Mercurial > repos > lecorguille > xcms_merge

comparison xcms_merge.r @ 3:f439ed7a8f03 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author lecorguille
date Tue, 18 Sep 2018 16:09:25 -0400
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children a26679f68d4d
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2:3a5204f14fff 3:f439ed7a8f03
1 #!/usr/bin/env Rscript
2
3 #Import the different functions
4 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
5 source_local("lib.r")
6 source_local("lib-xcms3.x.x.r")
7
8 pkgs <- c("xcms","batch")
9 loadAndDisplayPackages(pkgs)
10 cat("\n\n");
11
12 args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
13
14
15 cat("\tXSET MERGING...\n")
16
17 mergeXDataReturn <- mergeXData(args)
18 xdata <- mergeXDataReturn$xdata
19 singlefile <- mergeXDataReturn$singlefile
20 md5sumList <- mergeXDataReturn$md5sumList
21 sampleNamesList <- mergeXDataReturn$sampleNamesList
22 chromTIC <- mergeXDataReturn$chromTIC
23 chromBPI <- mergeXDataReturn$chromBPI
24
25 # Create a sampleMetada file
26 sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")
27
28 cat("\n\n")
29
30 cat("\tXCMSnExp OBJECT INFO\n")
31 print(pData(xdata))
32 print(xdata)
33 cat("\n\n")
34
35 cat("\txcmsSet OBJECT INFO\n")
36 # Get the legacy xcmsSet object
37 xset <- getxcmsSetObject(xdata)
38 print(xset@phenoData)
39 print(xset)
40 cat("\n\n")
41
42 cat("\tSAVE RData\n")
43 #saving R data in .Rdata file to save the variables used in the present tool
44 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList", "chromTIC", "chromBPI")
45 save(list=objects2save[objects2save %in% ls()], file="merged.RData")