cwlProcess methods

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.

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 cwlProcess
$(x, name)

# S4 method for 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)
#> [1] "v1.0"
cwlClass(echo)
#> [1] "CommandLineTool"
baseCommand(echo)
#> [1] "echo"
hints(echo)
#> list()
requirements(echo)
#> list()
inputs(echo)
#> inputs:
#>   sth (string):  
outputs(echo)
#> outputs:
#> output:
#>   type: stdout
stdOut(echo)
#> character(0)
extensions(echo)
#> list()

s1 <- cwlWorkflow()
runs(s1)
#> List of length 0
#> names(0): 
s1
#> class: cwlWorkflow 
#>  cwlClass: Workflow 
#>  cwlVersion: v1.0 
#> inputs:
#> outputs:
#> output:
#>   type: stdout
#> steps:
#> {}
short(s1)
#> inputs: []
#> outputs: output
#> steps: []