Mercurial > repos > lecorguille > xcms_summary

annotate xcms_summary.r @ 45:43122259be1f draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 15:56:21 +0000
parents 9df658383852
children 18d050f7b9d4
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dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
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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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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) {
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17 argv <- commandArgs(trailingOnly = FALSE)
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18 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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19 source(paste(base_dir, fname, sep = "/"))
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20 }
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21 source_local("lib.r")
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23 pkgs <- c("CAMERA", "batch")
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24 loadAndDisplayPackages(pkgs)
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25 cat("\n\n")
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28 # ----- FUNCTION -----
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29 writehtml <- function(...) {
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30 cat(..., "\n", file = htmlOutput, append = TRUE, sep = "")
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31 }
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32 writeraw <- function(htmlOutput, object, open = "at") {
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33 log_file <- file(htmlOutput, open = open)
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34 sink(log_file)
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35 sink(log_file, type = "output")
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36 print(object)
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37 sink()
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38 close(log_file)
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39 }
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40 getSampleNames <- function(xobject) {
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41 if (class(xobject) == "xcmsSet")
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42 return(sampnames(xobject))
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43 if (class(xobject) == "XCMSnExp")
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44 return(xobject@phenoData@data$sample_name)
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45 }
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46 getFilePaths <- function(xobject) {
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47 if (class(xobject) == "xcmsSet")
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48 return(xobject@filepaths)
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49 if (class(xobject) == "XCMSnExp")
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50 return(fileNames(xobject))
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51 }
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52 equalParams <- function(param1, param2) {
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53 writeraw("param1.txt", param1, open = "wt")
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54 writeraw("param2.txt", param2, open = "wt")
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55 return(tools::md5sum("param1.txt") == tools::md5sum("param2.txt"))
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56 }
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59 # ----- ARGUMENTS -----
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60
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61 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
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64 # ----- ARGUMENTS PROCESSING -----
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65
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66 #image is an .RData file necessary to use xset variable given by previous tools
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67 load(args$image)
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68
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69 htmlOutput <- "summary.html"
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70 if (!is.null(args$htmlOutput)) htmlOutput <- args$htmlOutput
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72 user_email <- NULL
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73 if (!is.null(args$user_email)) user_email <- args$user_email
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75 # if the RData come from XCMS 1.x
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76 if (exists("xset")) {
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77 xobject <- xset
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78 # retrocompatability
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79 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(sampnames(xobject)))
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80 }
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81 # if the RData come from CAMERA
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82 if (exists("xa")) {
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83 xobject <- xa@xcmsSet
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84 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xa@xcmsSet@phenoData$sample_name))
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85 }
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86 # if the RData come from XCMS 3.x
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87 if (exists("xdata")) {
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88 xobject <- xdata
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89 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xdata@phenoData@data$sample_name))
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90 }
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91
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92 if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.")
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94
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95 # ----- MAIN PROCESSING INFO -----
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96 writehtml("<!DOCTYPE html>")
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97 writehtml("<HTML lang='en'>")
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99 writehtml("<HEAD>")
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100 writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />")
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101
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102 writehtml("<title>[W4M] XCMS analysis summary</title>")
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104 writehtml("<style>")
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105 writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }")
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106 writehtml("td, th { padding: 5px; padding-right: 12px; }")
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107 writehtml("th { background: #898989; text-align:left;color: white;}")
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108 writehtml("h2 { color: #FFA212; }")
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109 writehtml("ul li { margin-bottom:10px; }")
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110 writehtml("</style>")
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111 writehtml("</HEAD>")
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112
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113 writehtml("<BODY>")
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114 writehtml("<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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115 # to pass the planemo shed_test
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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116 if (user_email != "test@bx.psu.edu") {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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117 if (!is.null(user_email)) writehtml("By: ", user_email, " - ")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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118 writehtml("Date: ", format(Sys.time(), "%y%m%d-%H:%M:%S"))
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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119 }
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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120 writehtml("</div>")
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121
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122 writehtml("<h2>Samples used:</h2>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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123 writehtml("<div><table>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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124 if (all(getSampleNames(xobject) == sampleNamesList$sampleNamesMakeNames)) {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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125 sampleNameHeaderHtml <- paste0("<th>sample</th>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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126 sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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127 } else {
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128 sampleNameHeaderHtml <- paste0("<th>sample</th><th>sample renamed</th>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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129 sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td><td>", sampleNamesList$sampleNamesMakeNames, "</td>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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130 }
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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131
45
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132 if (!exists("md5sumList")) {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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133 md5sumHeaderHtml <- ""
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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134 md5sumHtml <- ""
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135 md5sumLegend <- ""
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136 } else if (is.null(md5sumList$removalBadCharacters)) {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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137 md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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138 md5sumHtml <- paste0("<td>", md5sumList$origin, "</td>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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139 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."
