Mercurial > repos > lecorguille > xcms_merge
comparison xcms_merge.r @ 14:5bd125a3f3b0 draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author | workflow4metabolomics |
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date | Wed, 07 Apr 2021 12:07:13 +0000 |
parents | 772290533d6e |
children | 58b5a4b6e1da |
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13:39797c768bba | 14:5bd125a3f3b0 |
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1 #!/usr/bin/env Rscript | 1 #!/usr/bin/env Rscript |
2 | 2 |
3 #Import the different functions | 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="/")) } | 4 source_local <- function(fname) { |
5 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/")) | |
6 } | |
5 source_local("lib.r") | 7 source_local("lib.r") |
6 | 8 |
7 pkgs <- c("xcms","batch") | 9 pkgs <- c("xcms", "batch") |
8 loadAndDisplayPackages(pkgs) | 10 loadAndDisplayPackages(pkgs) |
9 cat("\n\n"); | 11 cat("\n\n"); |
10 | 12 |
11 args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects | 13 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects |
12 | 14 |
13 | 15 |
14 cat("\tXSET MERGING...\n") | 16 cat("\tXSET MERGING...\n") |
15 | 17 |
16 mergeXDataReturn <- mergeXData(args) | 18 mergeXDataReturn <- mergeXData(args) |
20 sampleNamesList <- mergeXDataReturn$sampleNamesList | 22 sampleNamesList <- mergeXDataReturn$sampleNamesList |
21 chromTIC <- mergeXDataReturn$chromTIC | 23 chromTIC <- mergeXDataReturn$chromTIC |
22 chromBPI <- mergeXDataReturn$chromBPI | 24 chromBPI <- mergeXDataReturn$chromBPI |
23 | 25 |
24 # Create a sampleMetada file | 26 # Create a sampleMetada file |
25 sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv") | 27 sampleNamesList <- getSampleMetadata(xdata = xdata, sampleMetadataOutput = "sampleMetadata.tsv") |
26 | 28 |
27 cat("\n\n") | 29 cat("\n\n") |
28 | 30 |
29 cat("\tXCMSnExp OBJECT INFO\n") | 31 cat("\tXCMSnExp OBJECT INFO\n") |
30 print(pData(xdata)) | 32 print(pData(xdata)) |
39 cat("\n\n") | 41 cat("\n\n") |
40 | 42 |
41 cat("\tSAVE RData\n") | 43 cat("\tSAVE RData\n") |
42 #saving R data in .Rdata file to save the variables used in the present tool | 44 #saving R data in .Rdata file to save the variables used in the present tool |
43 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI") | 45 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI") |
44 save(list=objects2save[objects2save %in% ls()], file="merged.RData") | 46 save(list = objects2save[objects2save %in% ls()], file = "merged.RData") |