galaxy: Make a function available in Galaxy
In Bioconductor/RGalaxy: Make an R function available in the Galaxy web platform

Description Usage Arguments Value See Also Examples

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

galaxy(func, 
        package=getPackage(func),
        manpage=func, 
        name=getFriendlyName(func),
        version=getVersion(func),
        galaxyConfig,
        dirToRoxygenize,
        RserveConnection=NULL,
        path.to.R="",
        functionalTestDirectory)

`func`	Required. TA character vector naming 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).
`package`	The name of the package where `func` lives, or NULL if it is not in a package. By default, `RGalaxy` will try to determine which package the code lives in and set the parameter to NULL if it cannot.
`manpage`	The full path to the Rd-formatted manual page for the function, or if the `func` is in a package, an alias that will pull up that manpage.
`name`	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".
`version`	The version of this function. If `func` lives in a package, defaults to the version of `package`.
`galaxyConfig`	Required. A `link{GalaxyConfig}` object describing your Galaxy configuration.
`dirToRoxygenize`	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.
`RserveConnection`	If set (by calling `RserveConnection`), sends the function to a running Rserve for evaluation. This can make functions run faster since dependencies have already been loaded. If NULL (the default), function is run normally. See vignette for more information.
`path.to.R`	If not empty, Galaxy will look for R in this directory. This is useful if there are multiple versions of R on your system and your Galaxy configuration prevents you from setting your PATH to point to the right one.
`functionalTestDirectory`	If `package` is not specified, this directory is searched for functional test fixtures.

invisible(NULL)

GalaxyConfig, GalaxyOutput, GalaxyParam

## 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)

## Not run: 
galaxy("functionToGalaxify",
    galaxyConfig=GalaxyConfig(galaxyHome, "mytool",
      "Test Section", "testSectionId"),
    RserveConnection=RserveConnection())

## End(Not run)