AllClasses: All classes defined in the package of 'Rcwl' and the class...

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

All classes defined in the package of 'Rcwl' and the class constructor functions.

Description

InputArrayParam: Parameters for array inputs. To specify an array parameter, the array definition is nested under the type field with 'type: array' and items defining the valid data types that may appear in the array.

InputParam: parameter for a command line tool.

InputParamList: A list of 'InputParam' objects.

OutputArrayParam: Parameters for array outputs.

OutputParam: An output parameter for a Command Line Tool.

OutputParamList: A list of 'InputParam' objects.

stepInParam: The input parameter of a workflow step.

stepInParamList: A list of 'stepInParam' objects.

cwlStepList: A list of 'cwlStep' objects.

Usage

InputArrayParam(
  label = "",
  doc = character(),
  name = character(),
  type = "array",
  items = character(),
  prefix = "",
  separate = TRUE,
  itemSeparator = character(),
  valueFrom = character()
)

InputParam(
  id,
  label = "",
  type = "string",
  doc = character(),
  secondaryFiles = character(),
  streamable = logical(),
  format = character(),
  loadListing = character(),
  loadContents = logical(),
  position = 0L,
  prefix = "",
  separate = TRUE,
  itemSeparator = character(),
  valueFrom = character(),
  shellQuote = logical(),
  default = character(),
  value = character()
)

InputParamList(...)

OutputArrayParam(
  label = character(),
  doc = character(),
  name = character(),
  type = "array",
  items = character()
)

OutputParam(
  id = "output",
  label = character(),
  doc = character(),
  type = "stdout",
  format = character(),
  secondaryFiles = character(),
  streamable = logical(),
  glob = character(),
  loadContents = logical(),
  loadListing = character(),
  outputEval = character(),
  outputSource = character(),
  linkMerge = character(),
  pickValue = character()
)

OutputParamList(out = OutputParam(), ...)

stepInParam(
  id,
  source = character(),
  linkMerge = character(),
  pickValue = character(),
  loadContents = logical(),
  loadListing = character(),
  default = character(),
  valueFrom = character()
)

stepInParamList(...)

cwlStepList(...)

Arguments

label	A short, human-readable label of this object.
doc	A documentation string for this object, or an array of strings which should be concatenated.
name	The identifier for this type.
type	Specify valid types of data that may be assigned to this parameter.
items	Defines the type of the array elements.
prefix	Command line prefix to add before the value.
separate	If true (default), then the prefix and value must be added as separate command line arguments; if false, prefix and value must be concatenated into a single command line argument.
itemSeparator	Join the array elements into a single string with the elements separated by by itemSeparator.
valueFrom	value from string or expression.
id	A unique identifier for this workflow input parameter.
secondaryFiles	Provides a pattern or expression specifying files or directories. Only valid when type: File or is an array of items: File.
streamable	A value of true indicates that the file is read or written sequentially without seeking. Only valid when type: File or is an array of items: File.
format	Only valid when type: File or is an array of items: File. This is the file format that will be assigned to the output File object.
loadListing	Only valid when type: Directory or is an array of items: Directory. "no_listing", "shallow_listing" or "deep_listing".
loadContents	Only valid when type: File or is an array of items: File.
position	The position for this parameter.
shellQuote	If ShellCommandRequirement is in the requirements for the current command, this controls whether the value is quoted on the command line (default is true).
default	The default value for this parameter to use if either there is no source field, or the value produced by the source is null.
value	Assigned value for this parameter
...	A list of 'cwlStep' objects.
glob	Pattern to find files relative to the output directory.
outputEval	Evaluate an expression to generate the output value.
outputSource	Specifies one or more workflow parameters that supply the value of to the output parameter.
linkMerge	The method to use to merge multiple inbound links into a single array.
pickValue	The method to use to choose non-null elements among multiple sources. "first_non_null", "the_only_non_null", or "all_non_null".
out	The default stdout parameter.
source	Specifies one or more workflow parameters that will provide input to the underlying step parameter.

Details

More details of 'InputArrayParam', see: https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputArraySchema

More details for 'InputParam', see: https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter

More details for 'OutputArrayParam', see: https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputArraySchema

More details for 'OutputParam', see: https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter

More details for 'stepInParam', see: https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput

Value

InputArrayParam: An object of class 'InputArrayParam'.

An object of class 'InputParam'.

InputParamList: An object of class 'InputParamList'.

An object of class 'OutputArrayParam'.

OutputParam: An object of class 'OutputParam'.

OutputParamList: An object of class 'OutputParamList'.

stepInParam: An object of class 'stepInParam'.

An object of class 'stepInParamList'.

cwlStepList: An object of class 'cwlStepList'.

Examples

InputArrayParam(items = "string", prefix="-B=", separate = FALSE)
input1 <- InputParam(id = "sth")
InputParamList(input1)
OutputParam(id = "b", type = OutputArrayParam(items = "File"), glob = "*.txt")
o1 <- OutputParam(id = "file", type = "File", glob = "*.txt")
o1

o1 <- OutputParam(id = "file", type = "File", glob = "*.txt")
OutputParamList(o1)
s1 <- stepInParam(id = "s1")

s1 <- stepInParam(id = "s1")
stepInParamList(s1)
s1 <- cwlStep(id = "s1")
cwlStepList(s1)

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