cwlProcess-methods: cwlProcess methods

In hubentu/Rcwl: An R interface to the Common Workflow Language

cwlProcess methods

Description

Some useful methods for 'cwlProcess' objects.

'$': Extract input values for 'cwlProcess' object. (Can auto-complete the input names using tab)

'$<-': Set input values for 'cwlProcess' object by name.

outputs: The outputs of a 'cwlProcess' object.

stdOut: stdout of 'cwlProcess' object.

extensions: Extensions and metadata of 'cwlProcess' object.

short: The function to show a short summary of 'cwlProcess' or 'cwlWorkflow' object.

Usage

cwlVersion(cwl)

cwlVersion(cwl) <- value

cwlClass(cwl)

cwlClass(cwl) <- value

baseCommand(cwl)

baseCommand(cwl) <- value

arguments(cwl, step = NULL)

arguments(cwl, step = NULL) <- value

hints(cwl)

hints(cwl) <- value

requirements(cwl, step = NULL)

requirements(cwl, step = NULL) <- value

inputs(cwl)

## S4 method for signature 'cwlProcess'
x$name

## S4 replacement method for signature 'cwlProcess'
x$name <- value

outputs(cwl)

stdOut(cwl)

stdOut(cwl) <- value

extensions(cwl)

extensions(cwl) <- value

short(cwl)

Arguments

cwl	A 'cwlProcess' (or 'cwlWorkflow') object.
value	To assign a list of 'requirements' value.
step	To specifiy a step ID when 'cwl' is a workflow.
x	A 'cwlProcess' object.
name	One of input list.

Value

cwlVersion: cwl document version

cwlClass: CWL class of 'cwlProcess' or 'cwlWorkflow' object.

baseCommand: base command for the 'cwlProcess' object.

arguments: CWL arguments.

hints: CWL hints.

requirements: CWL requirments.

inputs: A list of 'InputParam'.

'$': the 'InputParam' value for 'cwlProcess' object.

outputs: A list of 'OutputParam'.

stdOut: CWL stdout.

extensions: A list of extensions or metadata.

short: A short summary of an object of 'cwlProcess' or 'cwlWorkflow'.

Examples

ip <- InputParam(id = "sth")
echo <- cwlProcess(baseCommand = "echo", inputs = InputParamList(ip))
cwlVersion(echo)
cwlClass(echo)
baseCommand(echo)
hints(echo)
requirements(echo)
inputs(echo)
outputs(echo)
stdOut(echo)
extensions(echo)

s1 <- cwlWorkflow()
runs(s1)
s1
short(s1)

hubentu/Rcwl documentation built on May 9, 2024, 2:14 a.m.