sevenbridges (version 1.2.4)

CLB: Shorthand functions for cwl packages constructors

Description

Shorthand functions for cwl packages constructors

Arguments

type

[ANY] Specify valid types of data that may be assigned to this parameter.

label

[character] A short, human-readable label of this parameter object.

description

[character] A long, human-readable description of this parameter object.

streamable

[logical] Currently only applies if type is File. A value of true indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: false.

default

[ANY] The default value for this parameter if not provided in the input object.

...

For InputParameter, it will be passed to [CommandLineBinding], which could be created by command CLB. For parameters that accepted please check CommandLineBiding in cwl package. For your convenience, this manual also contain a section for CommandLineBinding. For OutPar or OutputParameter, it will be passed to CommandOutputParameter. Please check the following section as well.

Shorthand

CLB <- CommandLineBinding argslist <- CLBList <- CommandLineBindingList COB <- CommandOutputBinding IPList <- InputParameterList OPList <- OutputParameterList InPar <- InputParameter OutPar <- OutputParameter

CommandLineBinding

position

[integer] The sorting key. Default position is 0.

prefix

[character] Command line prefix to add before the value.

separate

[logical] 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

[character] Join the array elements into a single string with the elements separated by by itemSeparator.

valueFrom

[characterOrExpression] If valueFrom is a constant string value, use this as the value and apply the binding rules above. If valueFrom is an expression, evaluate the expression to yield the actual value to use to build the command line and apply the binding rules above. If the inputBinding is associated with an input parameter, the "context" of the expression will be the value of the input parameter. When a binding is part of the CommandLineTool.arguments field, the valueFrom field is required.

CommandOutputParameter

glob

[characterORExpression] Find files relative to the output directory, using POSIX glob(3) pathname matching. If provided an array, match all patterns in the array. If provided an expression, the expression must return a string or an array of strings, which will then be evaluated as a glob pattern. Only files which actually exist will be matched and returned.

outputEval

[Expression] Evaluate an expression to generate the output value. If glob was specified, the script context will be an array containing any files that were matched. Additionally, if loadContents is true, the file objects will include up to the first 64 KiB of file contents in the contents field.

Following fields inherited from Binding

loadContents

[logical] Only applies when type is File. Read up to the first 64 KiB of text from the file and place it in the "contents" field of the file object for manipulation by expressions.

secondaryFiles

Only applies when type is File. Describes files that must be included alongside the primary file. If the value is Expression, the context of the expression is the input or output File parameter to which this binding applies. Where the value is a string, it specifies that the following pattern should be applied to the primary file: If string begins with one or more caret characters, for each caret, remove the last file extension from the path (the last period . and all following characters). If there are no file extensions, the path is unchanged. Append the remainder of the string to the end of the file path.

Examples

ipl <- IPList(
    input(id = "bam",
          type = "File",
          label = "Bam file",
          description = "Input bam file",
          position = 1L,
          separate = TRUE),
    input(id = "level",
          type = "Integer",
          label = "Compression Level",
          description = "Set compression level, from 0 (uncompressed) to 9 (best)",
          position = 2L),
    input(id = "prefix",
          type = "String",
          label = "Prefix",
          description = "Write temporary files to PREFIX.nnnn.bam",
          position = 3L)
)