RGalaxy: Make an R function available in the Galaxy web platform
Version 1.20.0

Given an R function and its manual page, make the documented function available in Galaxy.

AuthorDan Tenenbaum
Bioconductor views Infrastructure
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.20.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RGalaxy")

Popular man pages

addTwoNumbersWithTest: Add two numbers (with functional test)
galaxy: Make a function available in Galaxy
GalaxyClasses: Galaxy Parameter Classes
GalaxyConfig-class: Class '"GalaxyConfig"'
GalaxyOutput-class: Class '"GalaxyOutput"'
testFunctionWithGalaxySelectParam: A variation on functionToGalaxify that takes a...
testFunctionWithSelect: A variation on functionToGalaxify that takes a...
See all...

All man pages Function index File listing

Man pages

addTwoNumbers: Add two numbers
addTwoNumbersWithTest: Add two numbers (with functional test)
anotherTestFunction: Add two matrices
foo: a foo function
functionToGalaxify: Add two matrices
galaxy: Make a function available in Galaxy
GalaxyClasses: Galaxy Parameter Classes
GalaxyConfig-class: Class '"GalaxyConfig"'
GalaxyInputFile-class: Class '"GalaxyInputFile"'
GalaxyOutput-class: Class '"GalaxyOutput"'
getFriendlyName: Change a camelCase name to a friendlier version
probeLookup: Get the PFAM and SYMBOL names for a set of Affymetrix probe...
RserveConnection-class: Class '"RserveConnection"'
runFunctionalTest: Run the functional test associated with a function.
testFunctionWithGalaxySelectParam: A variation on functionToGalaxify that takes a...
testFunctionWithSelect: A variation on functionToGalaxify that takes a...
utilities: Sends informational, warning, and error messages to the user.

Functions

GalaxyCharacterParam Man page
GalaxyCharacterParam-class Man page
GalaxyClasses Man page
GalaxyConfig Man page Source code
GalaxyConfig-class Man page
GalaxyInputFile Man page Source code
GalaxyInputFile-class Man page
GalaxyIntegerParam Man page
GalaxyIntegerParam-class Man page
GalaxyLogicalParam Man page
GalaxyLogicalParam-class Man page
GalaxyNumericParam Man page
GalaxyNumericParam-class Man page
GalaxyOutput Man page Source code
GalaxyOutput-class Man page
GalaxyParam Man page Source code
GalaxySelectParam Man page
GalaxySelectParam-class Man page
RserveConnection Man page
RserveConnection-class Man page
addTwoNumbers Man page Source code
addTwoNumbersWithTest Man page Source code
anotherTestFunction Man page Source code
checkInputs Source code
createScriptFile Source code
displayFunction Source code
editToolConfXML Source code
foo Man page Source code
functionToGalaxify Man page Source code
galaxy Man page Source code
generateHelpText Source code
getFriendlyName Man page Source code
getFuncInfo Source code
getFuncName Source code
getHelp Source code
getHelpFromText Source code
getManPage Source code
getManSection Source code
getPackage Source code
getSupportedExtensions Source code
getTitle Source code
getVersion Source code
gmessage Man page Source code
gstop Man page Source code
gwarning Man page Source code
isTestable Source code
msg Source code
parseSectionFromText Source code
printf Source code Source code
probeLookup Man page Source code
runFunctionalTest Man page Source code
testFunctionWithGalaxySelectParam Man page Source code
testFunctionWithSelect Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/galaxy.R
R/man.R
R/test_functions.R
R/utils.R
build
build/vignette.rds
inst
inst/Rserve
inst/Rserve/Rserv.conf
inst/doc
inst/doc/RGalaxy-vignette.R
inst/doc/RGalaxy-vignette.Rmd
inst/doc/RGalaxy-vignette.html
inst/extdata
inst/extdata/a.tsv
inst/extdata/b.tsv
inst/extdata/foo.Rd
inst/extdata/functionToGalaxify2.R
inst/extdata/functionToGalaxify2.Rd
inst/functionalTests
inst/functionalTests/addTwoNumbersWithTest
inst/functionalTests/addTwoNumbersWithTest/sum
inst/functionalTests/functionToGalaxify
inst/functionalTests/functionToGalaxify/inputfile1
inst/functionalTests/functionToGalaxify/inputfile2
inst/functionalTests/functionToGalaxify/outputfile1
inst/functionalTests/functionToGalaxify/outputfile2
inst/functionalTests/probeLookup
inst/functionalTests/probeLookup/outputfile
inst/galaxy
inst/galaxy/datatypes_conf.xml
inst/galaxy/tool_conf.xml
inst/samplePkg
inst/samplePkg/DESCRIPTION
inst/samplePkg/NAMESPACE
inst/samplePkg/R
inst/samplePkg/R/functions.R
inst/samplePkg/man
inst/samplePkg/man/testCheckboxes.Rd
inst/samplePkg/man/testMissingParams.Rd
inst/samplePkg/man/testRequiredOption.Rd
inst/template
inst/template/template.R
inst/unitTests
inst/unitTests/test_galaxy.R
man
man/GalaxyClasses.Rd
man/GalaxyConfig-class.Rd
man/GalaxyInputFile-class.Rd
man/GalaxyOutput-class.Rd
man/RserveConnection-class.Rd
man/addTwoNumbers.Rd
man/addTwoNumbersWithTest.Rd
man/anotherTestFunction.Rd
man/foo.Rd
man/functionToGalaxify.Rd
man/galaxy.Rd
man/getFriendlyName.Rd
man/probeLookup.Rd
man/runFunctionalTest.Rd
man/testFunctionWithGalaxySelectParam.Rd
man/testFunctionWithSelect.Rd
man/utilities.Rd
tests
tests/runTests.R
vignettes
vignettes/RGalaxy-vignette.Rmd
vignettes/RGalaxy.css
vignettes/addTwoNumbers.jpg
vignettes/addTwoNumbers_result.jpg
vignettes/tools
vignettes/tools/mytool
vignettes/tools/mytool/addTwoNumbers.R
vignettes/tools/mytool/addTwoNumbers.xml
vignettes/tools/mytool/functionToGalaxify.R
vignettes/tools/mytool/functionToGalaxify.xml
RGalaxy documentation built on May 20, 2017, 9:44 p.m.

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