Mercurial > repos > lecorguille > xcms_xcmsset

annotate lib.r @ 11:91311aa08cdc draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
author lecorguille
date Mon, 30 Jan 2017 08:52:59 -0500
parents 0888f7ef739a
children 15646e937936
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0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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1 #Authors ABiMS TEAM
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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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
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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6 #version 2.3: yguitton
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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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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91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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9 # correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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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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11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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15 #@author G. Le Corguille
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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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(dataData, numDigitsRT=0, numDigitsMZ=0) {
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31 return(make.unique(paste0("M",round(dataData[,"mz"],numDigitsMZ),"T",round(dataData[,"rt"],numDigitsRT))))
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32 }
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34 #@author G. Le Corguille
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35 # value: intensity values to be used into, maxo or intb
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36 getPeaklistW4M <- function(xset, intval="into",convertRTMinute=F,numDigitsMZ=4,numDigitsRT=0,variableMetadataOutput,dataMatrixOutput) {
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37 groups <- xset@groups
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38 values <- groupval(xset, "medret", value=intval)
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40 # renamming of the column rtmed to rt to fit with camera peaklist function output
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41 colnames(groups)[colnames(groups)=="rtmed"] <- "rt"
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42 colnames(groups)[colnames(groups)=="mzmed"] <- "mz"
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44 ids <- formatIonIdentifiers(groups, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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45 groups = RTSecondToMinute(groups, convertRTMinute)
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47 rownames(groups) = ids
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48 rownames(values) = ids
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50 #@TODO: add "name" as the first column name
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51 #colnames(groups)[1] = "name"
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52 #colnames(values)[1] = "name"
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54 write.table(groups, file=variableMetadataOutput,sep="\t",quote=F,row.names = T,col.names = NA)
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55 write.table(values, file=dataMatrixOutput,sep="\t",quote=F,row.names = T,col.names = NA)
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56 }
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58 #@author Y. Guitton
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59 getBPC <- function(file,rtcor=NULL, ...) {
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60 object <- xcmsRaw(file)
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61 sel <- profRange(object, ...)
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62 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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63 #plotChrom(xcmsRaw(file), base=T)
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64 }
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66 #@author Y. Guitton
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67 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
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68 cat("Creating BIC pdf...\n")
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70 if (is.null(xcmsSet)) {
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71 cat("Enter an xcmsSet \n")
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72 stop()
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73 } else {
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74 files <- filepaths(xcmsSet)
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75 }
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77 class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
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79 classnames<-vector("list",length(class))
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80 for (i in 1:length(class)){
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81 classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i])
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82 }
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84 N <- dim(phenoData(xcmsSet))[1]
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86 TIC <- vector("list",N)
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89 for (j in 1:N) {
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91 TIC[[j]] <- getBPC(files[j])
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92 #good for raw
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93 # seems strange for corrected
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parents:
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94 #errors if scanrange used in xcmsSetgeneration
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95 if (!is.null(xcmsSet) && rt == "corrected")
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96 rtcor <- xcmsSet@rt$corrected[[j]] else
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97 rtcor <- NULL
11
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98
6
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99 TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
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100 # TIC[[j]][,1]<-rtcor
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101 }
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102
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103
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104
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105 pdf(pdfname,w=16,h=10)
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parents:
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106 cols <- rainbow(N)
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107 lty = 1:N
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108 pch = 1:N
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109 #search for max x and max y in BPCs
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110 xlim = range(sapply(TIC, function(x) range(x[,1])))
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111 ylim = range(sapply(TIC, function(x) range(x[,2])))
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112 ylim = c(-ylim[2], ylim[2])
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113
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114
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115 ##plot start
11
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116
6
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117 if (length(class)>2){
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118 for (k in 1:(length(class)-1)){
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119 for (l in (k+1):length(class)){
11
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120 #print(paste(class[k],"vs",class[l],sep=" "))
6
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121 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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122 colvect<-NULL
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123 for (j in 1:length(classnames[[k]])) {
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124 tic <- TIC[[classnames[[k]][j]]]
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125 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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126 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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127 colvect<-append(colvect,cols[classnames[[k]][j]])
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128 }
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129 for (j in 1:length(classnames[[l]])) {
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130 # i=class2names[j]
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131 tic <- TIC[[classnames[[l]][j]]]
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132 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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133 colvect<-append(colvect,cols[classnames[[l]][j]])
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134 }
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diff changeset
135 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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136 }
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137 }
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138 }#end if length >2
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139
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diff changeset
140 if (length(class)==2){
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141 k=1
