Mercurial > repos > lecorguille > xcms_merge

comparison xcms_merge.r @ 9:35b9bb3205d8 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1444e7c7ebd2bb5bdadede71c60a39f560721a98
author lecorguille
date Mon, 05 Mar 2018 09:31:22 -0500
parents 6b5504f877ff
children 47e953d9da82
comparison
equal deleted inserted replaced
8:6b5504f877ff 9:35b9bb3205d8
8 loadAndDisplayPackages(pkgs) 8 loadAndDisplayPackages(pkgs)
9 cat("\n\n"); 9 cat("\n\n");
10 10
11 args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects 11 args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
12 12
13 # Handle infiles
14 if (!exists("singlefile")) singlefile <- NULL
15 if (!exists("zipfile")) zipfile <- NULL
16 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
17 zipfile <- rawFilePath$zipfile
18 singlefile <- rawFilePath$singlefile
19 args <- rawFilePath$args
20 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
21 13
22 cat("\tXSET MERGING...\n") 14 cat("\tXSET MERGING...\n")
23 15
24 for(image in args$images) { 16 for(image in args$images) {
25 load(image) 17 load(image)
18
19 # Handle infiles
20 if (!exists("singlefile")) singlefile <- NULL
21 if (!exists("zipfile")) zipfile <- NULL
22 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
23 zipfile <- rawFilePath$zipfile
24 singlefile <- rawFilePath$singlefile
25 args <- rawFilePath$args
26 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
27
26 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") 28 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
27 cat(sampleNamesList$sampleNamesOrigin,"\n") 29 cat(sampleNamesList$sampleNamesOrigin,"\n")
28 if (!exists("xdata_merged")) { 30 if (!exists("xdata_merged")) {
29 xdata_merged <- xdata 31 xdata_merged <- xdata
30 singlefile_merged <- singlefile 32 singlefile_merged <- singlefile