Mercurial > repos > lecorguille > xcms_group
annotate xcms.r @ 7:5c37c1d214a2 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2aff6f6ced8185ed35371d7ad637e5a44f8a250c
author | lecorguille |
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date | Mon, 04 Jul 2016 11:55:02 -0400 |
parents | 2db1d1d0f131 |
children | 2c1d7df89cf6 |
rev | line source |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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1 #!/usr/bin/env Rscript |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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2 # xcms.r version="2.2.0" |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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3 #Authors ABIMS TEAM |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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4 #BPC Addition from Y.guitton |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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5 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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6 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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7 # ----- LOG FILE ----- |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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8 log_file=file("log.txt", open = "wt") |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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9 sink(log_file) |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
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10 sink(log_file, type = "output") |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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11 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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12 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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13 # ----- PACKAGE ----- |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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14 cat("\tPACKAGE INFO\n") |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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15 #pkgs=c("xcms","batch") |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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16 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch") |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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changeset
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17 for(pkg in pkgs) { |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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18 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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19 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="") |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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20 } |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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21 source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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22 cat("\n\n"); |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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23 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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24 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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25 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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26 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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27 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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changeset
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28 # ----- ARGUMENTS ----- |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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29 cat("\tARGUMENTS INFO\n") |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
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30 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
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31 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t') |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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32 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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changeset
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33 cat("\n\n"); |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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34 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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35 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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36 # ----- ARGUMENTS PROCESSING ----- |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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37 cat("\tINFILE PROCESSING INFO\n") |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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38 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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39 #image is an .RData file necessary to use xset variable given by previous tools |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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40 if (!is.null(listArguments[["image"]])){ |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
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41 load(listArguments[["image"]]); listArguments[["image"]]=NULL |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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42 } |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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43 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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44 #Import the different functions |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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45 source_local("lib.r") |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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46 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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47 cat("\n\n") |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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48 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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49 #Import the different functions |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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50 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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51 # ----- PROCESSING INFILE ----- |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff
changeset
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52 cat("\tARGUMENTS PROCESSING INFO\n") |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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53 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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54 # Save arguments to generate a report |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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55 if (!exists("listOFlistArguments")) listOFlistArguments=list() |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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56 listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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57 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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58 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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59 #saving the commun parameters |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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60 thefunction = listArguments[["xfunction"]]; listArguments[["xfunction"]]=NULL #delete from the list of arguments |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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61 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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62 xsetRdataOutput = paste(thefunction,"RData",sep=".") |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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63 if (!is.null(listArguments[["xsetRdataOutput"]])){ |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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64 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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65 } |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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66 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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67 rplotspdf = "Rplots.pdf" |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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68 if (!is.null(listArguments[["rplotspdf"]])){ |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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69 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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70 } |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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71 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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72 sampleMetadataOutput = "sampleMetadata.tsv" |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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73 if (!is.null(listArguments[["sampleMetadataOutput"]])){ |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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74 sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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75 } |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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76 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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77 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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78 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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79 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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80 if (thefunction %in% c("xcmsSet","retcor")) { |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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81 ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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82 bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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83 } |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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84 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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85 #necessary to unzip .zip file uploaded to Galaxy |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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86 #thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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87 |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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88 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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89 if (!is.null(listArguments[["zipfile"]])){ |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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90 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
91 } |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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92 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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93 if (!is.null(listArguments[["library"]])){ |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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94 directory=listArguments[["library"]]; listArguments[["library"]]=NULL |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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95 if(!file.exists(directory)){ |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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96 error_message=paste("Cannot access the directory:",directory,". Please verify if the directory exists or not.") |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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97 print(error_message) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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98 stop(error_message) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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99 } |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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100 } |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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101 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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102 # We unzip automatically the chromatograms from the zip files. |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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103 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) { |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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104 if(exists("zipfile") && (zipfile!