Mercurial > repos > lecorguille > xcms_summary

annotate xcms_summary.r @ 26:db6549f27ad1 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8"
author workflow4metabolomics
date Tue, 12 May 2020 16:39:28 -0400
parents 46be2c523a7f
children bed23aa27b4b
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1 #!/usr/bin/env Rscript
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5 # ----- ARGUMENTS BLACKLIST -----
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6 #xcms.r
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7 argBlacklist <- c("zipfile", "singlefile_galaxyPath", "singlefile_sampleName", "xfunction", "xsetRdataOutput", "sampleMetadataOutput", "ticspdf", "bicspdf", "rplotspdf")
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8 #CAMERA.r
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9 argBlacklist <- c(argBlacklist, "dataMatrixOutput", "variableMetadataOutput", "new_file_path")
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10
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12 # ----- PACKAGE -----
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13 cat("\tSESSION INFO\n")
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15 #Import the different functions
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16 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
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17 source_local("lib.r")
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19 pkgs <- c("CAMERA","batch")
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20 loadAndDisplayPackages(pkgs)
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21 cat("\n\n");
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24 # ----- FUNCTION -----
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25 writehtml <- function(...) { cat(...,"\n", file=htmlOutput,append = TRUE,sep="") }
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26 writeraw <- function(htmlOutput, object, open="at") {
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27 log_file <- file(htmlOutput, open = open)
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28 sink(log_file)
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29 sink(log_file, type = "output")
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30 print(object)
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31 sink()
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32 close(log_file)
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33 }
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34 getSampleNames <- function(xobject) {
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35 if (class(xobject) == "xcmsSet")
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36 return (sampnames(xobject))
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37 if (class(xobject) == "XCMSnExp")
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38 return (xobject@phenoData@data$sample_name)
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39 }
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40 getFilePaths <- function(xobject) {
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41 if (class(xobject) == "xcmsSet")
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42 return (xobject@filepaths)
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43 if (class(xobject) == "XCMSnExp")
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44 return (fileNames(xobject))
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45 }
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46 equalParams <- function(param1, param2) {
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47 writeraw("param1.txt", param1, open="wt")
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48 writeraw("param2.txt", param2, open="wt")
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49 return(tools::md5sum("param1.txt") == tools::md5sum("param2.txt"))
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50 }
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53 # ----- ARGUMENTS -----
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54
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55 args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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58 # ----- ARGUMENTS PROCESSING -----
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59
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60 #image is an .RData file necessary to use xset variable given by previous tools
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61 load(args$image);
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62
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63 htmlOutput <- "summary.html"
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64 if (!is.null(args$htmlOutput)) htmlOutput = args$htmlOutput;
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66 user_email <- NULL
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67 if (!is.null(args$user_email)) user_email = args$user_email;
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69 # if the RData come from XCMS 1.x
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70 if (exists("xset")) {
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71 xobject <- xset
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72 # retrocompatability
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73 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject)))
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74 }
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75 # if the RData come from CAMERA
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76 if (exists("xa")) xobject <- xa@xcmsSet
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77 # if the RData come from XCMS 3.x
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78 if (exists("xdata")) {
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79 xobject <- xdata
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80 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(xdata@phenoData@data$sample_name))
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81 }
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82
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83 if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.")
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84
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86 # ----- MAIN PROCESSING INFO -----
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87 writehtml("<!DOCTYPE html>")
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88 writehtml("<HTML lang='en'>")
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90 writehtml("<HEAD>")
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91 writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />")
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93 writehtml("<title>[W4M] XCMS analysis summary</title>")
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94
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95 writehtml("<style>")
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96 writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }")
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97 writehtml("td,th { padding: 5px; padding-right: 12px; }")
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98 writehtml("th { background: #898989; text-align:left;color: white;}")
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99 writehtml("h2 { color: #FFA212; }")
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100 writehtml("ul li { margin-bottom:10px; }")
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101 writehtml("</style>")
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102 writehtml("</HEAD>")
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103
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104 writehtml("<BODY>")
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105 writehtml("<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>")
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106 # to pass the planemo shed_test
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107 if (user_email != "test@bx.psu.edu") {
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108 if (!is.null(user_email)) writehtml("By: ", user_email," - ")
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109 writehtml("Date: ", format(Sys.time(), "%y%m%d-%H:%M:%S"))
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110 }
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111 writehtml("</div>")
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112
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113 writehtml("<h2>Samples used:</h2>")
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114 writehtml("<div><table>")
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115 if (all(getSampleNames(xobject) == sampleNamesList$sampleNamesMakeNames)) {
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116 sampleNameHeaderHtml <- paste0("<th>sample</th>")
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117 sampleNameHtml <- paste0("<td>",getSampleNames(xobject),"</td>")
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118 } else {
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119 sampleNameHeaderHtml <- paste0("<th>sample</th><th>sample renamed</th>")
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120 sampleNameHtml <- paste0("<td>",getSampleNames(xobject),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>")
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121 }
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122
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123 if (!exists("md5sumList")) {
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124 md5sumHeaderHtml <- ""
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125 md5sumHtml <- ""
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126 md5sumLegend <- ""
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127 } else if (is.null(md5sumList$removalBadCharacters)) {
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128 md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th>")
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129 md5sumHtml <- paste0("<td>",md5sumList$origin,"</td>")
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130 md5sumLegend <- "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process."
