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Commit f7642e81 authored by Martin Kuhl's avatar Martin Kuhl
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adding ARC

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2021-09-07 09:57:30.4430 minimal TRACE Input file: /FuNLno/mzlite/minimal.mzlite
2021-09-07 09:57:30.4508 minimal TRACE Output directory: /FuNLno/quant
2021-09-07 09:57:30.4618 minimal TRACE Parameters: { PerformLabeledQuantification = true
XicExtraction =
{ ScanTimeWindow = 2.0
MzWindow_Da = Fixed 0.7
XicProcessing =
Wavelet
{ Borderpadding = None
BorderPadMethod = Random
InternalPaddingMethod =
LinearInterpolation
HugeGapPaddingMethod = Zero
HugeGapPaddingDistance = 100.0
MinPeakDistance = None
MinPeakLength = Some 0.1
MaxPeakLength = 1.5
NoiseQuantile = 0.01
MinSNR = 0.01 }
TopKPSMs = None }
BaseLineCorrection = Some { MaxIterations = 10
Lambda = 6
P = 0.05 } }
2021-09-07 09:57:30.4717 minimal TRACE Now performing Quantification using: /FuNLno/mzlite/minimal.mzlite and /FuNLno/psmstats/minimal.qpsm, Results will be written to: /FuNLno/quant
2021-09-07 09:57:30.4789 minimal TRACE outFilePath:/FuNLno/quant/minimal.quant
2021-09-07 09:57:30.4921 minimal TRACE plotDirectory:/FuNLno/quant/minimal_plots
2021-09-07 09:57:30.4921 minimal TRACE Copy peptide DB into Memory
2021-09-07 09:57:30.5098 minimal TRACE Copy peptide DB into Memory: finished
2021-09-07 09:57:30.5098 minimal TRACE Get peptide lookUp function
2021-09-07 09:57:30.5814 minimal TRACE Get peptide lookUp function: finished
2021-09-07 09:57:30.5814 minimal TRACE Init connection to mass spectrum data.
2021-09-07 09:57:30.6131 minimal TRACE Create RetentionTime index
2021-09-07 09:57:30.7196 minimal TRACE Create RetentionTime index:finished
2021-09-07 09:57:30.7287 minimal TRACE Read and sort ms1s
2021-09-07 09:57:30.7657 minimal TRACE Read and sort ms1s:finished
2021-09-07 09:57:30.7757 minimal TRACE Read scored PSMs
2021-09-07 09:57:30.8056 minimal TRACE Read scored PSMs:finished
2021-09-07 09:57:30.8141 minimal TRACE Estimate precursor mz standard deviation and mz correction.
2021-09-07 09:57:30.8309 minimal TRACE Estimate precursor mz standard deviation and mz correction.:finished, standard deviation: 0.000920
2021-09-07 09:57:30.8411 minimal TRACE init lookup functions
2021-09-07 09:57:30.8459 minimal TRACE init lookup functions:finished
2021-09-07 09:57:30.8459 minimal TRACE init quantification functions
2021-09-07 09:57:30.8459 minimal TRACE init quantification functions:finished
2021-09-07 09:57:30.8579 minimal TRACE executing quantification
2021-09-07 09:57:30.8670 minimal TRACE 0 peptides quantified
2021-09-07 09:57:31.2593 minimal TRACE executing quantification:finished
cwlVersion: v1.2
class: Workflow
requirements:
MultipleInputFeatureRequirement: {}
inputs:
cores: int
outputDB: string
outputMzML: string
outputPSM: string
outputPSMStats: string
outputQuant: string
outputProt: string
inputDB: File
inputPSM: Directory
paramsDB: File
paramsMzML: File
paramsPSM: File
paramsPSMStats: File
paramsPSMBasedQuant: File
paramsProt: File
steps:
#MzMLToMzlite:
# run: ./../../workflows/MzMLToMzlite/proteomiqon-mzmltomzlite.cwl
# in:
# stageDirectory: stage
# inputDirectory: inputMzML
# params: paramsMzML
# outputDirectory: outputMzML
# parallelismLevel: cores
# out: [dir]
PeptideDB:
run: ./../../workflows/PeptideDB/proteomiqon-peptidedb.cwl
in:
inputFile: inputDB
params: paramsDB
outputDirectory: outputDB
out: [db, dbFolder]
PeptideSpectrumMatching:
run: ./../../workflows/PeptideSpectrumMatching/proteomiqon-peptidespectrummatching.cwl
in:
inputDirectory: inputPSM
database: PeptideDB/db
params: paramsPSM
outputDirectory: outputPSM
parallelismLevel: cores
out: [dir]
PSMStatistics:
run: ./../../workflows/PSMStatistics/proteomiqon-psmstatistics.cwl
in:
