Man pages for PacificBiosciences/pbcommandR
R Package for generating reports using SMRT-Link

chkClassHelper function for verifying arguments
chkPngCheck the file ends as a png
dictToResolvedToolContractConvert a dict to a Resolved Task Contract
dToToolContractconvert the json to ToolContract instance
examplefastaReportExample Task for Testing with emitting a report
examplefilterFastaTaskExample Task for testing inputs = [FileTypes.Fasta] outputs =...
FileType-classFile Type
FileTypesRegistry for all the PacBio defined file types
getExamplePlotGroupExample Plot Group
getParserFundamental argument parser to emit tool contracts and Run...
getPBColorScaleGet the default color scheme, adding more colors if they are...
getPBFillScaleGet the default color scheme for fills, adding more colors if...
getPBThemeReturns a default there for making plots.
InputFileType-classTool Contract Task Input File Type
loadJsonFromFileGeneral func to load JSON from a file
loadReseqConditionsFromPathLoad Condition
loadResolvedToolContractFromPathLoad a Resolved Tool contract from json file
loadToolContractFromPathLoad Tool Contract from Path
mainRegisteryMainArgsCLI entry point. Parses CLI args and calls registery Runner
OutputFileType-classTool Contract Task Input File Type
pbreporterSugar object to make it easier to generate reports.
pbReseqJobCreate a resequencing job tool wrapper using a function that...
printConditionCSVConvert a resolved condition JSON into a CSV for resubmission...
RegisteredToolContract-classRegistered Tool Contract
ReseqCondition-classModel For Reseq Condition
ReseqConditions-classModel for ReseqConditions
ResolvedToolContract-classResolved Tool Contract
ResolvedToolContractTask-classResolved Tool Contract Task
ResourceTypesSymbol types used in Tool Contract and Resolved Tool...
SymbolTypesSymbol types used in Tool Contract and Resolved Tool...
TaskTypesPacBio Defined task types
ToolContract-classTool Contract
ToolContractTask-classTool Contract
toolContractToDConvert Tool Contract into list/dict
ToolDriver-classTool Driver has the driver exe and env (to be added)
writeToolContractWrite Tool Contract to JSON file
PacificBiosciences/pbcommandR documentation built on Oct. 4, 2017, 12:08 a.m.