Mercurial > repos > ethevenot > profia

annotate profia_wrapper.R @ 3:5215be2bdc9e draft

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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
author ethevenot
date Tue, 09 Jan 2018 12:44:23 -0500
parents e29c563df582
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 2
diff changeset
1 #!/usr/bin/env Rscript
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 2
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 2
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3 library(batch) ## parseCommandArgs
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 2
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5 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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7 ##------------------------------
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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8 ## Initializing
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 2
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9 ##------------------------------
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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12 ## libraries
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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13 ##----------
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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15 suppressMessages(library(proFIA))
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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18 ## constants
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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19 ##----------
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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21 modNamC <- "proFIA" ## module name
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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24 ## log file
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 2
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25 ##---------
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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27 sink(argVc["information"])
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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29 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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30 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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33 ## arguments
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 2
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34 ##----------
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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37 if("zipfile" %in% names(argVc)) {
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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39 zipfile <- argVc["zipfile"]
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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41 ## We unzip automatically the raw files from the zip file
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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ethevenot
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43 if(exists("zipfile") && (zipfile!="")) {
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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44 if(!file.exists(zipfile)){
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
parents: 2
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45 error_message=paste("Cannot access the Zip file:", zipfile)
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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46 print(error_message)
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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47 stop(error_message)
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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48 }
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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ethevenot
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50 ## unzip
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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52 suppressWarnings(unzip(zipfile, unzip="unzip"))
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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54 ## get the directory name
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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56 filesInZip=unzip(zipfile, list=T);
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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57 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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58 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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59 directory = "."
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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60 if (length(directories) == 1) directory = directories
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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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)) {
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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68 directory <- argVc["library"]
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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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.")
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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73 print(error_message)
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74 stop(error_message)
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76 }
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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78 } else {
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80 error_message <- "No zipfile nor input library available"
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
ethevenot
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81 print(error_message)
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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82 stop(error_message)
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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84 }
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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86 ##------------------------------
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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87 ## Computations
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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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
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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96 cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "")
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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98 if("sizeMinN" %in% names(argVc) && argVc["sizeMinN"] != "none") {
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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99 if("scanMaxI" %in% names(argVc) && argVc["scanMaxI"] != "none") {
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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100 fiaset <- proFIAset(directory,
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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101 ppm = as.numeric(argVc["ppmN"]),
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102 dmz = as.numeric(argVc["dmzN"]),
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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103 bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")),
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104 sizeMin = as.numeric(argVc["sizeMinN"]),
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105 scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")),
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106 scanmax = as.numeric(argVc["scanMaxI"]),
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107 parallel = TRUE)
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108 } else {
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109 fiaset <- proFIAset(directory,
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110 ppm = as.numeric(argVc["ppmN"]),
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111 dmz = as.numeric(argVc["dmzN"]),
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112 bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")),
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113 sizeMin = as.numeric(argVc["sizeMinN"]),
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114 scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")),
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115 parallel = TRUE)
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116 }
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117 } else {
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118 if("scanMaxI" %in% names(argVc) && argVc["scanMaxI"] != "none") {
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119 fiaset <- proFIAset(directory,
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120 ppm = as.numeric(argVc["ppmN"]),
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121 dmz = as.numeric(argVc["dmzN"]),
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122 bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")),
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123 scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")),
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124 scanmax = as.numeric(argVc["scanMaxI"]),
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125 parallel = TRUE)
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126 } else {
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127 fiaset <- proFIAset(directory,
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128 ppm = as.numeric(argVc["ppmN"]),
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129 dmz = as.numeric(argVc["dmzN"]),
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130 bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")),
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131 scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")),
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132 parallel = TRUE)
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133 }
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134 }
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135
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136 stpI <- stpI + 1
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137
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138 cat("\n", stpI, ") Peak alignment ('group.FIA'):\n", sep = "")
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139
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140 fiaset <- group.FIA(fiaset,
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141 ppmGroup = as.numeric(argVc["ppmGroupN"]),
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142 dmz = as.numeric(argVc["dmzGroupN"]),
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143 fracGroup = as.numeric(argVc["fracGroupN"]))
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144
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145 stpI <- stpI + 1
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146
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147 cat("\n", stpI, ") Creating the peak table ('makeDataMatrix'):\n", sep = "")
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148
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149 fiaset <- makeDataMatrix(fiaset,
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150 maxo = FALSE)
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151
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152 stpI <- stpI + 1
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153
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154
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155 if(argVc["imputeC"] == "randomForest") {
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156
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157 cat("\n", stpI, ") Imputing missing values ('impute.randomForest'):\n", sep = "")
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158
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159 set.seed(123)
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160
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161 fiaset <- impute.randomForest(fiaset,
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162 parallel = FALSE)
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163
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164 set.seed(NULL)
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165
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166 stpI <- stpI + 1
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167 }
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168 ###TODO Fix the error message to set 'parallel' to TRUE: You must register a 'foreach' parallel backend to run 'missForest' in parallel. Set 'parallelize' to 'no' to compute serially.
