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annotate NmrBucketing_wrapper.R @ 0:a99a6026c972 draft

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
author marie-tremblay-metatoul
date Fri, 08 Apr 2016 10:56:14 -0400
parents
children d61f6ceef5d6
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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1 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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2
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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3 ## 070115_NmrBucketing2galaxy_v1.R
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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4 ## Marie Tremblay-Franco
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5 ## MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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6 ## www.metabohub.fr/en
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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7 ## marie.tremblay-franco@toulouse.inra.fr
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8
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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9 runExampleL <- FALSE
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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10
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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11 if(runExampleL) {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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12 ##------------------------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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13 ## Example of arguments
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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14 ##------------------------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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15 argLs <- list(StudyDir = "Tlse_BPASourisCerveau",
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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16 upper = "10.0",
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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17 lower = "0.50",
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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18 bucket.width = "0.01",
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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19 exclusion = "TRUE",
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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20 exclusion.zone = list(c(6.5,4.5)),
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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21 graph="Overlay")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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22
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23 argLs <- c(argLs,
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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24 list(dataMatrixOut = paste(directory,"_NmrBucketing_dataMatrix.tsv",sep=""),
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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25 sampleMetadataOut = paste(directory,"_NmrBucketing_sampleMetadata.tsv",sep=""),
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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26 variableMetadataOut = paste(directory,"_NmrBucketing_variableMetadata.tsv",sep=""),
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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27 graphOut = paste(directory,"_NmrBucketing_graph.pdf",sep=""),
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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28 logOut = paste(directory,"_NmrBucketing_log.txt",sep="")))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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29 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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31 ##------------------------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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32 ## Options
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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33 ##------------------------------
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34 strAsFacL <- options()$stringsAsFactors
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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35 options(stringsAsFactors = FALSE)
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36
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38 ##------------------------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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39 ## Libraries laoding
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40 ##------------------------------
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41 # For parseCommandArgs function
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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42 library(batch)
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43 # For cumtrapz function
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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44 library(pracma)
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45
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46 # R script call
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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47 source_local <- function(fname)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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48 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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49 argv <- commandArgs(trailingOnly = FALSE)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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50 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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51 source(paste(base_dir, fname, sep="/"))
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52 }
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53 #Import the different functions
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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54 source_local("NmrBucketing_script.R")
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55
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56 ##------------------------------
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57 ## Errors ?????????????????????
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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58 ##------------------------------
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59
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60
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61 ##------------------------------
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62 ## Constants
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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63 ##------------------------------
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64 topEnvC <- environment()
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65 flagC <- "\n"
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66
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67
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68 ##------------------------------
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69 ## Script
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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70 ##------------------------------
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71 if(!runExampleL)
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72 argLs <- parseCommandArgs(evaluate=FALSE)
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73
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74 ## sink(argLs[["logOut"]])
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75
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76
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77 ## Parameters Loading
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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78 ##-------------------
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79 # Inputs
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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80 if (!is.null(argLs[["zipfile"]])){
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81 zipfile= argLs[["zipfile"]]
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82 directory=unzip(zipfile, list=F)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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83 directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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84 } else if (!is.null(argLs[["library"]])){
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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85 directory=argLs[["library"]]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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86 if(!file.exists(directory)){
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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87 error_message=paste("Cannot access the directory :",directory,".Please verify if the directory exists or not.")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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88 print(error_message)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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89 stop(error_message)
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90 }
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91 }
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92
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93 leftBorder <- argLs[["left_border"]]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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94 rightBorder <- argLs[["right_border"]]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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95 bucketSize <- argLs[["bucket_width"]]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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96 exclusionZones <- argLs[["zone_exclusion_choices.choice"]]
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97
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98 exclusionZonesBorders <- NULL
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99 if (!is.null(argLs$zone_exclusion_left))
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marie-tremblay-metatoul
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100 {
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101 for(i in which(names(argLs)=="zone_exclusion_left"))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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102 {
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marie-tremblay-metatoul
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103 exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]])))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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104 }
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105 }
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106
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107 graphique <- argLs[["graphType"]]
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108
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109 # Outputs
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110 nomGraphe <- argLs[["graphOut"]]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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111 dataMatrixOut <- argLs[["dataMatrixOut"]]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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112 sampleMetadataOut <- argLs[["sampleOut"]]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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113 variableMetadataOut <- argLs[["variableOut"]]
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marie-tremblay-metatoul
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114 log <- argLs[["logOut"]]
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115
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116 ## Checking arguments
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117 ##-------------------
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118 error.stock <- "\n"
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119
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120 if(length(error.stock) > 1)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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121 stop(error.stock)
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122
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123
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124 ## Computation
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125 ##------------
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126 outputs <- NmrBucketing(directory,leftBorder,rightBorder,bucketSize,exclusionZones,exclusionZonesBorders,graphique,nomGraphe,log)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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127 data_bucket <- outputs[[1]]
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128 data_sample <- outputs[[2]]
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129 data_variable <- outputs[[3]]
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130
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131 ## Saving
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132 ##-------
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133 # Data
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134 data_bucket <- cbind(rownames(data_bucket),data_bucket)
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135 colnames(data_bucket) <- c("Bucket",colnames(data_bucket)[-1])
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136 write.table(data_bucket,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\t")
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137 # Sample
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138 data_sample <- cbind(rownames(data_sample),data_sample)
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139 colnames(data_sample) <- c("Sample",colnames(data_sample)[-1])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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140 write.table(data_sample,file=argLs$sampleOut,quote=FALSE,row.names=FALSE,sep="\t")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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141 # Variable
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142 data_variable <- cbind(rownames(data_variable),data_variable)
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143 colnames(data_variable) <- c("Bucket",colnames(data_variable)[-1])
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144 write.table(data_variable,file=argLs$variableOut,quote=FALSE,row.names=FALSE,sep="\t")
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145
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146
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147 ## Ending
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148 ##---------------------
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149
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150 cat("\nEnd of 'NMR bucketing' Galaxy module call: ", as.character(Sys.time()), sep = "")
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151
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152 ## sink(NULL)
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153
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154 options(stringsAsFactors = strAsFacL)
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155
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156 rm(list = ls())