Mercurial > repos > ethevenot > profia

annotate profia_wrapper.R @ 1:4753e64cf694 draft

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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 0a90b8ee1577263ace397124d8b0e34d1e630f51
author ethevenot
date Wed, 03 May 2017 10:49:08 -0400
parents 39ccace77270
children 3f8ae071bdda
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39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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1 #!/usr/bin/env Rscript
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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3 library(batch) ## parseCommandArgs
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5 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
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7 ##------------------------------
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8 ## Initializing
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9 ##------------------------------
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12 ## libraries
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13 ##----------
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15 suppressMessages(library(proFIA))
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18 ## constants
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19 ##----------
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21 modNamC <- "proFIA" ## module name
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24 ## log file
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25 ##---------
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27 sink(argVc["information"])
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29 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
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30 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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33 ## arguments
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34 ##----------
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37 if("zipfile" %in% names(argVc)) {
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39 zipfile <- argVc["zipfile"]
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41 ## We unzip automatically the raw files from the zip file
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43 if(exists("zipfile") && (zipfile!="")) {
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44 if(!file.exists(zipfile)){
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
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45 error_message=paste("Cannot access the Zip file:", zipfile)
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46 print(error_message)
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47 stop(error_message)
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48 }
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50 ## unzip
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52 suppressWarnings(unzip(zipfile, unzip="unzip"))
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54 ## get the directory name
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56 filesInZip=unzip(zipfile, list=T);
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57 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
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58 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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59 directory = "."
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60 if (length(directories) == 1) directory = directories
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62 cat("files_root_directory\t",directory,"\n")
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64 }
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66 } else if ("library" %in% names(argVc)) {
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68 directory <- argVc["library"]
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70 if(!file.exists(directory)) {
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72 error_message=paste("Cannot access the directory:", directory,". Please check that the directory really exists.")
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73 print(error_message)
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74 stop(error_message)
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76 }
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78 } else {
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80 error_message <- "No zipfile nor input library available"
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81 print(error_message)
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82 stop(error_message)
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84 }
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86 ##------------------------------
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87 ## Computations
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88 ##------------------------------
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91 optWrnN <- options()$warn
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92 options(warn = -1)
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94 stpI <- 1
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96 cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "")
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98 fiaset <- proFIAset(directory,
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99 ppm = as.numeric(argVc["ppmN"]),
1
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100 parallel = TRUE)
0
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102 stpI <- stpI + 1
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103
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104 cat("\n", stpI, ") Peak alignment ('group.FIA'):\n", sep = "")
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105
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106 fiaset <- group.FIA(fiaset,
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107 ppmGroup = as.numeric(argVc["ppmGroupN"]),
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108 fracGroup = as.numeric(argVc["fracGroupN"]))
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109
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110 stpI <- stpI + 1
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111
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112 cat("\n", stpI, ") Creating the peak table ('makeDataMatrix'):\n", sep = "")
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113
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114 fiaset <- makeDataMatrix(fiaset,
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115 maxo = FALSE)
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116
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117 stpI <- stpI + 1
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118
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119 kI <- as.integer(argVc["kI"])
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120
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121 if(kI > 0) {
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122
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123 cat("\n", stpI, ") Imputing missing values ('imputeMissingValues.WKNN_TN'):\n", sep = "")
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124
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125 fiaset <- imputeMissingValues.WKNN_TN(fiaset,
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126 k = kI)
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127
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128 stpI <- stpI + 1
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129 }
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130
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131 options(warn = optWrnN)
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132
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133
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134 ##------------------------------
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135 ## Ending
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136 ##------------------------------
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137
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138
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139 ## Plotting
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140 ##---------
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141
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142 cat("\n", stpI, ") Plotting ('plot'):\n", sep = "")
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143
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144 pdf(argVc["figure"])
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145
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146 plot(fiaset)
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147
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148 dev.off()
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149
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150 stpI <- stpI + 1
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151
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152 ## Printing
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153 ##---------
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154
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155 cat("\n", stpI, ") Printing ('show'):\n", sep = "")
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156
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157 fiaset
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158
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159 stpI <- stpI + 1
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160
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161 ## Exporting
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162 ##----------
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163
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164 cat("\n", stpI, ") Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'):\n", sep = "")
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165
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166 datMN <- exportDataMatrix(fiaset)
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167 samDF <- exportSampleMetadata(fiaset)
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168 varDF <- exportVariableMetadata(fiaset)
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169
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170 if(nrow(datMN) == nrow(samDF) && ncol(datMN) == nrow(varDF)) {
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171 datDF <- as.data.frame(t(datMN))
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172 } else {
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173 datDF <- as.data.frame(datMN)
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174 }
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175 rownames(varDF) <- rownames(datDF)
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176
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177 datDF <- cbind.data.frame(dataMatrix = rownames(datDF),
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178 datDF)
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179 write.table(datDF,
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180 file = argVc["dataMatrix_out"],
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181 quote = FALSE,
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182 row.names = FALSE,
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183 sep = "\t")
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184
1
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185 samDF <- cbind.data.frame(sampleMetadata = samDF[, "sampleID"],
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186 class = samDF[, "class"])
0
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187 write.table(samDF,
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188 file = argVc["sampleMetadata_out"],
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189 quote = FALSE,
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190 row.names = FALSE,
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191 sep = "\t")
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192
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193 varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
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194 varDF)
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195 write.table(varDF,
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196 file = argVc["variableMetadata_out"],
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197 quote = FALSE,
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198 row.names = FALSE,
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199 sep = "\t")
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200
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201
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202 ## Closing
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203 ##--------
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204
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parents:
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205 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff changeset
206 as.character(Sys.time()), "\n", sep = "")
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff changeset
207
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff changeset
208 sink()
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff changeset
209
39ccace77270 planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
ethevenot
parents:
diff changeset
210 rm(list = ls())