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planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
author workflow4metabolomics
date Mon, 11 Sep 2023 22:37:32 +0000
parents ae8de756dfcf
children
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1 #@author G. Le Corguille
ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
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2 # solve an issue with batch if arguments are logical TRUE/FALSE
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3 parseCommandArgs <- function(...) {
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4 args <- batch::parseCommandArgs(...)
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5 for (key in names(args)) {
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6 if (args[key] %in% c("TRUE", "FALSE"))
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7 args[key] <- as.logical(args[key])
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8 }
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9 return(args)
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10 }
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ae8de756dfcf "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
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12 #@author G. Le Corguille
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13 # This function will
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14 # - load the packages
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15 # - display the sessionInfo
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16 loadAndDisplayPackages <- function(pkgs) {
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17 for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
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18 sessioninfo <- sessionInfo()
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19 cat(sessioninfo$R.version$version.string, "\n")
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20 cat("Main packages:\n")
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21 for (pkg in names(sessioninfo$otherPkgs)) {
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22 cat(paste(pkg, packageVersion(pkg)), "\t")
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23 }
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24 cat("\n")
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25 cat("Other loaded packages:\n")
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26 for (pkg in names(sessioninfo$loadedOnly)) {
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27 cat(paste(pkg, packageVersion(pkg)), "\t")
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28 }
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29 cat("\n")
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30 }
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31
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32 ##
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33 ## This function launch IPO functions to get the best parameters for xcmsSet
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34 ## A sample among the whole dataset is used to save time
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35 ##
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36 ipo4xcmsSet <- function(directory, parametersOutput, args, samplebyclass = 4) {
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37 setwd(directory)
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38
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39 files <- list.files(".", recursive = TRUE) # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF"
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40 files <- files[!files %in% c("conda_activate.log", "log.txt")]
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41 files_classes <- basename(dirname(files)) # "KO", "KO", "WT", "WT"
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42
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43 mzmlfile <- files
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44 if (samplebyclass > 0) {
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45 #random selection of N files for IPO in each class
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46 classes <- unique(basename(dirname(files)))
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47 mzmlfile <- NULL
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48 for (class_i in classes){
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49 files_class_i <- files[files_classes == class_i]
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50 if (samplebyclass > length(files_class_i)) {
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51 mzmlfile <- c(mzmlfile, files_class_i)
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52 } else {
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53 mzmlfile <- c(mzmlfile, sample(files_class_i, samplebyclass))
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54 }
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55 }
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56 }
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57 #@TODO: else, must we keep the RData to been use directly by group?
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59 cat("\t\tSamples used:\n")
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60 print(mzmlfile)
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62 peakpickingParameters <- getDefaultXcmsSetStartingParams(args$method) #get default parameters of IPO
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64 # filter args to only get releavant parameters and complete with those that are not declared
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65 peakpickingParametersUser <- c(args[names(args) %in% names(peakpickingParameters)], peakpickingParameters[!(names(peakpickingParameters) %in% names(args))])
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66 peakpickingParametersUser$verbose.columns <- TRUE
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67 resultPeakpicking <- optimizeXcmsSet(mzmlfile, peakpickingParametersUser, nSlaves = args$nSlaves, subdir = "./IPO_results") #some images generated by IPO
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69 # export
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70 peakpicking_best_params <- resultPeakpicking$best_settings$parameters[!(names(resultPeakpicking$best_settings$parameters) %in% c("nSlaves", "verbose.columns"))]
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71 write.table(t(as.data.frame(peakpicking_best_params)), file = parametersOutput, sep = "\t", row.names = TRUE, col.names = FALSE, quote = FALSE) #can be read by user
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73 return(resultPeakpicking$best_settings$xset)
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74 }
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76 ##
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77 ## This function launch IPO functions to get the best parameters for group and retcor
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78 ##
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79 ipo4retgroup <- function(xset, directory, parametersOutput, args, samplebyclass = 4) {
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80 setwd(directory)
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82 files <- list.files(".", recursive = TRUE) # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF"
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83 files <- files[!files %in% c("conda_activate.log", "log.txt")]
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84 files_classes <- basename(dirname(files)) # "KO", "KO", "WT", "WT"
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86 retcorGroupParameters <- getDefaultRetGroupStartingParams(args$retcorMethod) #get default parameters of IPO
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87 print(retcorGroupParameters)
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88 # filter args to only get releavant parameters and complete with those that are not declared
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89 retcorGroupParametersUser <- c(args[names(args) %in% names(retcorGroupParameters)], retcorGroupParameters[!(names(retcorGroupParameters) %in% names(args))])
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90 print("retcorGroupParametersUser")
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91 print(retcorGroupParametersUser)
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92 resultRetcorGroup <- optimizeRetGroup(xset, retcorGroupParametersUser, nSlaves = args$nSlaves, subdir = "../IPO_results") #some images generated by IPO
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94 # export
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95 resultRetcorGroup_best_params <- resultRetcorGroup$best_settings
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96 write.table(t(as.data.frame(resultRetcorGroup_best_params)), file = parametersOutput, sep = "\t", row.names = TRUE, col.names = FALSE, quote = FALSE) #can be read by user
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97 }
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99
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100
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101 # This function check if XML contains special caracters. It also checks integrity and completness.
