Wrap Command Tools and Pipelines Using CWL


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Documentation for package ‘Rcwl’ version 1.3.1

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Rcwl-package Rcwl
$-method Input parameters InputParam
$<--method Input parameters InputParam
+-method Pipeline
arguments cwlParam methods
arguments<- cwlParam methods
baseCommand cwlParam methods
baseCommand<- cwlParam methods
cwlClass cwlParam methods
cwlClass<- cwlParam methods
cwlParam Parameters for CWL
cwlParam-class Parameters for CWL
cwlShiny cwlShiny
cwlStepParam cwlStepParam
cwlStepParam-class cwlStepParam
cwlVersion cwlParam methods
cwlVersion<- cwlParam methods
extensions cwlParam methods
extensions<- cwlParam methods
hints cwlParam methods
hints<- cwlParam methods
InputArrayParam InputArrayParam
InputArrayParam-class InputArrayParam
InputParam Input parameters InputParam
InputParam-class Input parameters InputParam
InputParamList InputParamList
InputParamList-class InputParamList
inputs InputParamList
OutputArrayParam Output array parameters
OutputArrayParam-class Output array parameters
OutputParam Output parameters
OutputParam-class Output parameters
OutputParamList OutputParamList
OutputParamList-class OutputParamList
outputs OutputParamList
plotCWL plotCWL
Rcwl Rcwl
readCWL Read CWL Function to read CWL command or workflow files.
requirements cwlParam methods
requirements<- cwlParam methods
runCWL run cwlParam
runCWLBatch run CWL with batchtools
runs runs
short short
stdOut cwlParam methods
stdOut<- cwlParam methods
Step Step function
stepInParam stepInParam
stepInParam-class stepInParam
stepInParamList stepInParamList
stepInParamList-class stepInParamList
stepParam stepParam
stepParam-class stepParam
stepParamList stepParamList
stepParamList-class stepParamList
steps Steps
steps<- Steps
writeCWL Write CWL