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131 } else {
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132 md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>")
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133 md5sumHtml <- paste0("<td>",md5sumList$origin,"</td><td>",md5sumList$removalBadCharacters,"</td>")
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134 md5sumLegend <- "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process.<br/><sup>**</sup>Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>"
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135 }
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136
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137 writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>")
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138 writehtml(paste0("<tr>",sampleNameHtml,"<td>",getFilePaths(xobject),"</td>",md5sumHtml,"</tr>"))
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139
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140 writehtml("</table>")
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141 writehtml(md5sumLegend)
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142 writehtml("</div>")
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143
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144 writehtml("<h2>Function launched:</h2>")
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145 writehtml("<div><table>")
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146 writehtml("<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>")
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147 # XCMS 3.x
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148 if (class(xobject) == "XCMSnExp") {
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149 xcmsFunction <- NULL
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150 params <- NULL
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151 for (processHistoryItem in processHistory(xobject)) {
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152 if ((xcmsFunction == processType(processHistoryItem)) && equalParams(params, processParam(processHistoryItem)))
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153 next
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154 timestamp <- processDate(processHistoryItem)
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155 xcmsFunction <- processType(processHistoryItem)
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156 params <- processParam(processHistoryItem)
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157 writehtml("<tr><td>",timestamp,"</td><td>",xcmsFunction,"</td><td colspan='2'><pre>")
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158 writeraw(htmlOutput, params)
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159 writehtml("</pre></td></tr>")
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160 }
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161 }
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162 # CAMERA and retrocompatability XCMS 1.x
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163 if (exists("listOFlistArguments")) {
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164 for(tool in names(listOFlistArguments)) {
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165 listOFlistArgumentsDisplay <- listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]
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166
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167 timestamp <- strsplit(tool,"_")[[1]][1]
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168 xcmsFunction <- strsplit(tool,"_")[[1]][2]
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169 writehtml("<tr><td rowspan='",length(listOFlistArgumentsDisplay),"'>",timestamp,"</td><td rowspan='",length(listOFlistArgumentsDisplay),"'>",xcmsFunction,"</td>")
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170 line_begin <- ""
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171 for (arg in names(listOFlistArgumentsDisplay)) {
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172 writehtml(line_begin,"<td>",arg,"</td><td>",unlist(listOFlistArgumentsDisplay[arg][1]),"</td></tr>")
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173 line_begin <- "<tr>"
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174 }
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175 }
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176 }
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177 writehtml("</table>")
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178 writehtml("<br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss")
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179 writehtml("</div>")
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180
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181 if (class(xobject) == "XCMSnExp") {
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182 writehtml("<h2>Informations about the XCMSnExp object:</h2>")
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183
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184 writehtml("<div><pre>")
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185 writeraw(htmlOutput, xobject)
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186 writehtml("</pre></div>")
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187 }
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188
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189 writehtml("<h2>Informations about the xcmsSet object:</h2>")
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190
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191 writehtml("<div><pre>")
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192 # Get the legacy xcmsSet object
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193 xset <- getxcmsSetObject(xobject)
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194 writeraw(htmlOutput, xset)
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195 writehtml("</pre></div>")
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196
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197 # CAMERA
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198 if (exists("xa")) {
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199 writehtml("<h2>Informations about the CAMERA object:</h2>")
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200
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201 writehtml("<div>")
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202 writehtml("Number of pcgroup: ",length(xa@pspectra))
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203 writehtml("</div>")
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204 }
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205
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206 writehtml("<h2>Citations:</h2>")
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207 writehtml("<div><ul>")
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208 writehtml("<li>To cite the <b>XCMS</b> package in publications use:")
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209 writehtml("<ul>")
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210 writehtml("<li>","Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)","</li>")
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211 writehtml("<li>","Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)","</li>")
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212 writehtml("<li>","H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)","</li>")
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213 writehtml("</ul>")
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214 writehtml("</li>")
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215
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216 writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")
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217 writehtml("<ul>")
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218 writehtml("<li>","Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)","</li>")
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219 writehtml("</ul>")
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220 writehtml("</li>")
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221
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222 writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")
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223 writehtml("<ul>")
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224 writehtml("<li>","Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813","</li>")
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225 writehtml("</ul>")
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226 writehtml("</li>")
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227 writehtml("</ul></div>")
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228
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229 writehtml("</BODY>")
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230
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231 writehtml("</HTML>")