writeTargetsout {systemPipeR} | R Documentation

## Write updated targets out to file

### Description

Convenience write function for generating targets files with updated `FileName` columns containing the paths to files generated by input/output processes. These processes can be commandline- or R-based software. Typically, the paths to the inputs are stored in the targets infile (`targetsin(args)`) and the outputs are stored in the targets outfile (`targetsout(args)`). Note: by default the function cannot overwrite any existing files. If a file exists then the user has to explicitly remove it or set `overwrite=TRUE`.

### Usage

    writeTargetsout(x, file = "default", silent = FALSE, overwrite=FALSE, ...)

### Arguments

`x` | Object of class `SYSargs`.
`file` | Name and path of output file. If set to "default" then the name of the output file will have the pattern 'targets_<software>.txt', where <software> will be what `software(x)` returns.
`silent` | If set to `TRUE`, all messages returned by the function will be suppressed.
`overwrite` | If set to `TRUE`, existing files of same name will be overwritten.
`...` | To pass on additional arguments.

### Value

Writes tabular targes files containing the header/comment lines from `targetsheader(x)` and the columns from `targetsout(x)`.

### Author(s)

Thomas Girke

### See Also

`writeTargetsRef`

### Examples

    ## Create SYSargs object
    param <- system.file("extdata", "tophat.param", package="systemPipeR")
    targets <- system.file("extdata", "targets.txt", package="systemPipeR")
    args <- systemArgs(sysma=param, mytargets=targets)

    ## Not run:
    ## Write targets out file
    writeTargetsout(x=args, file="default")

    ## End(Not run)

[Package systemPipeR version 1.16.1 Index]