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Storeys method +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.calculateQValueLogReg``1(System.Double,``0[],Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double})"> +<summary> + Gives a function to calculate the q value for a score in a dataset using Lukas method and Levenberg Marguardt fitting +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.calculateFDRwithDecoyTargetRatio(ProteomIQon.ProteinInference'.InferredProteinClassItemScored[])"> +<summary> + Calculates Decoy/Target ratio +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.calculateFDRwithMAYU(ProteomIQon.ProteinInference'.InferredProteinClassItemScored[],System.Tuple{System.String,System.String}[])"> +<summary> + Calculates the fdr of the data using the MAYU method. The proteinsFromDB is the DB that was used for the inference. +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.expectedFP(ProteomIQon.ProteinInference'.InferredProteinClassItemScored[])"> +<summary> + Calculates the expected false positives for every protein bin and sums them up. +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.binProteinsLength(ProteomIQon.ProteinInference'.InferredProteinClassItemScored[],System.Tuple{System.String,System.String}[],System.Double)"> +<summary> + Returns proteins sorted into bins according to their size. + proteins are the proteins which were found in either the reverse or forward proteininference, proteinsFromDB are the proteins with peptide sequence + on which the inference was performed. +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.estimatePi0HG(System.Double,System.Double,System.Double)"> +<summary> + Estimates the false positives given the total number of entries, the number of target hits and the number of decoy hits +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.getQValues``1(System.Double,Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},``0[])"> +<summary> + Calculates q values for target/decoy dataset +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.getQValueFunc``1(System.Double,System.Double,Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},``0[])"> +<summary> + Calculates q value mapping funtion for target/decoy dataset +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.binningFunction``1(System.Double,System.Double,Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},``0[])"> +<summary> + returns scores, pep, q +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.getLogisticRegressionFunction(FSharp.Stats.Vector{System.Double},FSharp.Stats.Vector{System.Double},System.Double)"> +<summary> + for given data, creates a logistic regression model and returns a mapping function for this model +</summary> +</member> +<member name="T:ProteomIQon.ProteinInference'.QValueInput"> +<summary> + Input for QValue calulation +</summary> +</member> +<member name="T:ProteomIQon.ProteinInference'.InferredProteinClassItemOut"> +<summary> + For a group of proteins, contains information about all peptides that are put into the output file. +</summary> +</member> +<member name="T:ProteomIQon.ProteinInference'.InferredProteinClassItemQValue"> +<summary> + For a group of proteins, contains information about all peptides that might be used for its quantification and score / q-value calculated for it. +</summary> +</member> +<member name="T:ProteomIQon.ProteinInference'.InferredProteinClassItemScored"> +<summary> + For a group of proteins, contains information about all peptides that might be used for its quantification and score calculated for it. +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.assignDecoyScoreToTargetScore(System.String,Microsoft.FSharp.Collections.FSharpMap{System.String,System.Tuple{System.Double,System.String[]}})"> +<summary> + Looks if the given protein accession is present in a map of identified decoy proteins and assigns its score when found. +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.assignPeptideScores(System.String[],Microsoft.FSharp.Collections.FSharpMap{System.String,System.Double})"> +<summary> + Sums up score of all peptide sequences +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.createPeptideProteinRelation``4(System.Collections.Generic.IEnumerable{Microsoft.FSharp.Core.FSharpOption{BioFSharp.PeptideClassification.ProteinModel{``0,``1,``2,Microsoft.FSharp.Collections.FSharpList{``3}}}})"> +<summary> + Creates a lookup data base to assign