sig
type output_type = [ `CSV of string | `HTML of string ]
type predictor_type =
[ `NetMHC
| `NetMHCIIpan
| `NetMHCcons
| `NetMHCcons_IEDB
| `NetMHCpan
| `NetMHCpan_IEDB
| `Random
| `SMM
| `SMM_IEDB
| `SMM_PMBEC
| `SMM_PMBEC_IEDB ]
val predictor_to_string :
[< `NetMHC
| `NetMHCIIpan
| `NetMHCcons
| `NetMHCcons_IEDB
| `NetMHCpan
| `NetMHCpan_IEDB
| `Random
| `SMM
| `SMM_IEDB
| `SMM_PMBEC
| `SMM_PMBEC_IEDB ] ->
string
val predictor_to_tool :
run_with:Biokepi_run_environment.Machine.t ->
[> `NetMHC | `NetMHCIIpan | `NetMHCcons | `NetMHCpan ] ->
(Biokepi_run_environment.Common.KEDSL.phony_workflow *
Biokepi_run_environment.Common.KEDSL.Program.t)
option
module Configuration :
sig
type t = {
name : string;
rna_gene_fpkm_tracking_file : string option;
rna_min_gene_expression : float;
rna_transcript_fpkm_tracking_file : string option;
rna_min_transcript_expression : float;
rna_transcript_fkpm_gtf_file : string option;
mhc_epitope_lengths : int list;
only_novel_epitopes : bool;
ic50_cutoff : float;
percentile_cutoff : float;
padding_around_mutation : int option;
self_filter_directory : string option;
skip_variant_errors : bool;
parameters : (string * string) list;
}
val to_json :
Biokepi_bfx_tools.Topiary.Configuration.t -> Yojson.Basic.json
val render : Biokepi_bfx_tools.Topiary.Configuration.t -> string list
val default : Biokepi_bfx_tools.Topiary.Configuration.t
val name : Biokepi_bfx_tools.Topiary.Configuration.t -> string
end
val run :
run_with:Biokepi_run_environment.Machine.t ->
configuration:Biokepi_bfx_tools.Topiary.Configuration.t ->
reference_build:string ->
vcfs:< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
path : string; .. >
Biokepi_run_environment.Common.KEDSL.workflow_node list ->
predictor:[< `NetMHC
| `NetMHCIIpan
| `NetMHCcons
| `NetMHCcons_IEDB
| `NetMHCpan
| `NetMHCpan_IEDB
| `Random
| `SMM
| `SMM_IEDB
| `SMM_PMBEC
| `SMM_PMBEC_IEDB
> `NetMHC `NetMHCIIpan `NetMHCcons `NetMHCpan ] ->
alleles_file:< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t
option;
path : string; .. >
Biokepi_run_environment.Common.KEDSL.workflow_node ->
output:[< `CSV of string | `HTML of string ] ->
< exists : Ketrew_pure.Target.Condition.t;
host : Biokepi_run_environment.Common.KEDSL.Host.t;
is_bigger_than : int -> Ketrew_pure.Target.Condition.t;
is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
path : string >
Biokepi_run_environment.Common.KEDSL.workflow_node
end