inputDirectory: PeptideSpectrumMatching/dir
database: PeptideDB/db
params: paramsPSMStats
outputDirectory: outputPSMStats
parallelismLevel: cores
out: [dir]
PSMBasedQuantification:
run: ./../../workflows/PSMBasedQuantification/proteomiqon-psmbasedquantification.cwl
in:
inputDirectoryI: inputPSM
inputDirectoryII: PSMStatistics/dir
database: PeptideDB/db
params: paramsPSMBasedQuant
outputDirectory: outputQuant
parallelismLevel: cores
out: [dir]
ProteinInference:
run: ./../../workflows/ProteinInference/proteomiqon-proteininference.cwl
in:
inputDirectory: PSMStatistics/dir
database: PeptideDB/db
params: paramsProt
outputDirectory: outputProt
out: [dir]
outputs:
#mzlite:
# type: Directory
# outputSource: MzMLToMzlite/dir
peptidedb:
type: Directory
outputSource: PeptideDB/dbFolder
psm:
type: Directory
outputSource: PeptideSpectrumMatching/dir
psmStats:
type: Directory
outputSource: PSMStatistics/dir
quant:
type: Directory
outputSource: PSMBasedQuantification/dir
prot:
type: Directory
outputSource: ProteinInference/dir
\ No newline at end of file
cores: 1
outputDB: db
outputMzML: mzlite
outputPSM: psm
outputPSMStats: psmstats
outputQuant: quant
outputProt: prot
inputDB:
class: File
path: ./../../externals/example.fasta
inputPSM:
class: Directory
path: ./../../assays/assay1/dataset
paramsDB:
class: File
path: ./db/peptideDBParams.json
paramsMzML:
class: File
path: ./mzlite/preprocessingParams.json
paramsPSM:
class: File
path: ./psm/peptideSpectrumMatchingParams.json
paramsPSMStats:
class: File
path: ./psmstats/pSMStatisticsParamsFixed.json
paramsPSMBasedQuant:
class: File
path: ./quant/QuantificationParams.json
paramsProt:
class: File
path: ./prot/ProteinInferenceParams.json
\ No newline at end of file
FROM mcr.microsoft.com/dotnet/sdk:5.0
# Install tool in $HOME/.dotnet/tools
RUN dotnet tool install \
ProteomIQon.MzMLToMzLite \
--version 0.0.6 \
--tool-path /usr/local/bin
\ No newline at end of file
#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool
hints:
DockerRequirement:
dockerImageId: mzmltomzlite
dockerFile:
$include: ./Dockerfile
baseCommand: ['proteomiqon-mzmltomzlite']
inputs:
# inputtype that declares the directory to be staged?
stageDirectory:
type: Directory
inputDirectory:
type: Directory
inputBinding:
position: 1
prefix: -i
params:
type: File
inputBinding:
position: 2
prefix: -p
outputDirectory:
type: Directory
inputBinding:
position: 3
prefix: -o
parallelismLevel:
type: int
inputBinding:
position: 4
prefix: -c
requirements:
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.inputDirectory)
writable: true
#- entry: $(inputs.stageDirectory)
# writable: true
- entry: $(inputs.outputDirectory)
writable: true
outputs:
dir:
type: Directory
outputBinding:
glob: $(inputs.outputDirectory.basename)
FROM mcr.microsoft.com/dotnet/sdk:5.0
# Install tool in $HOME/.dotnet/tools
RUN dotnet tool install \
ProteomIQon.PSMBasedQuantification \
--version 0.0.7 \
--tool-path /usr/local/bin
#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool
hints:
DockerRequirement:
dockerImageId: psmbasedquantification
dockerFile:
$include: ./Dockerfile
baseCommand: ['proteomiqon-psmbasedquantification']
inputs:
inputDirectoryI:
type: Directory
inputBinding:
position: 1
prefix: -i
inputDirectoryII:
type: Directory
inputBinding:
position: 2
prefix: -ii
database:
type: File
inputBinding:
position: 3
prefix: -d
params:
type: File
inputBinding:
position: 4
prefix: -p
outputDirectory:
type: string
inputBinding:
position: 5
prefix: -o
parallelismLevel:
type: int
inputBinding:
position: 6
prefix: -c
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.inputDirectoryI)
writable: true
- entry: $(inputs.inputDirectoryII)
writable: true
- entry: "$({class: 'Directory', listing: []})"
entryname: inputs.OutputDirectory
writable: true
outputs:
dir:
type: Directory
