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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
author lecorguille
date Tue, 24 Oct 2017 11:47:49 -0400
parents b8be2b25957d
children c013ed353a2f
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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)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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391 polarity=xcmsRaw@polarity
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392 #Verify if all the scans have the same polarity
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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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
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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400 filename=basename(file)
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401 library(tools)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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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
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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405 sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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406
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407 #Delete xcmsRaw object because it creates a bug for the fillpeaks step
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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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
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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422 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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423 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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424 checkFilesCompatibilityWithXcms <- function(directory) {
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20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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425 cat("Checking files filenames compatibilities with xmcs...\n")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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426 # WHAT XCMS WILL FIND
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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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]")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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428 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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429 info <- file.info(directory)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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430 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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431 files <- c(directory[!info$isdir], listed)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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432 files_abs <- file.path(getwd(), files)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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433 exists <- file.exists(files_abs)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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434 files[exists] <- files_abs[exists]
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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435 files[exists] <- sub("//","/",files[exists])
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436
16
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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)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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439 filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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440
16
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lecorguille
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441 # COMPARISON
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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442 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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443 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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444 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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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.")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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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
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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455 checkXmlStructure <- function (directory) {
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20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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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;")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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459 capture=system(cmd,intern=TRUE)
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460
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lecorguille
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461 if (length(capture)>0){
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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462 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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463 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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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 }
15
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lecorguille
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467
6
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468 }
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lecorguille
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469
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lecorguille
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470
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471 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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472 ## This function check if XML contain special characters
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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473 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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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)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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480 for (i in l){
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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481 cmd=paste("LC_ALL=C grep '[^ -~]' \"",i,"\"",sep="")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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482 capture=suppressWarnings(system(cmd,intern=TRUE))
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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diff changeset
483 if (length(capture)>0){
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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484 cmd=paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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485 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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486 c=system(cmd,intern=TRUE)
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487 capture=""
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488 processed=T
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489 }
6
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490 }
16
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491 if (processed) cat("\n\n")
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492 return(processed)
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diff changeset
493 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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494
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lecorguille
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diff changeset
495
15
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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496 ##
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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497 ## This function will compute MD5 checksum to check the data integrity
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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498 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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499 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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diff changeset
500 getMd5sum <- function (directory) {
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
501 cat("Compute md5 checksum...\n")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
502 # WHAT XCMS WILL FIND
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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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]")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
504 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
505 info <- file.info(directory)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
506 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
507 files <- c(directory[!info$isdir], listed)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
508 exists <- file.exists(files)
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
509 files <- files[exists]
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
510
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
511 library(tools)
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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diff changeset
512
16
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lecorguille
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diff changeset
513 #cat("\n\n")
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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diff changeset
514
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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diff changeset
515 return(as.matrix(md5sum(files)))
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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diff changeset
516 }
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
517
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
518
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
519 # This function get the raw file path from the arguments
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 25
diff changeset
520 getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {
22
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
521 if (!is.null(listArguments[["zipfile"]])) zipfile = listArguments[["zipfile"]]
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
522 if (!is.null(listArguments[["zipfilePositive"]])) zipfile = listArguments[["zipfilePositive"]]
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
523 if (!is.null(listArguments[["zipfileNegative"]])) zipfile = listArguments[["zipfileNegative"]]
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
524
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lecorguille
parents: 19
diff changeset
525 if (!is.null(listArguments[["singlefile_galaxyPath"]])) {
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
526 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]];
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
527 singlefile_sampleNames = listArguments[["singlefile_sampleName"]]
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
528 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
529 if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) {
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
530 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]];
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
531 singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]]
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
532 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
533 if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) {
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
534 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]];
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
535 singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]]
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
536 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
537 if (exists("singlefile_galaxyPaths")){
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
538 singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
539 singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,","))
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
540
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
541 singlefile=NULL
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
542 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
543 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
544 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
545 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
546 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
547 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
548 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
549 listArguments[[argument]]=NULL
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
550 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
551 return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments))
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
552 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
553
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
554
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
555 # This function retrieve the raw file in the working directory
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
556 # - if zipfile: unzip the file with its directory tree
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
557 # - if singlefiles: set symlink with the good filename
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
558 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
559 if(!is.null(singlefile) && (length("singlefile")>0)) {
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
560 for (singlefile_sampleName in names(singlefile)) {
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
561 singlefile_galaxyPath = singlefile[[singlefile_sampleName]]
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
562 if(!file.exists(singlefile_galaxyPath)){
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
563 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
564 print(error_message); stop(error_message)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
565 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
566
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
567 file.symlink(singlefile_galaxyPath,singlefile_sampleName)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
568 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
569 directory = "."
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
570
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
571 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
572 if(!is.null(zipfile) && (zipfile!="")) {
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
573 if(!file.exists(zipfile)){
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
574 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
575 print(error_message)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
576 stop(error_message)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
577 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
578
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
579 #list all file in the zip file
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
580 #zip_files=unzip(zipfile,list=T)[,"Name"]
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
581
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
582 #unzip
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
583 suppressWarnings(unzip(zipfile, unzip="unzip"))
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
584
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
585 #get the directory name
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
586 filesInZip=unzip(zipfile, list=T);
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
587 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
588 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
589 directory = "."
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
590 if (length(directories) == 1) directory = directories
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
591
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
592 cat("files_root_directory\t",directory,"\n")
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
593
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
594 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
595 return (directory)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
diff changeset
596 }