peptides to the proteins they are contained in +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.assignTranscriptsToGenes(System.String,System.Collections.Generic.IEnumerable{BioFSharp.IO.GFF3.GFFLine{System.Collections.Generic.IEnumerable{System.Char}}})"> +<summary> + By reading GFF creates the protein models (relationships of proteins to each other) which basically means grouping the rnas over the gene loci + TODO: Don't group over order but rather group over id +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.createProteinModelInfoFromEntry(System.Int32,System.String,BioFSharp.IO.GFF3.GFFEntry)"> +<summary> + Reads geographical information about protein from gff entry and builds the modelinfo of it + This function takes an RNA gff3 entry and therefore will contain the splice variant id of the gene in its result. + This splice variant id should be the same in the given FastA-file. +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.isRNA(BioFSharp.IO.GFF3.GFFLine{System.Collections.Generic.IEnumerable{System.Char}})"> +<summary> +checks if GFF line describes rna +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.isGene(BioFSharp.IO.GFF3.GFFLine{System.Collections.Generic.IEnumerable{System.Char}})"> +<summary> +checks if GFF line describes gene +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.createScoreTargetDecoyCount(System.Double,System.Double,System.Double)"> +<summary> + Gives the decoy and target count at a specific score +</summary> +</member> +<member name="M:ProteomIQon.SearchDB'.getSDBParamsBy(System.Data.SQLite.SQLiteConnection)"> +<summary> + Returns SearchDbParams of a existing database by filePath +</summary> +</member> +<member name="M:ProteomIQon.SearchDB'.selectProteins(System.Data.SQLite.SQLiteConnection)"> +<summary> + Returns Accession and Sequence of Proteins from SearchDB +</summary> +</member> +<member name="M:ProteomIQon.SearchDB'.getProteinPeptideLookUpFromFileBy(System.Data.SQLite.SQLiteConnection)"> +<summary> + Prepares a function which returns a list of protein Accessions tupled with the peptide sequence whose ID they were retrieved by +</summary> +</member> +<member name="M:ProteomIQon.SearchDB'.DB'.SQLiteQuery'.prepareSelectPepSequenceByPepSequenceID(System.Data.SQLite.SQLiteConnection,System.Data.SQLite.SQLiteTransaction)"> +<summary> + Prepares statement to select a Peptide Sequence entry by ID +</summary> +</member> +<member name="M:ProteomIQon.SearchDB'.DB'.SQLiteQuery'.prepareSelectProteinAccessionByID(System.Data.SQLite.SQLiteConnection,System.Data.SQLite.SQLiteTransaction)"> +<summary> + Prepares statement to select a Protein Accession entry by ID +</summary> +</member> +<member name="M:ProteomIQon.Fitting'.NonLinearRegression'.LevenbergMarquardtConstrained'.estimatedParamsWithRSS(FSharp.Stats.Fitting.NonLinearRegression.Model,FSharp.Stats.Fitting.NonLinearRegression.SolverOptions,System.Double,System.Double,FSharp.Stats.Vector{System.Double},FSharp.Stats.Vector{System.Double},System.Double[],System.Double[])"> +<summary> + Returns a parameter vector tupled with its residual sum of squares (RSS) as a possible solution for linear least square based nonlinear fitting of a given dataset (xData, yData) with a given + model function. +</summary> +</member> +<member name="M:ProteomIQon.Fitting'.NonLinearRegression'.LevenbergMarquardtConstrained'.initialParamsOverRange(System.Double[],System.Double[],System.Double[])"> +<summary> + Returns an estimate for an initial parameter for the linear least square estimator for a given dataset (xData, yData). + The steepness is given as an array and not estimated. An initial estimate is returned for every given steepness. + The initial estimation is intended for a logistic function. +</summary> +</member> +<member name="M:ProteomIQon.Fitting'.NonLinearRegression'.LevenbergMarquardtConstrained'.initialParam(System.Double[],System.Double[])"> +<summary> + Returns an estimate for an initial parameter for the linear least square estimator for a given dataset (xData, yData). + The initial estimation is intended for a logistic function. +</summary> +</member> +<member name="P:ProteomIQon.Fitting'.NonLinearRegression'.LevenbergMarquardtConstrained'.LogisticFunction"> +<summary> + Logistic Function + Line model of the form "y = a * x + b" +</summary> +</member> +<member name="T:ProteomIQon.Domain.PSMStatisticsParams"> + +</member> +<member