galaxy {RGalaxy} | R Documentation |
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 |
manpage |
The full path to the Rd-formatted manual page for the function,
or if the |
name |
Text describe the action this function performs. Becomes a clickable
link in Galaxy. By default, if your function is called "fooBar",
|
version |
The version of this function. If |
galaxyConfig |
Required.
A |
dirToRoxygenize |
If present, points to the directory of a source package upon which to run
|
RserveConnection |
If set (by calling |
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 |
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)