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InputArrayParam-classR Documentation

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)

rworkflow/Rcwl documentation built on May 10, 2024, 6:21 a.m.