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142 l=2
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143 colvect<-NULL
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144 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k],"vs",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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145
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146 for (j in 1:length(classnames[[k]])) {
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147
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148 tic <- TIC[[classnames[[k]][j]]]
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149 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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150 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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151 colvect<-append(colvect,cols[classnames[[k]][j]])
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152 }
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153 for (j in 1:length(classnames[[l]])) {
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154 # i=class2names[j]
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155 tic <- TIC[[classnames[[l]][j]]]
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diff changeset
156 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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157 colvect<-append(colvect,cols[classnames[[l]][j]])
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158 }
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diff changeset
159 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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160
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161 }#end length ==2
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162
11
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163 #case where only one class
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164 if (length(class)==1){
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165 k=1
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166 ylim = range(sapply(TIC, function(x) range(x[,2])))
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167 colvect<-NULL
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168 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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169
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170 for (j in 1:length(classnames[[k]])) {
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171 tic <- TIC[[classnames[[k]][j]]]
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172 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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173 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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174 colvect<-append(colvect,cols[classnames[[k]][j]])
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175 }
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176
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177 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
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178
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179 }#end length ==1
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180
6
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181 dev.off() #pdf(pdfname,w=16,h=10)
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182
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183 invisible(TIC)
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184 }
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185
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186
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187
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diff changeset
188 #@author Y. Guitton
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189 getTIC <- function(file,rtcor=NULL) {
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190 object <- xcmsRaw(file)
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191 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object,mzrange=range(object@env$mz))$intensity)
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192 }
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193
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194 ##
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195 ## overlay TIC from all files in current folder or from xcmsSet, create pdf
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196 ##
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lecorguille
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197 #@author Y. Guitton
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198 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf",rt=c("raw","corrected")) {
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199 cat("Creating TIC pdf...\n")
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200
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201 if (is.null(xcmsSet)) {
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lecorguille
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202 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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203 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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204 if (is.null(files))
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205 files <- getwd()
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206 info <- file.info(files)
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207 listed <- list.files(files[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
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208 files <- c(files[!info$isdir], listed)
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209 } else {
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210 files <- filepaths(xcmsSet)
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211 }
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212
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213 class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
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214
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215 classnames<-vector("list",length(class))
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216 for (i in 1:length(class)){
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217 classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i])
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lecorguille
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218 }
11
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lecorguille
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219
6
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220 N <- length(files)
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lecorguille
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221 TIC <- vector("list",N)
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222
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223 for (i in 1:N) {
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224 if (!is.null(xcmsSet) && rt == "corrected")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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225 rtcor <- xcmsSet@rt$corrected[[i]] else
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226 rtcor <- NULL
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227 TIC[[i]] <- getTIC(files[i],rtcor=rtcor)
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lecorguille
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228 }
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229
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230 pdf(pdfname,w=16,h=10)
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lecorguille
parents:
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231 cols <- rainbow(N)
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232 lty = 1:N
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233 pch = 1:N
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234 #search for max x and max y in TICs
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235 xlim = range(sapply(TIC, function(x) range(x[,1])))
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236 ylim = range(sapply(TIC, function(x) range(x[,2])))
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lecorguille
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237 ylim = c(-ylim[2], ylim[2])
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238
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239
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lecorguille
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240 ##plot start
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
241 if (length(class)>2){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
242 for (k in 1:(length(class)-1)){
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243 for (l in (k+1):length(class)){
11
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244 #print(paste(class[k],"vs",class[l],sep=" "))
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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245 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
246 colvect<-NULL
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diff changeset
247 for (j in 1:length(classnames[[k]])) {
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248
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249 tic <- TIC[[classnames[[k]][j]]]
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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250 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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251 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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252 colvect<-append(colvect,cols[classnames[[k]][j]])
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parents:
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253 }
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diff changeset
254 for (j in 1:length(classnames[[l]])) {
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parents:
diff changeset
255 # i=class2names[j]
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lecorguille
parents:
diff changeset
256 tic <- TIC[[classnames[[l]][j]]]
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lecorguille
parents:
diff changeset
257 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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diff changeset
258 colvect<-append(colvect,cols[classnames[[l]][j]])
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parents:
diff changeset
259 }
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lecorguille
parents:
diff changeset
260 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
261 }
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lecorguille
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diff changeset
262 }
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lecorguille
parents:
diff changeset
263 }#end if length >2
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lecorguille
parents:
diff changeset
264 if (length(class)==2){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
265 k=1
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lecorguille
parents:
diff changeset
266 l=2
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267
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parents:
diff changeset
268 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k],"vs",class[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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diff changeset
269 colvect<-NULL
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diff changeset
270 for (j in 1:length(classnames[[k]])) {
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lecorguille
parents:
diff changeset
271 tic <- TIC[[classnames[[k]][j]]]
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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parents:
diff changeset
272 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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parents:
diff changeset
273 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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lecorguille
parents:
diff changeset
274 colvect<-append(colvect,cols[classnames[[k]][j]])
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lecorguille
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diff changeset
275 }
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
276 for (j in 1:length(classnames[[l]])) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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parents:
diff changeset
277 # i=class2names[j]
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parents:
diff changeset
278 tic <- TIC[[classnames[[l]][j]]]
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
279 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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lecorguille
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diff changeset
280 colvect<-append(colvect,cols[classnames[[l]][j]])
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281 }
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282 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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283
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284 }#end length ==2
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285
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286 #case where only one class
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287 if (length(class)==1){
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288 k=1
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289 ylim = range(sapply(TIC, function(x) range(x[,2])))
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290
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291 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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292 colvect<-NULL
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293 for (j in 1:length(classnames[[k]])) {
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294 tic <- TIC[[classnames[[k]][j]]]
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295 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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296 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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297 colvect<-append(colvect,cols[classnames[[k]][j]])
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298 }
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299
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300 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
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301
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302 }#end length ==1
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303
6
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304 dev.off() #pdf(pdfname,w=16,h=10)
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305
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306 invisible(TIC)
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307 }
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308
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309
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310
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311 ##
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312 ## Get the polarities from all the samples of a condition
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313 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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314 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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315 getSampleMetadata <- function(xcmsSet=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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316 cat("Creating the sampleMetadata file...\n")
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317
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318 #Create the sampleMetada dataframe
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319 sampleMetadata=xset@phenoData
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320 sampleNamesOrigin=rownames(sampleMetadata)
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321 sampleNamesMakeNames=make.names(sampleNamesOrigin)
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322
6
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323 if (any(duplicated(sampleNamesMakeNames))) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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324 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())
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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325 for (sampleName in sampleNamesOrigin) {
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326 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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327 }
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328 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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329 }
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diff changeset
330
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331 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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332 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")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
333 for (sampleName in sampleNamesOrigin) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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334 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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335 }
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336 }
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diff changeset
337
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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338 sampleMetadata$sampleMetadata=sampleNamesMakeNames
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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339 sampleMetadata=cbind(sampleMetadata["sampleMetadata"],sampleMetadata["class"]) #Reorder columns
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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340 rownames(sampleMetadata)=NULL
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341
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342 #Create a list of files name in the current directory
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343 list_files=xset@filepaths
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344 #For each sample file, the following actions are done
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345 for (file in list_files){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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346 #Check if the file is in the CDF format
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347 if (!mzR:::netCDFIsFile(file)){
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348
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349 # If the column isn't exist, with add one filled with NA
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350 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity=NA
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351
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352 #Create a simple xcmsRaw object for each sample
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353 xcmsRaw=xcmsRaw(file)
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354 #Extract the polarity (a list of polarities)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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355 polarity=xcmsRaw@polarity