="")) { |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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105 if(!file.exists(zipfile)){ |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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106 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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107 print(error_message) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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108 stop(error_message) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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109 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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110 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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111 #list all file in the zip file |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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112 #zip_files=unzip(zipfile,list=T)[,"Name"] |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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113 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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114 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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115 #unzip |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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116 suppressWarnings(unzip(zipfile, unzip="unzip")) |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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117 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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118 #get the directory name |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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119 filesInZip=unzip(zipfile, list=T); |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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120 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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121 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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122 directory = "." |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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123 if (length(directories) == 1) directory = directories |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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124 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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125 cat("files_root_directory\t",directory,"\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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126 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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127 # |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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128 md5sumList=list("origin"=getMd5sum(directory)) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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129 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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130 # Check and fix if there are non ASCII characters. If so, they will be removed from the *mzXML mzML files. |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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131 # Remove because can create issue with some clean files |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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132 #@TODO: fix me |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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133 #if (deleteXmlBadCharacters(directory)) { |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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134 # md5sumList=list("removalBadCharacters"=getMd5sum(directory)) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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135 #} |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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136 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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137 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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138 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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139 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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140 #addition of the directory to the list of arguments in the first position |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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141 if (thefunction == "xcmsSet") { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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142 checkXmlStructure(directory) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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143 checkFilesCompatibilityWithXcms(directory) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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144 listArguments=append(directory, listArguments) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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145 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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146 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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147 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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148 #addition of xset object to the list of arguments in the first position |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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149 if (exists("xset")){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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150 listArguments=append(list(xset), listArguments) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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151 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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152 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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153 cat("\n\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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154 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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155 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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156 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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157 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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158 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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159 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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160 # ----- MAIN PROCESSING INFO ----- |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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161 cat("\tMAIN PROCESSING INFO\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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162 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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163 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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164 #Verification of a group step before doing the fillpeaks job. |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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165 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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166 if (thefunction == "fillPeaks") { |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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167 res=try(is.null(groupnames(xset))) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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168 if (class(res) == "try-error"){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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169 error<-geterrmessage() |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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170 write(error, stderr()) |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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171 stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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172 } |
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173 |
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174 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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175 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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176 #change the default display settings |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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177 #dev.new(file="Rplots.pdf", width=16, height=12) |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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178 pdf(file=rplotspdf, width=16, height=12) |
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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179 if (thefunction == "group") { |
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180 par(mfrow=c(2,2)) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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181 } |
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182 #else if (thefunction == "retcor") { |
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183 #try to change the legend display |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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184 # par(xpd=NA) |
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185 # par(xpd=T, mar=par()$mar+c(0,0,0,4)) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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186 #} |
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187 |
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188 |
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189 #execution of the function "thefunction" with the parameters given in "listArguments" |
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190 xset = do.call(thefunction, listArguments) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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191 |
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192 |
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193 cat("\n\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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194 |
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195 dev.off() #dev.new(file="Rplots.pdf", width=16, height=12) |
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196 |
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197 if (thefunction == "xcmsSet") { |
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198 |
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199 #transform the files absolute pathways into relative pathways |
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200 xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths) |
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201 |
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202 if(exists("zipfile") && (zipfile!="")) { |
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203 |
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204 #Modify the samples names (erase the path) |
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205 for(i in 1:length(sampnames(xset))){ |
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206 |
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207 sample_name=unlist(strsplit(sampnames(xset)[i], "/")) |
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208 sample_name=sample_name[length(sample_name)] |
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209 sample_name= unlist(strsplit(sample_name,"[.]"))[1] |
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210 sampnames(xset)[i]=sample_name |
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211 |
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212 } |
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213 |
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214 } |
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215 |
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216 } |
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217 |
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218 # -- TIC -- |
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219 if (thefunction == "xcmsSet") { |
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220 sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput) |
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221 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw") |
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222 getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf) |
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223 } else if (thefunction == "retcor") { |
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224 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected") |
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225 getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf) |
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226 } |
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227 |
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228 cat("\n\n") |
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229 |
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230 |
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231 # ----- EXPORT ----- |
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232 |
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233 cat("\tXSET OBJECT INFO\n") |
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234 print(xset) |
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235 #delete the parameters to avoid the passage to the next tool in .RData image |
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236 |
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237 |
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238 #saving R data in .Rdata file to save the variables used in the present tool |
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239 objects2save = c("xset","zipfile","listOFlistArguments","md5sumList","sampleNamesList") |
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240 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput) |
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241 |
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242 cat("\n\n") |
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243 |
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244 |
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245 cat("\tDONE\n") |
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246 |