Mercurial > repos > lecorguille > xcms_retcor
annotate xcms_retcor.r @ 25:aa252eec9229 draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author | workflow4metabolomics |
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date | Wed, 07 Apr 2021 12:08:25 +0000 |
parents | faf4a6b67304 |
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rev | line source |
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10
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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1 #!/usr/bin/env Rscript |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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2 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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3 # ----- LOG FILE ----- |
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aa252eec9229
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
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4 log_file <- file("log.txt", open = "wt") |
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8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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5 sink(log_file) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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6 sink(log_file, type = "output") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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7 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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8 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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9 # ----- PACKAGE ----- |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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10 cat("\tSESSION INFO\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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11 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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12 #Import the different functions |
25
aa252eec9229
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
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13 source_local <- function(fname) { |
aa252eec9229
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
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14 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/")) |
aa252eec9229
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
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15 } |
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8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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16 source_local("lib.r") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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17 |
25
aa252eec9229
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
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18 pkgs <- c("xcms", "batch", "RColorBrewer") |
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8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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19 loadAndDisplayPackages(pkgs) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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20 cat("\n\n"); |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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21 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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22 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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23 # ----- ARGUMENTS ----- |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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24 cat("\tARGUMENTS INFO\n") |
25
aa252eec9229
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
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25 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects |
aa252eec9229
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
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26 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t") |
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8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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27 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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28 cat("\n\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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29 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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30 # ----- PROCESSING INFILE ----- |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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31 cat("\tARGUMENTS PROCESSING INFO\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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32 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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33 #saving the specific parameters |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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34 method <- args$method |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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35 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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36 cat("\n\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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37 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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38 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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39 # ----- ARGUMENTS PROCESSING ----- |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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40 cat("\tINFILE PROCESSING INFO\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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41 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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42 #image is an .RData file necessary to use xset variable given by previous tools |
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aa252eec9229
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
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43 load(args$image); args$image <- NULL |
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8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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44 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.*") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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45 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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46 # Handle infiles |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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47 if (!exists("singlefile")) singlefile <- NULL |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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48 if (!exists("zipfile")) zipfile <- NULL |
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aa252eec9229
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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49 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) |
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8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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50 zipfile <- rawFilePath$zipfile |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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51 singlefile <- rawFilePath$singlefile |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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52 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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53 cat("\n\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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54 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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55 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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56 # ----- MAIN PROCESSING INFO ----- |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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57 cat("\tMAIN PROCESSING INFO\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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58 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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59 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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60 cat("\t\tCOMPUTE\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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61 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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62 cat("\t\t\tAlignment/Retention Time correction\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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63 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ... |
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aa252eec9229
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
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64 args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))] |
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8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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65 |
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aa252eec9229
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents:
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66 adjustRtimeParam <- do.call(paste0(method, "Param"), args) |
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8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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67 print(adjustRtimeParam) |
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faf4a6b67304
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
workflow4metabolomics
parents:
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68 |
faf4a6b67304
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
workflow4metabolomics
parents:
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69 if (hasAdjustedRtime(xdata)) { |
faf4a6b67304
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
workflow4metabolomics
parents:
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70 cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment") |
faf4a6b67304
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
workflow4metabolomics
parents:
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71 cat("Replace raw retention times with adjusted retention times.\n") |
faf4a6b67304
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
workflow4metabolomics
parents:
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72 xdata <- applyAdjustedRtime(xdata) |
faf4a6b67304
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
workflow4metabolomics
parents:
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73 } |
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aa252eec9229
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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74 xdata <- adjustRtime(xdata, param = adjustRtimeParam) |
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8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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75 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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76 cat("\n\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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77 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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78 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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79 # -- TIC -- |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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80 cat("\t\tDRAW GRAPHICS\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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81 getPlotAdjustedRtime(xdata) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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82 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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83 cat("\n\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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84 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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85 # ----- EXPORT ----- |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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86 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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87 cat("\tXCMSnExp OBJECT INFO\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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88 print(xdata) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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89 cat("\n\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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90 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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91 cat("\txcmsSet OBJECT INFO\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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92 # Get the legacy xcmsSet object |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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93 xset <- getxcmsSetObject(xdata) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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94 print(xset) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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95 cat("\n\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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96 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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97 #saving R data in .Rdata file to save the variables used in the present tool |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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98 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") |
aa252eec9229
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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99 save(list = objects2save[objects2save %in% ls()], file = "retcor.RData") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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100 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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101 cat("\n\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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102 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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103 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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104 cat("\tDONE\n") |