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maw-metfrag.cwl
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maw-metfrag.cwl
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cwlVersion: v1.0
class: CommandLineTool
baseCommand: ['java', '-jar', '/usr/src/myapp/MetFragCommandLine-2.5.0.jar']
requirements:
DockerRequirement:
dockerPull: docker.io/zmahnoor/maw-metfrag_2.5.0:1.0.5
InlineJavascriptRequirement: {}
InitialWorkDirRequirement:
listing:
- entryname: metfrag.inputs
entry: |-
PeakListPath = $(inputs.PeakList.path)
IonizedPrecursorMass = $(inputs.IonizedPrecursorMass)
PrecursorIonMode = $(inputs.PrecursorIonMode)
MetFragDatabaseType = LocalCSV
LocalDatabasePath = $(inputs.LocalDatabasePath.path)
DatabaseSearchRelativeMassDeviation = 5
FragmentPeakMatchAbsoluteMassDeviation = 0.001
FragmentPeakMatchRelativeMassDeviation = 15
MetFragCandidateWriter = CSV
SampleName = $(inputs.SampleName)
#ResultsPath = $(runtime.outdir)/metfrag
ResultsPath = $(runtime.outdir)
MetFragPreProcessingCandidateFilter = UnconnectedCompoundFilter
MetFragPostProcessingCandidateFilter = InChIKeyFilter
MaximumTreeDepth = 2
NumberThreads = 1
inputs: # additional inputs for all files; make them to show certain paths
PeakList:
type: File
IonizedPrecursorMass:
type: string
PrecursorIonMode:
type: int
LocalDatabasePath:
type: File
SampleName:
type: string
# MetFragDatabaseType:
# type: string
# DatabaseSearchRelativeMassDeviation:
# type: int
# FragmentPeakMatchAbsoluteMassDeviation:
# type: float
# FragmentPeakMatchRelativeMassDeviation:
# type: float
# MetFragCandidateWriter:
# type: string
# MetFragPreProcessingCandidateFilter:
# type: string
# MetFragPostProcessingCandidateFilter:
# type: string
# MaximumTreeDepth:
# type: int
# NumberThreads:
# type: int
arguments:
#- $(runtime.outdir)/cwl.output.json
- $(runtime.outdir)/metfrag.inputs
outputs:
metfrag_candidate_list:
type: File
outputBinding:
#glob: "$(runtime.outdir)/metfrag/*.csv"
glob: "$(runtime.outdir)/*.csv"
#loadContents: true