annotate CAMERA.r @ 4:87570e9b71f5 draft

planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b

#!/usr/bin/env Rscript
# CAMERA.r version="2.2.1"



# ----- PACKAGE -----
cat("\tPACKAGE INFO\n")

setRepositories(graphics=F, ind=31)

#pkgs=c("xcms","batch")
pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","igraph","CAMERA","multtest","batch")
for(p in pkgs) {
  suppressPackageStartupMessages(suppressWarnings(library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
  cat(p,"\t",as.character(packageVersion(p)),"\n",sep="")
}
source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }

cat("\n\n"); 



# ----- ARGUMENTS -----
cat("\tARGUMENTS INFO\n")

listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')

cat("\n\n");


# ----- PROCESSING INFILE -----
cat("\tINFILE PROCESSING INFO\n")

#image is an .RData file necessary to use xset variable given by previous tools
if (!is.null(listArguments[["image"]])){
  load(listArguments[["image"]]); listArguments[["image"]]=NULL
}

if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) {
  load(listArguments[["image_pos"]])
  xaP=xa
  listOFlistArgumentsP=listOFlistArguments
  if (exists("xsAnnotate_object")) xaP=xsAnnotate_object
  
  diffrepP=NULL
  if (exists("diffrep")) diffrepP=diffrep

  load(listArguments[["image_neg"]])
  xaN=xa
  listOFlistArgumentsN=listOFlistArguments
  if (exists("xsAnnotate_object")) xaN=xsAnnotate_object

  diffrepN=NULL
  if (exists("diffrep")) diffrepN=diffrep
}


cat("\n\n")


# ----- ARGUMENTS PROCESSING -----
cat("\tARGUMENTS PROCESSING INFO\n")

# Save arguments to generate a report
if (!exists("listOFlistArguments")) listOFlistArguments=list()
listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments


#saving the commun parameters
thefunction = listArguments[["xfunction"]]
listArguments[["xfunction"]]=NULL #delete from the list of arguments

xsetRdataOutput = paste(thefunction,"RData",sep=".")
if (!is.null(listArguments[["xsetRdataOutput"]])){
  xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
}

rplotspdf = "Rplots.pdf"
if (!is.null(listArguments[["rplotspdf"]])){
  rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
}

dataMatrixOutput = "dataMatrix.tsv"
if (!is.null(listArguments[["dataMatrixOutput"]])){
  dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL
}

variableMetadataOutput = "variableMetadata.tsv"
if (!is.null(listArguments[["variableMetadataOutput"]])){
  variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
}

if (!is.null(listArguments[["new_file_path"]])){
  new_file_path = listArguments[["new_file_path"]]; listArguments[["new_file_path"]]=NULL
}

#Import the different functions
source_local("lib.r")

#necessary to unzip .zip file uploaded to Galaxy
#thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories


if (!is.null(listArguments[["zipfile"]])){
  zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
}

# We unzip automatically the chromatograms from the zip files.
if (thefunction %in% c("annotatediff"))  {
  if(exists("zipfile") && (zipfile!="")) {
    if(!file.exists(zipfile)){
      error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
      print(error_message)
      stop(error_message)
    }

    #unzip
    suppressWarnings(unzip(zipfile, unzip="unzip"))

    #get the directory name
    filesInZip=unzip(zipfile, list=T); 
    directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
    directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
    directory = "."
    if (length(directories) == 1) directory = directories
    
    cat("files_root_directory\t",directory,"\n")
  }
}



#addition of xset object to the list of arguments in the first position
if (exists("xset") != 0){
  listArguments=append(list(xset), listArguments)
}

cat("\n\n")




# ----- PROCESSING INFO -----
cat("\tMAIN PROCESSING INFO\n")

#change the default display settings
pdf(file=rplotspdf, width=16, height=12)


if (thefunction %in% c("annotatediff")) {
  results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput,new_file_path=new_file_path)
  xa=results_list[["xa"]]
  diffrep=results_list[["diffrep"]]
  variableMetadata=results_list[["variableMetadata"]]

  cat("\n\n")
  cat("\tXSET OBJECT INFO\n")
  print(xa)
}

if (thefunction %in% c("combinexsAnnos")) {
  cAnnot=combinexsAnnos_function(xaP=xaP,xaN=xaN,listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN,diffrepP=diffrepP,diffrepN=diffrepN,convert_param=listArguments[["convert_param"]],pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],variableMetadataOutput=variableMetadataOutput)
}

dev.off()


#saving R data in .Rdata file to save the variables used in the present tool
objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile")
save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)

cat("\n\n")

cat("\tDONE\n")