## ----setup, echo=FALSE--------------------------------------------------- options(width = 75) options(useFancyQuotes=FALSE) ## ----hook-printfun, echo=FALSE------------------------------------------- library(knitr) library(formatR) knit_hooks$set(printfun = function(before, options, envir) { if (before) return() txt = capture.output(dump(options$printfun, '', envir = envir)) ## reformat if tidy=TRUE if (options$tidy) txt = tidy.source(text=txt, output=FALSE, width.cutoff=30L, keep.comment=TRUE, keep.blank.line=FALSE)$text.tidy paste(c('\n```r\n', txt, '\n```\n'), collapse="\n") }) ## ----hook-printmanpage, echo=FALSE--------------------------------------- knit_hooks$set(printmanpage = function(before, options, envir) { if (before) return() manpage <- file.path("..", "man", sprintf("%s.Rd", options$printmanpage)) lines <- readLines(manpage) ret <- "\n" for (line in lines) { ret <- paste(ret, "\t", line, "\n", sep="") } ret }) ## ----library_RGalaxy_fake, eval=FALSE------------------------------------ # library(RGalaxy) ## ----library_RGalaxy_real, echo=FALSE, results="hide"-------------------- suppressPackageStartupMessages(library(RGalaxy)) ## ----addTwoNumbers, printfun='addTwoNumbers', echo=FALSE, tidy=FALSE----- #source code goes here ## ----run_addTwoNumbers--------------------------------------------------- t <- tempfile() addTwoNumbers(2, 2, t) readLines(t, warn=FALSE) ## ----addTwoNumbers_man, printmanpage='addTwoNumbers', echo=FALSE, tidy=FALSE---- #source code goes here ## ----galaxyHomeSetup, echo=FALSE, results="hide"------------------------- if (!exists("galaxyHome")) galaxyHome <- getwd() toolDir <- "RGalaxy_test_tool" funcName <- "functionToGalaxify" file.copy(system.file("galaxy", "tool_conf.xml", package="RGalaxy"), file.path(galaxyHome, "tool_conf.xml"), overwrite=FALSE) if(!file.exists("test-data")) dir.create("test-data", ) ## ----run_galaxy, tidy=FALSE---------------------------------------------- galaxy("addTwoNumbers", galaxyConfig= GalaxyConfig(galaxyHome, "mytool", "Test Section", "testSectionId") ) ## ----addTwoNumbersWithTest, printfun='addTwoNumbersWithTest', echo=FALSE, tidy=FALSE---- #source code goes here ## ----runFunctionalTest--------------------------------------------------- runFunctionalTest(addTwoNumbersWithTest) ## ----withRserve, tidy=FALSE, eval=FALSE---------------------------------- # galaxy("addTwoNumbersWithTest", # galaxyConfig= # GalaxyConfig(galaxyHome, "mytool", "Test Section", # "testSectionId"), # RserveConnection=RserveConnection() # ) ## ----install_RSclient, eval=FALSE---------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("RSclient", site_repository="http://www.rforge.net") ## ----RserveConnection---------------------------------------------------- RserveConnection(host="mymachine", port=2012L) ## ----probeLookup, printfun='probeLookup', echo=FALSE, tidy=FALSE--------- #source code goes here ## ----test_probeLookup---------------------------------------------------- runFunctionalTest(probeLookup)