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169 ###TODO add the impute.KNN_TN method
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170
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171
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172 options(warn = optWrnN)
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173
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174
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175 ##------------------------------
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176 ## Ending
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177 ##------------------------------
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178
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179
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180 ## Plotting
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181 ##---------
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182
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183 cat("\n", stpI, ") Plotting ('plot'):\n", sep = "")
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184
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185 pdf(argVc["figure"])
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186
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187 plot(fiaset)
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188
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189 dev.off()
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190
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191 stpI <- stpI + 1
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192
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193 ## Printing
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194 ##---------
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195
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196 cat("\n", stpI, ") Printing ('show'):\n", sep = "")
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197
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198 fiaset
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199
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200 stpI <- stpI + 1
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201
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202 ## Exporting
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203 ##----------
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204
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205 cat("\n", stpI, ") Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'):\n", sep = "")
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206
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207 datMN <- exportDataMatrix(fiaset)
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208 samDF <- exportSampleMetadata(fiaset)
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209 varDF <- exportVariableMetadata(fiaset)
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210
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211 if(nrow(datMN) == nrow(samDF) && ncol(datMN) == nrow(varDF)) {
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212 datDF <- as.data.frame(t(datMN))
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213 } else {
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214 datDF <- as.data.frame(datMN)
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215 }
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216 rownames(varDF) <- rownames(datDF)
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217
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218 datDF <- cbind.data.frame(dataMatrix = rownames(datDF),
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219 datDF)
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220 write.table(datDF,
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221 file = argVc["dataMatrix_out"],
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222 quote = FALSE,
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223 row.names = FALSE,
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224 sep = "\t")
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225
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226 samDF <- cbind.data.frame(sampleMetadata = samDF[, "sampleID"],
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227 class = samDF[, "class"])
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228 write.table(samDF,
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229 file = argVc["sampleMetadata_out"],
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230 quote = FALSE,
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231 row.names = FALSE,
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232 sep = "\t")
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233
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234 varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
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235 varDF)
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236 write.table(varDF,
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237 file = argVc["variableMetadata_out"],
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238 quote = FALSE,
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239 row.names = FALSE,
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240 sep = "\t")
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241
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242
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243 ## Closing
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244 ##--------
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245
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246 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
5215be2bdc9e planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
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247 as.character(Sys.time()), "\n", sep = "")
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248
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249 cat("\n\n\n============================================================================")
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250 cat("\nAdditional information about the call:\n")
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251 cat("\n1) Parameters:\n")
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252 print(cbind(value = argVc))
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253
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254 cat("\n2) Session Info:\n")
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255 sessioninfo <- sessionInfo()
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256 cat(sessioninfo$R.version$version.string,"\n")
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257 cat("Main packages:\n")
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258 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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259 cat("Other loaded packages:\n")
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260 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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261
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262 cat("============================================================================\n")
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263
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264 sink()
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265
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266 rm(list = ls())