_tm": {
"description": "Minimum melting temperature of primer degrees Celsius",
"type": "number",
"default": 58
},
"primer_max_tm": {
"description": "Maximum melting temperature in degrees Celsius",
"type": "number",
"default": 62
},
"primer_num_return": {
"description": "Number of returned primers. Increase to increase search space",
"type": "integer",
"default": 200
}
}
}
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