Mercurial > repos > workflow4metabolomics > camera_combinexsannos
comparison CAMERA_combinexsAnnos.r @ 6:2443150161b4 draft default tip
planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58
| author | workflow4metabolomics |
|---|---|
| date | Mon, 11 Sep 2023 22:41:22 +0000 |
| parents | 4c4945bce185 |
| children |
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| 5:617cf0705775 | 6:2443150161b4 |
|---|---|
| 3 # ----- PACKAGE ----- | 3 # ----- PACKAGE ----- |
| 4 cat("\tSESSION INFO\n") | 4 cat("\tSESSION INFO\n") |
| 5 | 5 |
| 6 #Import the different functions | 6 #Import the different functions |
| 7 source_local <- function(fname) { | 7 source_local <- function(fname) { |
| 8 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/")) | 8 argv <- commandArgs(trailingOnly = FALSE) |
| 9 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
| 10 source(paste(base_dir, fname, sep = "/")) | |
| 9 } | 11 } |
| 10 source_local("lib.r") | 12 source_local("lib.r") |
| 11 | 13 |
| 12 pkgs <- c("CAMERA", "multtest", "batch") | 14 pkgs <- c("CAMERA", "multtest", "batch") |
| 13 loadAndDisplayPackages(pkgs) | 15 loadAndDisplayPackages(pkgs) |
| 14 cat("\n\n"); | 16 cat("\n\n") |
| 15 | 17 |
| 16 # ----- ARGUMENTS ----- | 18 # ----- ARGUMENTS ----- |
| 17 cat("\tARGUMENTS INFO\n") | 19 cat("\tARGUMENTS INFO\n") |
| 18 | 20 |
| 19 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects | 21 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects |
| 20 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t") | 22 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t") |
| 21 | 23 |
| 22 cat("\n\n"); | 24 cat("\n\n") |
| 23 | 25 |
| 24 | 26 |
| 25 # ----- PROCESSING INFILE ----- | 27 # ----- PROCESSING INFILE ----- |
| 26 cat("\tINFILE PROCESSING INFO\n") | 28 cat("\tINFILE PROCESSING INFO\n") |
| 27 | 29 |
| 54 | 56 |
| 55 # ----- PROCESSING INFO ----- | 57 # ----- PROCESSING INFO ----- |
| 56 cat("\tMAIN PROCESSING INFO\n") | 58 cat("\tMAIN PROCESSING INFO\n") |
| 57 | 59 |
| 58 cAnnot <- combinexsAnnos_function( | 60 cAnnot <- combinexsAnnos_function( |
| 59 xaP = xaP, xaN = xaN, | 61 xaP = xaP, xaN = xaN, |
| 60 diffrepP = diffrepP, diffrepN = diffrepN, | 62 diffrepP = diffrepP, diffrepN = diffrepN, |
| 61 pos = args$pos, tol = args$tol, ruleset = args$ruleset, keep_meta = args$keep_meta, | 63 pos = args$pos, tol = args$tol, ruleset = args$ruleset, keep_meta = args$keep_meta, |
| 62 convertRTMinute = args$convertRTMinute, numDigitsMZ = args$numDigitsMZ, numDigitsRT = args$numDigitsRT, | 64 convertRTMinute = args$convertRTMinute, numDigitsMZ = args$numDigitsMZ, numDigitsRT = args$numDigitsRT, |
| 63 variableMetadataOutput = "variableMetadata.tsv" | 65 variableMetadataOutput = "variableMetadata.tsv" |
| 64 ) | 66 ) |
| 65 | 67 |
| 66 # ----- EXPORT ----- | 68 # ----- EXPORT ----- |
| 67 | 69 |
| 68 #saving R data in .Rdata file to save the variables used in the present tool | 70 #saving R data in .Rdata file to save the variables used in the present tool |