name="P:ProteomIQon.Domain.AndromedaParams.PMinPMax"> +<summary> + selects the minimum and maximum amount of peaks retained in a 100 Da window, all combinations are tested and the best result is kept. +</summary> +</member> +<member name="P:ProteomIQon.Domain.WaveletPeakPickingParams.NumberOfScales"> +<summary> + Centroidization +</summary> +</member> +<member name="T:ProteomIQon.Dto.QuantificationResult"> + +</member> +<member name="T:ProteomIQon.Dto"> + +</member> +<member name="M:ProteomIQon.Core.MzIO.Peaks.unzipIMzliteArray(MzIO.Commons.Arrays.IMzIOArray{MzIO.Binary.Peak1D})"> + +</member> +<member name="M:ProteomIQon.Core.MzIO.Reader.beginTransaction(MzIO.IO.IMzIODataReader)"> +<summary> + Initializes a transaction scope. +</summary> +</member> +<member name="M:ProteomIQon.Core.MzIO.Reader.getDefaultRunID(MzIO.IO.IMzIODataReader)"> +<summary> + Returns the default runID used by manufacturers +</summary> +</member> +</members> +</doc> diff --git a/workflows/ProteomIQon_0.0.2_Tools/Preprocessing_64/net47/System.AppContext.dll b/workflows/ProteomIQon_0.0.2_Tools/Preprocessing_64/net47/System.AppContext.dll new file mode 100644 index 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+<assembly><name>ProteomIQon</name></assembly> +<members> +<member name="M:ProteomIQon.FDRControl'.calculateQValueStorey``1(``0[],Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double})"> +<summary> + Gives a function to calculate the q value for a score in a dataset using Storeys method +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.calculateQValueLogReg``1(System.Double,``0[],Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double})"> +<summary> + Gives a function to calculate the q value for a score in a dataset using Lukas method and Levenberg Marguardt fitting +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.calculateFDRwithDecoyTargetRatio(ProteomIQon.ProteinInference'.InferredProteinClassItemScored[])"> +<summary> + Calculates Decoy/Target ratio +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.calculateFDRwithMAYU(ProteomIQon.ProteinInference'.InferredProteinClassItemScored[],System.Tuple{System.String,System.String}[])"> +<summary> + Calculates the fdr of the data using the MAYU method. The proteinsFromDB is the DB that was used for the inference. +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.expectedFP(ProteomIQon.ProteinInference'.InferredProteinClassItemScored[])"> +<summary> + Calculates the expected false positives for every protein bin and sums them up. +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.binProteinsLength(ProteomIQon.ProteinInference'.InferredProteinClassItemScored[],System.Tuple{System.String,System.String}[],System.Double)"> +<summary> + Returns proteins sorted into bins according to their size. + proteins are the proteins which were found in either the reverse or forward proteininference, proteinsFromDB are the proteins with peptide sequence + on which the inference was performed. +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.estimatePi0HG(System.Double,System.Double,System.Double)"> +<summary> + Estimates the false positives given the total number of entries, the number of target hits and the number of decoy hits +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.getQValues``1(System.Double,Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},``0[])"> +<summary> + Calculates q values for target/decoy dataset +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.getQValueFunc``1(System.Double,System.Double,Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},``0[])"> +<summary> + Calculates q value mapping funtion for target/decoy dataset +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.binningFunction``1(System.Double,System.Double,Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},``0[])"> +<summary> + returns scores, pep, q +</summary> +</member> +<member name="M:ProteomIQon.FDRControl'.getLogisticRegressionFunction(FSharp.Stats.Vector{System.Double},FSharp.Stats.Vector{System.Double},System.Double)"> +<summary> + for given data, creates a logistic regression model and returns a mapping function for this model +</summary> +</member> +<member name="T:ProteomIQon.ProteinInference'.QValueInput"> +<summary> + Input for QValue calulation +</summary> +</member> +<member name="T:ProteomIQon.ProteinInference'.InferredProteinClassItemOut"> +<summary> + For a group of proteins, contains information about all peptides that