outputBinding:
glob: $(inputs.outputDirectory)
FROM mcr.microsoft.com/dotnet/sdk:5.0
# Install tool in $HOME/.dotnet/tools
RUN dotnet tool install \
ProteomIQon.PSMStatistics \
--version 0.0.7 \
--tool-path /usr/local/bin
\ No newline at end of file
#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool
hints:
DockerRequirement:
dockerImageId: psmstatistics
dockerFile:
$include: ./Dockerfile
baseCommand: ['proteomiqon-psmstatistics']
inputs:
inputDirectory:
type: Directory
inputBinding:
position: 1
prefix: -i
database:
type: File
inputBinding:
position: 2
prefix: -d
params:
type: File
inputBinding:
position: 3
prefix: -p
outputDirectory:
type: string
inputBinding:
position: 4
prefix: -o
parallelismLevel:
type: int
inputBinding:
position: 5
prefix: -c
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.inputDirectory)
writable: true
- entry: "$({class: 'Directory', listing: []})"
entryname: inputs.OutputDirectory
writable: true
outputs:
dir:
type: Directory
outputBinding:
glob: $(inputs.outputDirectory)
FROM mcr.microsoft.com/dotnet/sdk:5.0
# Install tool in $HOME/.dotnet/tools
RUN dotnet tool install \
ProteomIQon.PeptideDB \
--version 0.0.7 \
--tool-path /usr/local/bin
\ No newline at end of file
#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool
hints:
DockerRequirement:
dockerImageId: peptidedb
dockerFile:
$include: ./Dockerfile
baseCommand: ['proteomiqon-peptidedb']
inputs:
inputFile:
type: File
inputBinding:
position: 1
prefix: -i
params:
type: File
inputBinding:
position: 2
prefix: -p
outputDirectory:
type: string
inputBinding:
position: 3
prefix: -o
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: "$({class: 'Directory', listing: []})"
entryname: inputs.outputDirectory
writable: true
outputs:
db:
type: File
outputBinding:
glob: "*/*.db"
dbFolder:
type: Directory
outputBinding:
glob: $(inputs.outputDirectory)
FROM mcr.microsoft.com/dotnet/sdk:5.0
# Install tool
RUN dotnet tool install \
ProteomIQon.PeptideSpectrumMatching \
--version 0.0.7 \
--tool-path /usr/local/bin
#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool
hints:
DockerRequirement:
dockerImageId: peptidespectrummatching
dockerFile:
$include: ./Dockerfile
baseCommand: [ 'proteomiqon-peptidespectrummatching' ]
inputs:
inputDirectory:
type: Directory
inputBinding:
position: 1
prefix: -i
database:
type: File
inputBinding:
position: 2
prefix: -d
params:
type: File
inputBinding:
position: 3
prefix: -p
outputDirectory:
type: string
inputBinding:
position: 4
prefix: -o
parallelismLevel:
type: int
inputBinding:
position: 5
prefix: -c
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.inputDirectory)
writable: true
- entry: "$({class: 'Directory', listing: []})"
entryname: inputs.outputDirectory
writable: true
outputs:
dir:
type: Directory
outputBinding:
glob: $(inputs.outputDirectory)
FROM mcr.microsoft.com/dotnet/sdk:5.0
# Install tool in $HOME/.dotnet/tools
RUN dotnet tool install \
ProteomIQon.ProteinInference \
--version 0.0.7 \
--tool-path /usr/local/bin
\ No newline at end of file
#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool
hints:
DockerRequirement:
dockerImageId: proteininference
dockerFile:
$include: ./Dockerfile
baseCommand: ['proteomiqon-proteininference']
inputs:
inputDirectory:
type: Directory
inputBinding:
position: 1
prefix: -i
database:
type: File
inputBinding:
position: 2
prefix: -d
params:
type: File
inputBinding:
position: 3
prefix: -p
outputDirectory:
type: string
inputBinding:
position: 4
prefix: -o
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.inputDirectory)
writable: true
- entry: "$({class: 'Directory', listing: []})"
entryname: inputs.outputDirectory
writable: true
outputs:
dir:
type: Directory
outputBinding:
glob: $(inputs.outputDirectory)
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