Mercurial > repos > lecorguille > xcms_retcor

comparison xcms.r @ 7:bb602a5b8819 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
author lecorguille
date Mon, 30 Jan 2017 08:53:30 -0500
parents 54cc3edfe35c
children 4bfef820569b
comparison
equal deleted inserted replaced
6:123824c7eaa8 7:bb602a5b8819
17 for(pkg in pkgs) { 17 for(pkg in pkgs) {
18 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) 18 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
19 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="") 19 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
20 } 20 }
21 source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } 21 source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
22 cat("\n\n"); 22 cat("\n\n");
23 23
24 24
25 25
26 26
27 27
62 xsetRdataOutput = paste(thefunction,"RData",sep=".") 62 xsetRdataOutput = paste(thefunction,"RData",sep=".")
63 if (!is.null(listArguments[["xsetRdataOutput"]])){ 63 if (!is.null(listArguments[["xsetRdataOutput"]])){
64 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL 64 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
65 } 65 }
66 66
67 #saving the specific parameters
67 rplotspdf = "Rplots.pdf" 68 rplotspdf = "Rplots.pdf"
68 if (!is.null(listArguments[["rplotspdf"]])){ 69 if (!is.null(listArguments[["rplotspdf"]])){
69 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL 70 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
70 } 71 }
71
72 sampleMetadataOutput = "sampleMetadata.tsv" 72 sampleMetadataOutput = "sampleMetadata.tsv"
73 if (!is.null(listArguments[["sampleMetadataOutput"]])){ 73 if (!is.null(listArguments[["sampleMetadataOutput"]])){
74 sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL 74 sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL
75 } 75 }
76 76 variableMetadataOutput = "variableMetadata.tsv"
77 77 if (!is.null(listArguments[["variableMetadataOutput"]])){
78 78 variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
79 }
80 dataMatrixOutput = "dataMatrix.tsv"
81 if (!is.null(listArguments[["dataMatrixOutput"]])){
82 dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL
83 }
84 if (!is.null(listArguments[["convertRTMinute"]])){
85 convertRTMinute = listArguments[["convertRTMinute"]]; listArguments[["convertRTMinute"]]=NULL
86 }
87 if (!is.null(listArguments[["numDigitsMZ"]])){
88 numDigitsMZ = listArguments[["numDigitsMZ"]]; listArguments[["numDigitsMZ"]]=NULL
89 }
90 if (!is.null(listArguments[["numDigitsRT"]])){
91 numDigitsRT = listArguments[["numDigitsRT"]]; listArguments[["numDigitsRT"]]=NULL
92 }
93 if (!is.null(listArguments[["intval"]])){
94 intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL
95 }
79 96
80 if (thefunction %in% c("xcmsSet","retcor")) { 97 if (thefunction %in% c("xcmsSet","retcor")) {
81 ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL 98 ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
82 bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL 99 bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
83 } 100 }
114 131
115 #unzip 132 #unzip
116 suppressWarnings(unzip(zipfile, unzip="unzip")) 133 suppressWarnings(unzip(zipfile, unzip="unzip"))
117 134
118 #get the directory name 135 #get the directory name
119 filesInZip=unzip(zipfile, list=T); 136 filesInZip=unzip(zipfile, list=T);
120 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); 137 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
121 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] 138 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
122 directory = "." 139 directory = "."
123 if (length(directories) == 1) directory = directories 140 if (length(directories) == 1) directory = directories
124 141
125 cat("files_root_directory\t",directory,"\n") 142 cat("files_root_directory\t",directory,"\n")
126 143
127 # 144 #
128 md5sumList=list("origin"=getMd5sum(directory)) 145 md5sumList=list("origin"=getMd5sum(directory))
129 146
130 # Check and fix if there are non ASCII characters. If so, they will be removed from the *mzXML mzML files. 147 # Check and fix if there are non ASCII characters. If so, they will be removed from the *mzXML mzML files.
131 # Remove because can create issue with some clean files 148 # Remove because can create issue with some clean files
132 #@TODO: fix me 149 #@TODO: fix me
185 # par(xpd=T, mar=par()$mar+c(0,0,0,4)) 202 # par(xpd=T, mar=par()$mar+c(0,0,0,4))
186 #} 203 #}
187 204
188 205
189 #execution of the function "thefunction" with the parameters given in "listArguments" 206 #execution of the function "thefunction" with the parameters given in "listArguments"
207
208 cat("\t\tCOMPUTE\n")
190 xset = do.call(thefunction, listArguments) 209 xset = do.call(thefunction, listArguments)
191 210
192 211
193 cat("\n\n") 212 cat("\n\n")
194 213
198 217
199 #transform the files absolute pathways into relative pathways 218 #transform the files absolute pathways into relative pathways
200 xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths) 219 xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
201 220
202 if(exists("zipfile") && (zipfile!="")) { 221 if(exists("zipfile") && (zipfile!="")) {
203 222
204 #Modify the samples names (erase the path) 223 #Modify the samples names (erase the path)
205 for(i in 1:length(sampnames(xset))){ 224 for(i in 1:length(sampnames(xset))){
206 225
207 sample_name=unlist(strsplit(sampnames(xset)[i], "/")) 226 sample_name=unlist(strsplit(sampnames(xset)[i], "/"))
208 sample_name=sample_name[length(sample_name)] 227 sample_name=sample_name[length(sample_name)]
215 234
216 } 235 }
217 236
218 # -- TIC -- 237 # -- TIC --
219 if (thefunction == "xcmsSet") { 238 if (thefunction == "xcmsSet") {
239 cat("\t\tGET TIC GRAPH\n")
220 sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput) 240 sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
221 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw") 241 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")
222 getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf) 242 getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)
223 } else if (thefunction == "retcor") { 243 } else if (thefunction == "retcor") {
244 cat("\t\tGET TIC GRAPH\n")
224 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected") 245 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")
225 getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf) 246 getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)
226 } 247 }
227 248
228 cat("\n\n") 249 if (thefunction == "fillPeaks") {
229 250 cat("\t\tGET THE PEAK LIST\n")
251 getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput)
252 }
253
254
255 cat("\n\n")
230 256
231 # ----- EXPORT ----- 257 # ----- EXPORT -----
232 258
233 cat("\tXSET OBJECT INFO\n") 259 cat("\tXSET OBJECT INFO\n")
234 print(xset) 260 print(xset)
241 267
242 cat("\n\n") 268 cat("\n\n")
243 269
244 270
245 cat("\tDONE\n") 271 cat("\tDONE\n")
246