are put into the output file. +</summary> +</member> +<member name="T:ProteomIQon.ProteinInference'.InferredProteinClassItemQValue"> +<summary> + For a group of proteins, contains information about all peptides that might be used for its quantification and score / q-value calculated for it. +</summary> +</member> +<member name="T:ProteomIQon.ProteinInference'.InferredProteinClassItemScored"> +<summary> + For a group of proteins, contains information about all peptides that might be used for its quantification and score calculated for it. +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.assignDecoyScoreToTargetScore(System.String,Microsoft.FSharp.Collections.FSharpMap{System.String,System.Tuple{System.Double,System.String[]}})"> +<summary> + Looks if the given protein accession is present in a map of identified decoy proteins and assigns its score when found. +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.assignPeptideScores(System.String[],Microsoft.FSharp.Collections.FSharpMap{System.String,System.Double})"> +<summary> + Sums up score of all peptide sequences +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.createPeptideProteinRelation``4(System.Collections.Generic.IEnumerable{Microsoft.FSharp.Core.FSharpOption{BioFSharp.PeptideClassification.ProteinModel{``0,``1,``2,Microsoft.FSharp.Collections.FSharpList{``3}}}})"> +<summary> + Creates a lookup data base to assign peptides to the proteins they are contained in +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.assignTranscriptsToGenes(System.String,System.Collections.Generic.IEnumerable{BioFSharp.IO.GFF3.GFFLine{System.Collections.Generic.IEnumerable{System.Char}}})"> +<summary> + By reading GFF creates the protein models (relationships of proteins to each other) which basically means grouping the rnas over the gene loci + TODO: Don't group over order but rather group over id +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.createProteinModelInfoFromEntry(System.Int32,System.String,BioFSharp.IO.GFF3.GFFEntry)"> +<summary> + Reads geographical information about protein from gff entry and builds the modelinfo of it + This function takes an RNA gff3 entry and therefore will contain the splice variant id of the gene in its result. + This splice variant id should be the same in the given FastA-file. +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.isRNA(BioFSharp.IO.GFF3.GFFLine{System.Collections.Generic.IEnumerable{System.Char}})"> +<summary> +checks if GFF line describes rna +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.isGene(BioFSharp.IO.GFF3.GFFLine{System.Collections.Generic.IEnumerable{System.Char}})"> +<summary> +checks if GFF line describes gene +</summary> +</member> +<member name="M:ProteomIQon.ProteinInference'.createScoreTargetDecoyCount(System.Double,System.Double,System.Double)"> +<summary> + Gives the decoy and target count at a specific score +</summary> +</member> +<member name="M:ProteomIQon.SearchDB'.getSDBParamsBy(System.Data.SQLite.SQLiteConnection)"> +<summary> + Returns SearchDbParams of a existing database by filePath +</summary> +</member> +<member name="M:ProteomIQon.SearchDB'.selectProteins(System.Data.SQLite.SQLiteConnection)"> +<summary> + Returns Accession and Sequence of Proteins from SearchDB +</summary> +</member> +<member name="M:ProteomIQon.SearchDB'.getProteinPeptideLookUpFromFileBy(System.Data.SQLite.SQLiteConnection)"> +<summary> + Prepares a function which returns a list of protein Accessions tupled with the peptide sequence whose ID they were retrieved by +</summary> +</member> +<member name="M:ProteomIQon.SearchDB'.DB'.SQLiteQuery'.prepareSelectPepSequenceByPepSequenceID(System.Data.SQLite.SQLiteConnection,System.Data.SQLite.SQLiteTransaction)"> +<summary> + Prepares statement to select a Peptide Sequence entry by ID +</summary> +</member> +<member name="M:ProteomIQon.SearchDB'.DB'.SQLiteQuery'.prepareSelectProteinAccessionByID(System.Data.SQLite.SQLiteConnection,System.Data.SQLite.SQLiteTransaction)"> +<summary> + Prepares statement to select a Protein Accession entry by ID +</summary> +</member> +<member name="M:ProteomIQon.Fitting'.NonLinearRegression'.LevenbergMarquardtConstrained'.estimatedParamsWithRSS(FSharp.Stats.Fitting.NonLinearRegression.Model,FSharp.Stats.Fitting.NonLinearRegression.SolverOptions,System.Double,System.Double,FSharp.Stats.Vector{System.Double},FSharp.Stats.Vector{System.Double},System.Double[],System.Double[])"> +<summary> + Returns