cwlProcess: Parameters for CWL

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

Parameters for CWL

Description

The main CWL parameter class and constructor for command tools. More details: https://www.commonwl.org/v1.0/CommandLineTool.html

Usage

cwlProcess(
  cwlVersion = "v1.0",
  cwlClass = "CommandLineTool",
  baseCommand = character(),
  requirements = list(),
  hints = list(),
  arguments = list(),
  id = character(),
  label = character(),
  doc = character(),
  inputs = InputParamList(),
  outputs = OutputParamList(),
  stdout = character(),
  stdin = character(),
  expression = character(),
  extensions = list(),
  intent = list()
)

Arguments

cwlVersion	CWL version
cwlClass	"CommandLineTool"
baseCommand	Specifies the program or R function to execute
requirements	A list of requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process.
hints	Any or a list for the workflow engine.
arguments	Command line bindings which are not directly associated with input parameters.
id	The unique identifier for this process object.
label	A short, human-readable label of this process object.
doc	A documentation string for this object, or an array of strings which should be concatenated.
inputs	A object of 'InputParamList'.
outputs	A object of 'OutputParamList'.
stdout	Capture the command's standard output stream to a file written to the designated output directory.
stdin	A path to a file whose contents must be piped into the command's standard input stream.
expression	Javascripts for ExpressionTool class.
extensions	A list of extensions and metadata
intent	An identifier for the type of computational operation, of this Process.

Details

https://www.commonwl.org/v1.0/CommandLineTool.html

Value

A 'cwlProcess' class object.

Examples

input1 <- InputParam(id = "sth")
echo <- cwlProcess(baseCommand = "echo", inputs = InputParamList(input1))

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