Mercurial > repos > lecorguille > xcms_fillpeaks

comparison xcms.r @ 23:7e289788d37d draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
author lecorguille
date Wed, 01 Mar 2017 16:58:07 -0500
parents 02bb34af0921
children 7a01dfc8be41
comparison
equal deleted inserted replaced
22:a6938c381d4e 23:7e289788d37d
69 if (!is.null(listArguments[["rplotspdf"]])){ 69 if (!is.null(listArguments[["rplotspdf"]])){
70 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL 70 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
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 variableMetadataOutput = "variableMetadata.tsv" 76 variableMetadataOutput = "variableMetadata.tsv"
77 if (!is.null(listArguments[["variableMetadataOutput"]])){ 77 if (!is.null(listArguments[["variableMetadataOutput"]])){
78 variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL 78 variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
79 } 79 }
97 if (thefunction %in% c("xcmsSet","retcor")) { 97 if (thefunction %in% c("xcmsSet","retcor")) {
98 ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL 98 ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
99 bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL 99 bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
100 } 100 }
101 101
102 #necessary to unzip .zip file uploaded to Galaxy 102
103 #thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories
104
105
106 if (!is.null(listArguments[["zipfile"]])){
107 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
108 }
109
110 if (!is.null(listArguments[["singlefile_galaxyPath"]])){
111 singlefile_galaxyPaths = unlist(strsplit(listArguments[["singlefile_galaxyPath"]],",")); listArguments[["singlefile_galaxyPath"]]=NULL
112 singlefile_sampleNames = unlist(strsplit(listArguments[["singlefile_sampleName"]],",")); listArguments[["singlefile_sampleName"]]=NULL
113
114 singlefile=NULL
115 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
116 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]
117 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]
118 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
119 }
120 }
121
122 # We unzip automatically the chromatograms from the zip files.
123 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) { 103 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) {
124 if(exists("singlefile") && (length("singlefile")>0)) { 104 rawFilePath = getRawfilePathFromArguments(listArguments)
125 for (singlefile_sampleName in names(singlefile)) { 105 zipfile = rawFilePath$zipfile
126 singlefile_galaxyPath = singlefile[[singlefile_sampleName]] 106 singlefile = rawFilePath$singlefile
127 if(!file.exists(singlefile_galaxyPath)){ 107 listArguments = rawFilePath$listArguments
128 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") 108 directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
129 print(error_message); stop(error_message) 109 md5sumList=list("origin"=getMd5sum(directory))
130 }
131
132 file.symlink(singlefile_galaxyPath,singlefile_sampleName)
133 }
134 directory = "."
135
136 md5sumList=list("origin"=getMd5sum(directory))
137
138 }
139 if(exists("zipfile") && (zipfile!="")) {
140 if(!file.exists(zipfile)){
141 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
142 print(error_message)
143 stop(error_message)
144 }
145
146 #list all file in the zip file
147 #zip_files=unzip(zipfile,list=T)[,"Name"]
148
149 #unzip
150 suppressWarnings(unzip(zipfile, unzip="unzip"))
151
152 #get the directory name
153 filesInZip=unzip(zipfile, list=T);
154 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
155 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
156 directory = "."
157 if (length(directories) == 1) directory = directories
158
159 cat("files_root_directory\t",directory,"\n")
160
161 md5sumList=list("origin"=getMd5sum(directory))
162 }
163 } 110 }
164 111
165 #addition of the directory to the list of arguments in the first position 112 #addition of the directory to the list of arguments in the first position
166 if (thefunction == "xcmsSet") { 113 if (thefunction == "xcmsSet") {
167 checkXmlStructure(directory) 114 checkXmlStructure(directory)
221 168
222 if (thefunction == "xcmsSet") { 169 if (thefunction == "xcmsSet") {
223 170
224 #transform the files absolute pathways into relative pathways 171 #transform the files absolute pathways into relative pathways
225 xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths) 172 xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
226 173 print(zipfile)
227 if(exists("zipfile") && (zipfile!="")) { 174 if(exists("zipfile") && !is.null(zipfile) && (zipfile!="")) {
228 175
229 #Modify the samples names (erase the path) 176 #Modify the samples names (erase the path)
230 for(i in 1:length(sampnames(xset))){ 177 for(i in 1:length(sampnames(xset))){
231 178
232 sample_name=unlist(strsplit(sampnames(xset)[i], "/")) 179 sample_name=unlist(strsplit(sampnames(xset)[i], "/"))