a parameter vector tupled with its residual sum of squares (RSS) as a possible solution for linear least square based nonlinear fitting of a given dataset (xData, yData) with a given + model function. +</summary> +</member> +<member name="M:ProteomIQon.Fitting'.NonLinearRegression'.LevenbergMarquardtConstrained'.initialParamsOverRange(System.Double[],System.Double[],System.Double[])"> +<summary> + Returns an estimate for an initial parameter for the linear least square estimator for a given dataset (xData, yData). + The steepness is given as an array and not estimated. An initial estimate is returned for every given steepness. + The initial estimation is intended for a logistic function. +</summary> +</member> +<member name="M:ProteomIQon.Fitting'.NonLinearRegression'.LevenbergMarquardtConstrained'.initialParam(System.Double[],System.Double[])"> +<summary> + Returns an estimate for an initial parameter for the linear least square estimator for a given dataset (xData, yData). + The initial estimation is intended for a logistic function. +</summary> +</member> +<member name="P:ProteomIQon.Fitting'.NonLinearRegression'.LevenbergMarquardtConstrained'.LogisticFunction"> +<summary> + Logistic Function + Line model of the form "y = a * x + b" +</summary> +</member> +<member name="T:ProteomIQon.Domain.PSMStatisticsParams"> + +</member> +<member name="P:ProteomIQon.Domain.AndromedaParams.PMinPMax"> +<summary> + selects the minimum and maximum amount of peaks retained in a 100 Da window, all combinations are tested and the best result is kept. +</summary> +</member> +<member name="P:ProteomIQon.Domain.WaveletPeakPickingParams.NumberOfScales"> +<summary> + Centroidization +</summary> +</member> +<member name="T:ProteomIQon.Dto.QuantificationResult"> + +</member> +<member name="T:ProteomIQon.Dto"> + +</member> +<member name="M:ProteomIQon.Core.MzIO.Peaks.unzipIMzliteArray(MzIO.Commons.Arrays.IMzIOArray{MzIO.Binary.Peak1D})"> + +</member> +<member name="M:ProteomIQon.Core.MzIO.Reader.beginTransaction(MzIO.IO.IMzIODataReader)"> +<summary> + Initializes a transaction scope. +</summary> +</member> +<member name="M:ProteomIQon.Core.MzIO.Reader.getDefaultRunID(MzIO.IO.IMzIODataReader)"> +<summary> + Returns the default runID used by manufacturers +</summary> +</member> +</members> +</doc> diff --git a/workflows/ProteomIQon_0.0.2_Tools/Preprocessing_64/netcoreapp2.1/baf2sql_c.dll b/workflows/ProteomIQon_0.0.2_Tools/Preprocessing_64/netcoreapp2.1/baf2sql_c.dll new file mode 100644 index 0000000000000000000000000000000000000000..070ad3e0afb14b9968d0707c7a975d85a825a005 Binary files /dev/null and b/workflows/ProteomIQon_0.0.2_Tools/Preprocessing_64/netcoreapp2.1/baf2sql_c.dll differ diff --git a/workflows/ProteomIQon_0.0.2_Tools/ProteomIQon.cwl b/workflows/ProteomIQon_0.0.2_Tools/ProteomIQon.cwl index 4d3977fb8755566e3eff77c6b0ed27f2a9619d24..499b5a446cbb0fee9bcef695796ceb9e8cb57750 100644 --- a/workflows/ProteomIQon_0.0.2_Tools/ProteomIQon.cwl +++ b/workflows/ProteomIQon_0.0.2_Tools/ProteomIQon.cwl @@ -35,7 +35,7 @@ steps: run: proteomiqon-peptidespectrummatching.cwl in: stageDirectory: stage - inputDirectory: Preprocessing/dir + inputDirectory: outputMzML database: db params: paramsPSM outputDirectory: outputPSM @@ -55,7 +55,7 @@ steps: run: proteomiqon-psmbasedquantification.cwl in: stageDirectory: stage - inputDirectoryI: Preprocessing/dir + inputDirectoryI: outputMzML inputDirectoryII: PSMStatistics/dir database: db params: paramsPSMBasedQuant @@ -75,7 +75,7 @@ steps: outputs: mzlite: type: Directory - outputSource: Preprocessing/dir + outputSource: outputMzML psm: type: Directory outputSource: PeptideSpectrumMatching/dir diff --git a/workflows/ProteomIQon_0.0.2_Tools/proteomiqon-preprocessing.cwl b/workflows/ProteomIQon_0.0.2_Tools/proteomiqon-preprocessing.cwl index 40254c73702ff8a902ca573e4ef98b7089c72e51..707157878b818d2cfd7a7dea35634f4f84693c4f 100644 --- a/workflows/ProteomIQon_0.0.2_Tools/proteomiqon-preprocessing.cwl +++ b/workflows/ProteomIQon_0.0.2_Tools/proteomiqon-preprocessing.cwl @@ -2,7 +2,7 @@ cwlVersion: v1.2 class: CommandLineTool -baseCommand: D:\Lukas\CPN2060_CoIP\workflows\ProteomIQon_0.0.2_Tools\Preprocessing\net4.7\ProteomIQon.Preprocessing.exe +baseCommand: D:\Lukas\CPN2060_CoIP\workflows\ProteomIQon_0.0.2_Tools\Preprocessing_64\net47\Preprocessing.exe inputs: # inputtype that declares the directory to be staged? stageDirectory: