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annotate lib.r @ 27:36b470f3ebcf draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
author lecorguille
date Tue, 24 Oct 2017 11:47:07 -0400
parents dcff3c4a8c80
children a18fc7554c6d
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1 #Authors ABiMS TEAM
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2 #Lib.r for Galaxy Workflow4Metabolomics xcms tools
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3 #
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4 #version 2.4: lecorguille
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5 # add getPeaklistW4M
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6 #version 2.3: yguitton
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7 # correction for empty PDF when only 1 class
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8 #version 2.2
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9 # correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet
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10 # Note if scanrange is used a warning is prompted in R console but do not stop PDF generation
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11 #version 2.1: yguitton
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12 # Modifications made by Guitton Yann
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15 #@author G. Le Corguille
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16 #This function convert if it is required the Retention Time in minutes
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17 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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18 if (convertRTMinute){
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19 #converting the retention times (seconds) into minutes
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20 print("converting the retention times into minutes in the variableMetadata")
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21 variableMetadata[,"rt"]=variableMetadata[,"rt"]/60
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22 variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60
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23 variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60
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24 }
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25 return (variableMetadata)
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26 }
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28 #@author G. Le Corguille
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29 #This function format ions identifiers
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30 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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31 splitDeco = strsplit(as.character(variableMetadata$name),"_")
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32 idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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33 namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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34 variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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35 return(variableMetadata)
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36 }
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38 #@author G. Le Corguille
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39 # value: intensity values to be used into, maxo or intb
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40 getPeaklistW4M <- function(xset, intval="into",convertRTMinute=F,numDigitsMZ=4,numDigitsRT=0,variableMetadataOutput,dataMatrixOutput) {
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41 variableMetadata_dataMatrix = peakTable(xset, method="medret", value=intval)
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42 variableMetadata_dataMatrix = cbind(name=groupnames(xset),variableMetadata_dataMatrix)
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44 dataMatrix = variableMetadata_dataMatrix[,(make.names(colnames(variableMetadata_dataMatrix)) %in% c("name", make.names(sampnames(xset))))]
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46 variableMetadata = variableMetadata_dataMatrix[,!(make.names(colnames(variableMetadata_dataMatrix)) %in% c(make.names(sampnames(xset))))]
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47 variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute)
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48 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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50 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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51 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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52 }
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54 #@author G. Le Corguille
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55 exportTicBpcTabular <- function(dataset, filenameBase, ticORbpc, rt='raw') {
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57 rawORcorrected = ''
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58 title = ''
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59 if (rt=='corrected') {
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60 rawORcorrected = '_corrected'
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61 title = ' corrected by retcor'
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62 }
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64 if (ticORbpc == "TIC") {
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65 section_name = paste0('TIC',rawORcorrected)
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66 title = paste0('Total Ion Current (TIC) chromatogram',title)
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67 description = 'Sum of intensity (Y) of all ions detected at each retention time(X)'
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68 } else if (ticORbpc == "BPC") {
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69 section_name = paste0('BPC',rawORcorrected)
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70 title = paste0('Base Peak Chromatogram (BPC)',title)
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71 description = 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
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72 }
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74 filename=paste0(basename(file_path_sans_ext(filenameBase)),"-",ticORbpc,rawORcorrected,"_mqc.out")
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76 # Headers for MultiQC
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77 cat("# file_format: 'tsv'\n", sep="", file = filename)
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78 cat("# section_name: '",section_name,"'\n", sep="", file = filename, append = T)
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79 cat("# title: '",title,"'\n", sep="", file = filename, append = T)
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80 cat("# description: '",description,"'\n", sep="", file = filename, append = T)
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81 cat("# plot_type: 'linegraph'\n", sep="", file = filename, append = T)
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82 cat("# pconfig:\n", sep="", file = filename, append = T)
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83 cat("# id: '",ticORbpc,rawORcorrected,"_lineplot'\n", sep="", file = filename, append = T)
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84 cat("# ylab: 'Base Peak Intensity'\n", sep="", file = filename, append = T)
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85 cat("# xlab: 'Retention Time'\n", sep="", file = filename, append = T)
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86 cat("Intensity\tRT\n", file = filename, append = T)
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87 write.table(dataset, filename ,row.names = F, col.names = F, sep = "\t", append = T, quote = F)
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88 }
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89
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90 #@author Y. Guitton
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91 getBPC <- function(file,rtcor=NULL, ...) {
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92 object <- xcmsRaw(file)
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93 sel <- profRange(object, ...)
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94 cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
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95 #plotChrom(xcmsRaw(file), base=T)
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96 }
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97
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98 #@author Y. Guitton
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99 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
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100 cat("Creating BIC pdf...\n")
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101
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102 if (is.null(xcmsSet)) {
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103 cat("Enter an xcmsSet \n")
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104 stop()
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105 } else {
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106 files <- filepaths(xcmsSet)
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107 }
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108
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109 phenoDataClass<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
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110
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111 classnames<-vector("list",length(phenoDataClass))
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112 for (i in 1:length(phenoDataClass)){
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113 classnames[[i]]<-which( xcmsSet@phenoData[,1]==phenoDataClass[i])
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114 }
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115
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116 N <- dim(phenoData(xcmsSet))[1]
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117
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118 TIC <- vector("list",N)
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119
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120
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121 for (j in 1:N) {
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122
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123 TIC[[j]] <- getBPC(files[j])
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124 #good for raw
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125 # seems strange for corrected
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126 #errors if scanrange used in xcmsSetgeneration
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127 if (!is.null(xcmsSet) && rt == "corrected")
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128 rtcor <- xcmsSet@rt$corrected[[j]]
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129 else
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130 rtcor <- NULL
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131
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132 TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
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133
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134 exportTicBpcTabular(TIC[[j]], files[j], "BPC", rt=rt)
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135
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136 # TIC[[j]][,1]<-rtcor
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137 }
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138
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139
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140
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141 pdf(pdfname,w=16,h=10)
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142 cols <- rainbow(N)
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143 lty = 1:N
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144 pch = 1:N
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145 #search for max x and max y in BPCs
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146 xlim = range(sapply(TIC, function(x) range(x[,1])))
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147 ylim = range(sapply(TIC, function(x) range(x[,2])))
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148 ylim = c(-ylim[2], ylim[2])
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149
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150
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151 ##plot start
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152
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153 if (length(phenoDataClass)>2){
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154 for (k in 1:(length(phenoDataClass)-1)){
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155 for (l in (k+1):length(phenoDataClass)){
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156 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
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157 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
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158 colvect<-NULL
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159 for (j in 1:length(classnames[[k]])) {
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160 tic <- TIC[[classnames[[k]][j]]]
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161 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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162 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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163 colvect<-append(colvect,cols[classnames[[k]][j]])
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164 }
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165 for (j in 1:length(classnames[[l]])) {
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166 # i=class2names[j]
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167 tic <- TIC[[classnames[[l]][j]]]
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168 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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169 colvect<-append(colvect,cols[classnames[[l]][j]])
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170 }
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171 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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172 }
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173 }
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174 }#end if length >2
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175
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176 if (length(phenoDataClass)==2){
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177 k=1
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178 l=2
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179 colvect<-NULL
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180 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
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181
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182 for (j in 1:length(classnames[[k]])) {
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183
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184 tic <- TIC[[classnames[[k]][j]]]
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185 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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186 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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187 colvect<-append(colvect,cols[classnames[[k]][j]])
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188 }
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189 for (j in 1:length(classnames[[l]])) {
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190 # i=class2names[j]
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191 tic <- TIC[[classnames[[l]][j]]]
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192 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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193 colvect<-append(colvect,cols[classnames[[l]][j]])
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194 }
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195 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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196
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197 }#end length ==2
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198
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199 #case where only one class
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200 if (length(phenoDataClass)==1){
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201 k=1
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202 ylim = range(sapply(TIC, function(x) range(x[,2])))
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203 colvect<-NULL
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204 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
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205
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206 for (j in 1:length(classnames[[k]])) {
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207 tic <- TIC[[classnames[[k]][j]]]
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208 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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209 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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210 colvect<-append(colvect,cols[classnames[[k]][j]])
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211 }
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212
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213 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
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214
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215 }#end length ==1
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216
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217 dev.off() #pdf(pdfname,w=16,h=10)
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218
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219 invisible(TIC)
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220 }
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221
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222
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223
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224 #@author Y. Guitton
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225 getTIC <- function(file,rtcor=NULL) {
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226 object <- xcmsRaw(file)
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227 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object,mzrange=range(object@env$mz))$intensity)
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228 }
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229
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230 ##
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231 ## overlay TIC from all files in current folder or from xcmsSet, create pdf
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232 ##
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233 #@author Y. Guitton
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234 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf",rt=c("raw","corrected")) {
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235 cat("Creating TIC pdf...\n")
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236
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237 if (is.null(xcmsSet)) {
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238 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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239 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
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240 if (is.null(files))
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241 files <- getwd()
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242 info <- file.info(files)
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243 listed <- list.files(files[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
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244 files <- c(files[!info$isdir], listed)
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245 } else {
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246 files <- filepaths(xcmsSet)
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247 }
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248
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249 phenoDataClass<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
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250 classnames<-vector("list",length(phenoDataClass))
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251 for (i in 1:length(phenoDataClass)){
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252 classnames[[i]]<-which( xcmsSet@phenoData[,1]==phenoDataClass[i])
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253 }
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254
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255 N <- length(files)
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256 TIC <- vector("list",N)
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257
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258 for (i in 1:N) {
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259 if (!is.null(xcmsSet) && rt == "corrected")
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260 rtcor <- xcmsSet@rt$corrected[[i]] else
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261 rtcor <- NULL
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262 TIC[[i]] <- getTIC(files[i],rtcor=rtcor)
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263
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264 exportTicBpcTabular(TIC[[i]], files[i], "TIC", rt=rt)
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265 }
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266
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267 pdf(pdfname,w=16,h=10)
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268 cols <- rainbow(N)
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269 lty = 1:N
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270 pch = 1:N
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271 #search for max x and max y in TICs
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272 xlim = range(sapply(TIC, function(x) range(x[,1])))
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273 ylim = range(sapply(TIC, function(x) range(x[,2])))
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274 ylim = c(-ylim[2], ylim[2])
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275
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276
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277 ##plot start
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278 if (length(phenoDataClass)>2){
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279 for (k in 1:(length(phenoDataClass)-1)){
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280 for (l in (k+1):length(phenoDataClass)){
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281 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
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282 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
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283 colvect<-NULL
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284 for (j in 1:length(classnames[[k]])) {
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285 tic <- TIC[[classnames[[k]][j]]]
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286 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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287 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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288 colvect<-append(colvect,cols[classnames[[k]][j]])
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289 }
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290 for (j in 1:length(classnames[[l]])) {
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291 # i=class2names[j]
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292 tic <- TIC[[classnames[[l]][j]]]
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293 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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294 colvect<-append(colvect,cols[classnames[[l]][j]])
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295 }
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296 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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297 }
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298 }
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299 }#end if length >2
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300 if (length(phenoDataClass)==2){
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301 k=1
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302 l=2
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303
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304 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
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305 colvect<-NULL
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306 for (j in 1:length(classnames[[k]])) {
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307 tic <- TIC[[classnames[[k]][j]]]
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308 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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309 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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310 colvect<-append(colvect,cols[classnames[[k]][j]])
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311 }
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312 for (j in 1:length(classnames[[l]])) {
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313 # i=class2names[j]
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314 tic <- TIC[[classnames[[l]][j]]]
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315 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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316 colvect<-append(colvect,cols[classnames[[l]][j]])
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317 }
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318 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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319
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320 }#end length ==2
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321
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322 #case where only one class
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323 if (length(phenoDataClass)==1){
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324 k=1
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325 ylim = range(sapply(TIC, function(x) range(x[,2])))
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326
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327 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
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328 colvect<-NULL
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329 for (j in 1:length(classnames[[k]])) {
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330 tic <- TIC[[classnames[[k]][j]]]
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331 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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332 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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333 colvect<-append(colvect,cols[classnames[[k]][j]])
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334 }
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335
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336 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
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337
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338 }#end length ==1
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339
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340 dev.off() #pdf(pdfname,w=16,h=10)
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341
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342 invisible(TIC)
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343 }
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344
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345
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346
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347 ##
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348 ## Get the polarities from all the samples of a condition
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349 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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350 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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351 getSampleMetadata <- function(xcmsSet=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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352 cat("Creating the sampleMetadata file...\n")
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353
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354 #Create the sampleMetada dataframe
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355 sampleMetadata=xset@phenoData
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356 sampleNamesOrigin=rownames(sampleMetadata)
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357 sampleNamesMakeNames=make.names(sampleNamesOrigin)
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358
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359 if (any(duplicated(sampleNamesMakeNames))) {
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360 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
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361 for (sampleName in sampleNamesOrigin) {
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362 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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363 }
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364 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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365 }
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366
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367 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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368 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
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369 for (sampleName in sampleNamesOrigin) {
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370 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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371 }
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372 }
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373
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374 sampleMetadata$sampleMetadata=sampleNamesMakeNames
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375 sampleMetadata=cbind(sampleMetadata["sampleMetadata"],sampleMetadata["class"]) #Reorder columns
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376 rownames(sampleMetadata)=NULL
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377
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378 #Create a list of files name in the current directory
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379 list_files=xset@filepaths
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380 #For each sample file, the following actions are done
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381 for (file in list_files){
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382 #Check if the file is in the CDF format
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383 if (!mzR:::netCDFIsFile(file)){
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384
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385 # If the column isn't exist, with add one filled with NA
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386 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity=NA
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387
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388 #Create a simple xcmsRaw object for each sample
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389 xcmsRaw=xcmsRaw(file)
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390 #Extract the polarity (a list of polarities)
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391 polarity=xcmsRaw@polarity
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392 #Verify if all the scans have the same polarity
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393 uniq_list=unique(polarity)
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394 if (length(uniq_list)>1){
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395 polarity="mixed"
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396 } else {
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397 polarity=as.character(uniq_list)
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398 }
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399 #Transforms the character to obtain only the sample name
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400 filename=basename(file)
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401 library(tools)
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402 samplename=file_path_sans_ext(filename)
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403
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404 #Set the polarity attribute
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405 sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity
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406
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407 #Delete xcmsRaw object because it creates a bug for the fillpeaks step
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408 rm(xcmsRaw)
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409 }
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410
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411 }
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412
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413 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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414
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415 return(list("sampleNamesOrigin"=sampleNamesOrigin,"sampleNamesMakeNames"=sampleNamesMakeNames))
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416
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417 }
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418
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419
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420 ##
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421 ## This function check if xcms will found all the files
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422 ##
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423 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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424 checkFilesCompatibilityWithXcms <- function(directory) {
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425 cat("Checking files filenames compatibilities with xmcs...\n")
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426 # WHAT XCMS WILL FIND
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427 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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428 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
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429 info <- file.info(directory)
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430 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
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431 files <- c(directory[!info$isdir], listed)
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432 files_abs <- file.path(getwd(), files)
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433 exists <- file.exists(files_abs)
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434 files[exists] <- files_abs[exists]
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435 files[exists] <- sub("//","/",files[exists])
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436
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437 # WHAT IS ON THE FILESYSTEM
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438 filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T)
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439 filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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440
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441 # COMPARISON
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442 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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443 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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444 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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445 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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446 }
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447 }
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448
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449
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450
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451 ##
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452 ## This function check if XML contains special caracters. It also checks integrity and completness.
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453 ##
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454 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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455 checkXmlStructure <- function (directory) {
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456 cat("Checking XML structure...\n")
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457
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458 cmd=paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
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459 capture=system(cmd,intern=TRUE)
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460
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461 if (length(capture)>0){
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462 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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463 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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464 write(capture, stderr())
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465 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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466 }
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467
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468 }
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469
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470
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471 ##
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472 ## This function check if XML contain special characters
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473 ##
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474 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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475 deleteXmlBadCharacters<- function (directory) {
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476 cat("Checking Non ASCII characters in the XML...\n")
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477
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478 processed=F
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479 l=system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"),intern=TRUE)
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480 for (i in l){
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481 cmd=paste("LC_ALL=C grep '[^ -~]' \"",i,"\"",sep="")
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482 capture=suppressWarnings(system(cmd,intern=TRUE))
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483 if (length(capture)>0){
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diff changeset
484 cmd=paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
485 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
486 c=system(cmd,intern=TRUE)
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
487 capture=""
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
488 processed=T
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
489 }
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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diff changeset
490 }
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
491 if (processed) cat("\n\n")
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
492 return(processed)
4
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lecorguille
parents:
diff changeset
493 }
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
494
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lecorguille
parents:
diff changeset
495
13
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
496 ##
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
497 ## This function will compute MD5 checksum to check the data integrity
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
498 ##
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
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499 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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diff changeset
500 getMd5sum <- function (directory) {
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
501 cat("Compute md5 checksum...\n")
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
502 # WHAT XCMS WILL FIND
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
503 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
504 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
505 info <- file.info(directory)
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
506 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
507 files <- c(directory[!info$isdir], listed)
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
508 exists <- file.exists(files)
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
509 files <- files[exists]
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
510
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
511 library(tools)
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
512
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
513 #cat("\n\n")
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
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514
14
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 13
diff changeset
515 return(as.matrix(md5sum(files)))
4
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
516 }
20
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
517
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
518
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
519 # This function get the raw file path from the arguments
27
36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 23
diff changeset
520 getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {
20
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
521 if (!is.null(listArguments[["zipfile"]])) zipfile = listArguments[["zipfile"]]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
522 if (!is.null(listArguments[["zipfilePositive"]])) zipfile = listArguments[["zipfilePositive"]]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
523 if (!is.null(listArguments[["zipfileNegative"]])) zipfile = listArguments[["zipfileNegative"]]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
524
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
525 if (!is.null(listArguments[["singlefile_galaxyPath"]])) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
526 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]];
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
527 singlefile_sampleNames = listArguments[["singlefile_sampleName"]]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
528 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
529 if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
530 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]];
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
531 singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
532 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
533 if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
534 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]];
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
535 singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
536 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
537 if (exists("singlefile_galaxyPaths")){
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
538 singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
539 singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,","))
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
540
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
541 singlefile=NULL
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
542 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
543 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
544 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
545 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
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546 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
547 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
548 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
549 listArguments[[argument]]=NULL
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
550 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
551 return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments))
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
552 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
553
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
554
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
555 # This function retrieve the raw file in the working directory
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
556 # - if zipfile: unzip the file with its directory tree
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
557 # - if singlefiles: set symlink with the good filename
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
558 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
559 if(!is.null(singlefile) && (length("singlefile")>0)) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
560 for (singlefile_sampleName in names(singlefile)) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
561 singlefile_galaxyPath = singlefile[[singlefile_sampleName]]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
562 if(!file.exists(singlefile_galaxyPath)){
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
563 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
564 print(error_message); stop(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
565 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
566
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
567 file.symlink(singlefile_galaxyPath,singlefile_sampleName)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
568 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
569 directory = "."
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
570
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
571 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
572 if(!is.null(zipfile) && (zipfile!="")) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
573 if(!file.exists(zipfile)){
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
574 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
575 print(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
576 stop(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
577 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
578
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
579 #list all file in the zip file
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
580 #zip_files=unzip(zipfile,list=T)[,"Name"]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
581
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
582 #unzip
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
583 suppressWarnings(unzip(zipfile, unzip="unzip"))
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
584
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
585 #get the directory name
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
586 filesInZip=unzip(zipfile, list=T);
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
587 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
588 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
589 directory = "."
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
590 if (length(directories) == 1) directory = directories
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
591
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
592 cat("files_root_directory\t",directory,"\n")
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
593
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
594 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
595 return (directory)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
596 }