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EntireWorkflowOptions Type

Namespace: BioFSharp.BioContainers
Assembly: BioFSharp.BioContainers.dll
Parent Module: MoFF
Base Type: obj
All Interfaces: IEquatable<EntireWorkflowOptions> , IStructuralEquatable , IComparable<EntireWorkflowOptions> , IComparable , IStructuralComparable

Those options run the Entire Workflow module, which executes both, the Match between runs and Apex Intensity module. The options are identical for both apex and MBR modules. The output for the latter (MBR) is stored in the folder sample_folder/mbr_output, while the former (apex) generates files in the specified output_moff folder.Log files for both algorithms are generated in the respective folders.

Union cases

Union case Description

FileExtensionsInputFile string

Full Usage: FileExtensionsInputFile string

Parameters:
    Item : string

--ext file extention of the input file. Default .txt)

Item : string

FileNameMBRLogFile string

Full Usage: FileNameMBRLogFile string

Parameters:
    Item : string

--log_label filename for the mbr log file. Default moFF_mbr

Item : string

FilterInputFiles string

Full Usage: FilterInputFiles string

Parameters:
    Item : string

--sample reg exp to filter the input file names (only with --loc_in input option-

Item : string

FilterMatchedPeak bool

Full Usage: FilterMatchedPeak bool

Parameters:
    Item : bool

--match_filter If set, filtering on the matched peak is activated. Default value: False

Item : bool

FilteringThresholdQuantileValue float

Full Usage: FilteringThresholdQuantileValue float

Parameters:
    Item : float

--quantile_thr_filtering quantile value used to computed the filtering threshold for the matched peak . Default is 0.75

Item : float

GetPeakInRtWindow float

Full Usage: GetPeakInRtWindow float

Parameters:
    Item : float

--rt_peak_win time windows used to get the apex for the ms2 peptide/feature (minutes). Default value is 1

Item : float

GetPeakInRtWindowForMatches float

Full Usage: GetPeakInRtWindowForMatches float

Parameters:
    Item : float

--rt_peak_win_match time windows used to get the apex for machted features (minutes). Default value is 1.2

Item : float

MassTolerance int

Full Usage: MassTolerance int

Parameters:
    Item : int

--tol mass tollerance (ppm)

Item : int

MoffFile string

Full Usage: MoffFile string

Parameters:
    Item : string

--config_file specify a moFF parameter file

Item : string

OutlierFilter bool

Full Usage: OutlierFilter bool

Parameters:
    Item : bool

--out_flag if set, outliers for rt time allignment are filtered. Default value: True

Item : bool

OutputFileFolder string

Full Usage: OutputFileFolder string

Parameters:
    Item : string

--loc_out output folder

Item : string

PeptideSummaryFile

Full Usage: PeptideSummaryFile

--peptide_summary flag that allows have as output the peptided summary intensity file. Default is disable(0)

PeptideSummaryFileName string

Full Usage: PeptideSummaryFileName string

Parameters:
    Item : string

--tag_pepsum a tag that is used in the peptide summary file name

Item : string

PtmFile string

Full Usage: PtmFile string

Parameters:
    Item : string

--ptm_file modification json ptm file. Default file ptm_setting.json

Item : string

RtWindow float

Full Usage: RtWindow float

Parameters:
    Item : float

--xic_length rt windows for xic (minutes). Default value is 3 min

Item : float

SampleSizeForThreshold float

Full Usage: SampleSizeForThreshold float

Parameters:
    Item : float

--sample_size percentage of MS2 identified peptides used to estimated the threshold

Item : float

WeightedRTModelCombination bool

Full Usage: WeightedRTModelCombination bool

Parameters:
    Item : bool

--w_comb if set, RT model combination is weighted using traing model errors: Default value: False

Item : bool

WidthForOutlierFiltering int

Full Usage: WidthForOutlierFiltering int

Parameters:
    Item : int

--w_filt width value for outlier filtering. Default 3

Item : int

Static members

Static member Description

EntireWorkflowOptions.make

Full Usage: EntireWorkflowOptions.make

Returns: EntireWorkflowOptions -> string list
Returns: EntireWorkflowOptions -> string list

EntireWorkflowOptions.makeWith m

Full Usage: EntireWorkflowOptions.makeWith m

Parameters:
Returns: EntireWorkflowOptions -> string list
m : MountInfo
Returns: EntireWorkflowOptions -> string list

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