#install.packages("optparse")
library('rmarkdown')
library("optparse")
#minor comment
option_list = list(
make_option(c("-d", "--dir"), type="character", default=NULL,
help="Working directory that contains all parameter file", metavar="character"),
make_option(c("-p", "--parameterFile"), type="character", default="parameters.table.txt",
help="The name of the parameter file that contains all the info", metavar="character"),
make_option(c("-o", "--outputDir"), type="character", default="Working directory",
help="output directory were the report will end up ", metavar="character")
);
opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);
if (is.null(opt$dir)){
print_help(opt_parser)
stop("A working directory has to be called (--dir) \n", call.=FALSE)
}
parametersTable = read.table("parameters.table.txt", sep = "\t", header = TRUE)
workingDirectory = as.character(parametersTable$Value[which(parametersTable$Key == "ProjectWD")])
RfunctionsDirectory = as.character(parametersTable$Value[which(parametersTable$Key == "RscriptsDir")])
resultsDir = paste(workingDirectory, "RSeQC", sep = "/")
metaDataTableTxt= "metaData.table.txt"
sampleNameColumn= "sampleName"
metaDataTableRmd = 'metadata.table.Rmd'
paramsList = list(
workingDirectory = workingDirectory,
RfunctionsDirectory = RfunctionsDirectory,
resultsDir = resultsDir,
metaDataTableTxt = metaDataTableTxt,
sampleNameColumn = sampleNameColumn,
metaDataTableRmd = metaDataTableRmd)
rmarkdown::render(paste(RfunctionsDirectory,'RSeQCdocument.Rmd', sep = "/"),
output_dir = workingDirectory,
params = paramsList
)
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