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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140 } else {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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141 md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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142 md5sumHtml <- paste0("<td>", md5sumList$origin, "</td><td>", md5sumList$removalBadCharacters, "</td>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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143 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/>"
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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144 }
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145
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146 writehtml("<tr>", sampleNameHeaderHtml, "<th>filename</th>", md5sumHeaderHtml, "</tr>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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147 writehtml(paste0("<tr>", sampleNameHtml, "<td>", getFilePaths(xobject), "</td>", md5sumHtml, "</tr>"))
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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148
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149 writehtml("</table>")
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150 writehtml(md5sumLegend)
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151 writehtml("</div>")
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152
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153 writehtml("<h2>Function launched:</h2>")
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154 writehtml("<div><table>")
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155 writehtml("<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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156 # XCMS 3.x
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157 if (class(xobject) == "XCMSnExp") {
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158 xcmsFunction <- NULL
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159 params <- NULL
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160 for (processHistoryItem in processHistory(xobject)) {
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161 if ((xcmsFunction == processType(processHistoryItem)) && equalParams(params, processParam(processHistoryItem)))
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162 next
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163 timestamp <- processDate(processHistoryItem)
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164 xcmsFunction <- processType(processHistoryItem)
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165 params <- processParam(processHistoryItem)
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166 writehtml("<tr><td>", timestamp, "</td><td>", xcmsFunction, "</td><td colspan='2'><pre>")
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167 writeraw(htmlOutput, params)
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168 writehtml("</pre></td></tr>")
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169 }
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170 }
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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171 # CAMERA and retrocompatability XCMS 1.x
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172 if (exists("listOFlistArguments")) {
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173 for (tool in names(listOFlistArguments)) {
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174 listOFlistArgumentsDisplay <- listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]
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175
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176 timestamp <- strsplit(tool, "_")[[1]][1]
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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177 xcmsFunction <- strsplit(tool, "_")[[1]][2]
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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178 writehtml("<tr><td rowspan='", length(listOFlistArgumentsDisplay), "'>", timestamp, "</td><td rowspan='", length(listOFlistArgumentsDisplay), "'>", xcmsFunction, "</td>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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179 line_begin <- ""
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180 for (arg in names(listOFlistArgumentsDisplay)) {
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181 writehtml(line_begin, "<td>", arg, "</td><td>", unlist(listOFlistArgumentsDisplay[arg][1]), "</td></tr>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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182 line_begin <- "<tr>"
29
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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183 }
45
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184 }
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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185 }
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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186 writehtml("</table>")
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187 writehtml("<br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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188 writehtml("</div>")
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189
45
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190 if (class(xobject) == "XCMSnExp") {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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191 writehtml("<h2>Informations about the XCMSnExp object:</h2>")
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192 writehtml("<div><pre>")
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193 writeraw(htmlOutput, xobject)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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194 writehtml("</pre></div>")
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195 }
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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196
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197 writehtml("<h2>Informations about the xcmsSet object:</h2>")
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198
45
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199 writehtml("<div><pre>")
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200 # Get the legacy xcmsSet object
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201 xset <- getxcmsSetObject(xobject)
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202 writeraw(htmlOutput, xset)
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203 writehtml("</pre></div>")
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204
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205 # CAMERA
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206 if (exists("xa")) {
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207 writehtml("<h2>Informations about the CAMERA object:</h2>")
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208 writehtml("<div>")
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209 writehtml("Number of pcgroup: ", length(xa@pspectra))
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210 writehtml("</div>")
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211 }
0
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212
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213 writehtml("<h2>Citations:</h2>")
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214 writehtml("<div><ul>")
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215 writehtml("<li>To cite the <b>XCMS</b> package in publications use:")
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216 writehtml("<ul>")
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217 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>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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218 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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219 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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220 writehtml("</ul>")
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221 writehtml("</li>")
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222
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223 writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")
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224 writehtml("<ul>")
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225 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>")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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226 writehtml("</ul>")
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227 writehtml("</li>")
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228
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229 writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")
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230 writehtml("<ul>")
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231 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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232 writehtml("</ul>")
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233 writehtml("</li>")
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234 writehtml("</ul></div>")
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235
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236 writehtml("</BODY>")
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237
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238 writehtml("</HTML>")