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356 #Verify if all the scans have the same polarity
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
357 uniq_list=unique(polarity)
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diff changeset
358 if (length(uniq_list)>1){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
359 polarity="mixed"
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
360 } else {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
361 polarity=as.character(uniq_list)
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diff changeset
362 }
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
363 #Transforms the character to obtain only the sample name
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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364 filename=basename(file)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
365 library(tools)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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366 samplename=file_path_sans_ext(filename)
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diff changeset
367
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
368 #Set the polarity attribute
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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369 sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity
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370
6
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diff changeset
371 #Delete xcmsRaw object because it creates a bug for the fillpeaks step
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
372 rm(xcmsRaw)
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373 }
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374
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375 }
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376
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
377 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
378
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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diff changeset
379 return(list("sampleNamesOrigin"=sampleNamesOrigin,"sampleNamesMakeNames"=sampleNamesMakeNames))
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
380
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
381 }
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
382
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
383
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
384 ##
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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diff changeset
385 ## This function check if xcms will found all the files
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
386 ##
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
387 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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diff changeset
388 checkFilesCompatibilityWithXcms <- function(directory) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
389 cat("Checking files filenames compatibilities with xmcs...\n")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
390 # WHAT XCMS WILL FIND
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
391 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
392 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
393 info <- file.info(directory)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
394 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
395 files <- c(directory[!info$isdir], listed)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
396 files_abs <- file.path(getwd(), files)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
397 exists <- file.exists(files_abs)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
398 files[exists] <- files_abs[exists]
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
399 files[exists] <- sub("//","/",files[exists])
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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diff changeset
400
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
401 # WHAT IS ON THE FILESYSTEM
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
402 filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
403 filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
404
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
405 # COMPARISON
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 6
diff changeset
406 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
407 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
408 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
409 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
410
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
411 }
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
412 }
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
413
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
414
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
415
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
416 ##
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
417 ## This function check if XML contains special caracters. It also checks integrity and completness.
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
418 ##
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
419 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
420 checkXmlStructure <- function (directory) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
421 cat("Checking XML structure...\n")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
422
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
423 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;")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
424 capture=system(cmd,intern=TRUE)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
425
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
426 if (length(capture)>0){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
427 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
428 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
429 write(capture, stderr())
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
430 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
431 }
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 6
diff changeset
432
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
433 }
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
434
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
435
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
436 ##
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
437 ## This function check if XML contain special characters
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
438 ##
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
439 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
440 deleteXmlBadCharacters<- function (directory) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
441 cat("Checking Non ASCII characters in the XML...\n")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
442
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
443 processed=F
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 6
diff changeset
444 l=system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"),intern=TRUE)
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
445 for (i in l){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
446 cmd=paste("LC_ALL=C grep '[^ -~]' \"",i,"\"",sep="")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
447 capture=suppressWarnings(system(cmd,intern=TRUE))
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
448 if (length(capture)>0){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
449 cmd=paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
450 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
451 c=system(cmd,intern=TRUE)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
452 capture=""
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 6
diff changeset
453 processed=T
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
454 }
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
455 }
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
456 if (processed) cat("\n\n")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
457 return(processed)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
458 }
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
459
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
460
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 6
diff changeset
461 ##
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
462 ## This function will compute MD5 checksum to check the data integrity
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
463 ##
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
464 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
465 getMd5sum <- function (directory) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
466 cat("Compute md5 checksum...\n")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
467 # WHAT XCMS WILL FIND
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
468 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
469 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
470 info <- file.info(directory)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
471 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
472 files <- c(directory[!info$isdir], listed)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
473 exists <- file.exists(files)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
474 files <- files[exists]
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
475
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
476 library(tools)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
477
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
478 #cat("\n\n")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
479
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
480 return(as.matrix(md5sum(files)))
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
481 }