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102 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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103 checkXmlStructure <- function(directory) {
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104 cat("Checking XML structure...\n")
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105
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106 cmd <- paste0("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;")
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107 capture <- system(cmd, intern = TRUE)
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108
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109 if (length(capture) > 0) {
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110 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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111 write(capture, stderr())
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112 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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113 }
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114
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115 }
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116
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117
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118 # This function get the raw file path from the arguments
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119 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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120 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix = "") {
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121 if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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122
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123 if (!is.null(args[[paste0("zipfile", prefix)]])) zipfile <- args[[paste0("zipfile", prefix)]]
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124
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125 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
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126 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath", prefix)]]
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127 singlefile_sampleNames <- args[[paste0("singlefile_sampleName", prefix)]]
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128 }
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129 if (exists("singlefile_galaxyPaths")) {
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130 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths, "\\|"))
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131 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames, "\\|"))
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132
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133 singlefile <- NULL
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134 for (singlefile_galaxyPath_i in seq_along(length(singlefile_galaxyPaths))) {
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135 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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136 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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137 # In case, an url is used to import data within Galaxy
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138 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
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139 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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140 }
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141 }
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142 return(list(zipfile = zipfile, singlefile = singlefile))
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143 }
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144
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145 # This function retrieve the raw file in the working directory
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146 # - if zipfile: unzip the file with its directory tree
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147 # - if singlefiles: set symlink with the good filename
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148 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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149 retrieveRawfileInWD <- function(singlefile, zipfile) {
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150 if (!is.null(singlefile) && (length("singlefile") > 0)) {
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151 for (singlefile_sampleName in names(singlefile)) {
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152 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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153 if (!file.exists(singlefile_galaxyPath)) {
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154 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
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155 print(error_message)
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156 stop(error_message)
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157 }
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158
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159 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE)))
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160 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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161
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162 }
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163 directory <- "."
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164
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165 }
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166 if (!is.null(zipfile) && (zipfile != "")) {
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167 if (!file.exists(zipfile)) {
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168 error_message <- paste(
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169 "Cannot access the Zip file:",
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170 zipfile,
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171 ". Please, contact your administrator ... if you have one!"
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172 )
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173 print(error_message)
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174 stop(error_message)
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175 }
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176
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177 #unzip
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178 suppressWarnings(unzip(zipfile, unzip = "unzip"))
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179
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180 #get the directory name
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181 suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE))
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182 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
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183 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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184 directory <- "."
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185 if (length(directories) == 1) directory <- directories
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186
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187 cat("files_root_directory\t", directory, "\n")
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188
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189 }
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190 return(directory)
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191 }
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192
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193
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194 # This function retrieve a xset like object
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195 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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196 getxcmsSetObject <- function(xobject) {
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197 # XCMS 1.x
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198 if (class(xobject) == "xcmsSet")
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199 return(xobject)
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200 # XCMS 3.x
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201 if (class(xobject) == "XCMSnExp") {
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202 # Get the legacy xcmsSet object
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203 suppressWarnings(xset <- as(xobject, "xcmsSet"))
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204 if (!is.null(xset@phenoData$sample_group))
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205 sampclass(xset) <- xset@phenoData$sample_group
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206 else
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207 sampclass(xset) <- "."
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208 return(xset)
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209 }
1
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210 }