galaxy: Make a function available in Galaxy

In dtenenba/RGalaxy-vignette-changes: Make an R function available in the Galaxy web platform

Description

Makes an R function available in the Galaxy web platform. Automates all the work necessary to expose an R function in Galaxy. See the vignette for more information

Usage

galaxy(func, manpage, ..., name=getFriendlyName(deparse(substitute(func))), 
    package=NULL, is.exported=NULL, version, galaxyConfig, packageSourceDir)

Arguments

func	Required. The function to make available in Galaxy. This function should be entirely-self contained, and should accept as arguments the full paths to its input and output file(s).
manpage	Required. The full path to the Rd-formatted manual page for the function, or if package is specified, an alias that will pull up that manpage.
...	Required. A list of at least one GalaxyParam object and at least one GalaxyOutput objects.
name	Required. Text describe the action this function performs. Becomes a clickable link in Galaxy. By default, if your function is called "fooBar", name is set to "Foo Bar".
package	The name of the package where func lives, or NULL (the default) if it is not in a package.
is.exported	If package is supplied, a logical indicating whether func is exported from package.
version	The version of this function. If package is TRUE, defaults to the version of package.
galaxyConfig	Required. A link{GalaxyConfig} object describing your Galaxy configuration.
packageSourceDir	If present, points to the directory of a source package upon which to run roxygenize() from the roxygen2 package, creating manual pages from source code comments.

Value

invisible(NULL)

See Also

GalaxyParam, GalaxyConfig, GalaxyOutput

Examples

## set up galaxyHome (you don't need to do this if 
## you really have Galaxy installed)
galaxyHome <- tempdir()
dir.create(galaxyHome, recursive=TRUE, showWarnings=FALSE)
file.copy(system.file("galaxy", "tool_conf.xml", package="RGalaxy"),
    file.path(galaxyHome, "tool_conf.xml"), overwrite=FALSE)


galaxy(functionToGalaxify,
    manpage="functionToGalaxify",
    package="RGalaxy",
    version=packageDescription("RGalaxy")$Version,
    galaxyConfig=GalaxyConfig(galaxyHome, "mytool", "Test Section", "testSectionId"))

dtenenba/RGalaxy-vignette-changes documentation built on May 15, 2019, 4:54 p.m.