comparison AffyQCnormalization.R @ 8:7f74250a083d draft

planemo upload

7:f3c021bdc000

library(Biobase)
library(GEOquery)
library(GEOmetadb)
library(limma)
library(jsonlite)
library(affy)
library(affyPLM)
library(dplyr)

cargs<-commandArgs()
cargs<-cargs[(which(cargs=="--args")+1):length(cargs)]
nbargs=length(cargs)
celList=vector()
celFileNameList=vector()
for (i in seq(1,nbargs-7,2))
{
	celList=c(celList,cargs[[i]])
	celFileNameList=c(celFileNameList,cargs[[i+1]])
}


normalization=cargs[[nbargs-6]]
result_export_eset=cargs[[nbargs-5]]
result=cargs[[nbargs-4]]
result.path=cargs[[nbargs-3]]
result.template=cargs[[nbargs-2]]

dir.create(result.path, showWarnings = TRUE, recursive = TRUE)
for(i in 1:length(celList))
{
	file.copy(celList[i],paste0("./",celFileNameList[i]))

#}

dev.off()
htmlfile=gsub(x=htmlfile,pattern = "###PLOTMANORM###",replacement = plotMAnorm, fixed = TRUE)
file.copy(plotMAnorm,result.path)
#write.table(tolower(c(condition1Name,condition2Name)),quote = FALSE,col.names = FALSE, row.names=FALSE,file=result_export_conditions)
#saveConditions=c(condition1Name,condition2Name)
save(eset,file=result_export_eset)
write(htmlfile,result)

#l=list()
#for(i in 1:length(esets))
#{
#	l[[paste("study",i,sep="")]]<-res[[i]]
#}
#l[["Meta"]]=res[[length(res)-1]]
#showVenn(res,file.path(temp.files.path,"venn.png"))
#writeLines(c("<h2>Venn diagram</h2>"),file.conn)
#writeLines(c("<img src='venn.png'><br/><br/>"),file.conn)
#writeLines(c("</body></html>"),file.conn)
#close(file.conn)

8:7f74250a083d

#!/usr/bin/env Rscript
# setup R error handling to go to stderr
options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )

# we need that to not crash galaxy with an UTF8 error on German LC settings.
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

library("optparse")

##### Read options
option_list=list(
		make_option("--input",type="character",default="NULL",help="rdata object containing eset object"),
		make_option("--normalization",type="character",default=NULL,help="normalization method"),
		make_option("--nbresult",type="character",default=NULL,help="number of result displayed results"),
		make_option("--rdataoutput",type="character",default="NULL",help="output rdata object containing eset object"),
		make_option("--htmloutput",type="character",default=NULL,help="Output html report"),
		make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"),
		make_option("--htmltemplate",type="character",default=NULL,help="html template)")
);

opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);

if(is.null(opt$input)){
	print_help(opt_parser)
	stop("input required.", call.=FALSE)
}

#loading libraries

suppressPackageStartupMessages(require(Biobase))
suppressPackageStartupMessages(require(GEOquery))
suppressPackageStartupMessages(require(GEOmetadb))
suppressPackageStartupMessages(require(limma))
suppressPackageStartupMessages(require(jsonlite))
suppressPackageStartupMessages(require(affy))
suppressPackageStartupMessages(library(affyPLM))
suppressPackageStartupMessages(require(dplyr))

listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) )

celList=vector()
celFileNameList=vector()

for (i in 1:length(listInput))
{
	inputFileInfo <- unlist( strsplit( listInput[i], ';' ) )
	celList=c(celList,inputFileInfo[1])
	celFileNameList=c(celFileNameList,inputFileInfo[2])
}


normalization=opt$normalization
result_export_eset=opt$rdataoutput
result=opt$htmloutput
result.path=opt$htmloutputpath
result.template=opt$htmltemplate

dir.create(result.path, showWarnings = TRUE, recursive = TRUE)
for(i in 1:length(celList))
{
	file.copy(celList[i],paste0("./",celFileNameList[i]))

#}

dev.off()
htmlfile=gsub(x=htmlfile,pattern = "###PLOTMANORM###",replacement = plotMAnorm, fixed = TRUE)
file.copy(plotMAnorm,result.path)
save(eset,file=result_export_eset)
write(htmlfile,result)