Mercurial > repos > lecorguille > xcms_summary

annotate xcms_summary.r @ 31:1ae878634ab3 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:48:46 +0000
parents 2a2850fdf29e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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 }
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44 if (class(xobject) == "XCMSnExp") {
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45 return(xobject@phenoData@data$sample_name)
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46 }
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47 }
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48 getFilePaths <- function(xobject) {
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49 if (class(xobject) == "xcmsSet") {
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50 return(xobject@filepaths)
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51 }
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52 if (class(xobject) == "XCMSnExp") {
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53 return(fileNames(xobject))
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54 }
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55 }
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56 equalParams <- function(param1, param2) {
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57 writeraw("param1.txt", param1, open = "wt")
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58 writeraw("param2.txt", param2, open = "wt")
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59 return(tools::md5sum("param1.txt") == tools::md5sum("param2.txt"))
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60 }
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63 # ----- ARGUMENTS -----
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64
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65 args <- parseCommandArgs(evaluate = FALSE) # interpretation of arguments given in command line as an R list of objects
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68 # ----- ARGUMENTS PROCESSING -----
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69
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70 # image is an .RData file necessary to use xset variable given by previous tools
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71 load(args$image)
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73 htmlOutput <- "summary.html"
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74 if (!is.null(args$htmlOutput)) htmlOutput <- args$htmlOutput
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75
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76 user_email <- NULL
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77 if (!is.null(args$user_email)) user_email <- args$user_email
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78
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79 # if the RData come from XCMS 1.x
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80 if (exists("xset")) {
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81 xobject <- xset
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82 # retrocompatability
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83 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(sampnames(xobject)))
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84 }
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85 # if the RData come from CAMERA
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86 if (exists("xa")) {
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87 xobject <- xa@xcmsSet
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88 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xa@xcmsSet@phenoData$sample_name))
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89 }
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90 # if the RData come from XCMS 3.x
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91 if (exists("xdata")) {
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92 xobject <- xdata
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93 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xdata@phenoData@data$sample_name))
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94 }
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96 if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.")
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99 # ----- MAIN PROCESSING INFO -----
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100 writehtml("<!DOCTYPE html>")
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101 writehtml("<HTML lang='en'>")
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103 writehtml("<HEAD>")
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104 writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />")
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105
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106 writehtml("<title>[W4M] XCMS analysis summary</title>")
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108 writehtml("<style>")
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109 writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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110 writehtml("td, th { padding: 5px; padding-right: 12px; }")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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111 writehtml("th { background: #898989; text-align:left;color: white;}")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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112 writehtml("h2 { color: #FFA212; }")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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113 writehtml("ul li { margin-bottom:10px; }")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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114 writehtml("</style>")
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115 writehtml("</HEAD>")
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116
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117 writehtml("<BODY>")
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118 writehtml("<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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119 # to pass the planemo shed_test
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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120 if (user_email != "test@bx.psu.edu") {
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121 if (!is.null(user_email)) writehtml("By: ", user_email, " - ")
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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122 writehtml("Date: ", format(Sys.time(), "%y%m%d-%H:%M:%S"))
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2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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123 }
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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124 writehtml("</div>")
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125
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2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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126 writehtml("<h2>Samples used:</h2>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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127 writehtml("<div><table>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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128 if (all(getSampleNames(xobject) == sampleNamesList$sampleNamesMakeNames)) {
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1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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129 sampleNameHeaderHtml <- paste0("<th>sample</th>")
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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130 sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td>")
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131 } else {
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132 sampleNameHeaderHtml <- paste0("<th>sample</th><th>sample renamed</th>")
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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133 sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td><td>", sampleNamesList$sampleNamesMakeNames, "</td>")
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2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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134 }
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135
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136 if (!exists("md5sumList")) {
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137 md5sumHeaderHtml <- ""
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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138 md5sumHtml <- ""
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139 md5sumLegend <- ""
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2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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140 } else if (is.null(md5sumList$removalBadCharacters)) {
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1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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141 md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th>")
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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142 md5sumHtml <- paste0("<td>", md5sumList$origin, "</td>")
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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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."
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144 } else {
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145 md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>")
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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146 md5sumHtml <- paste0("<td>", md5sumList$origin, "</td><td>", md5sumList$removalBadCharacters, "</td>")
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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147 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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2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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148 }
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149
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150 writehtml("<tr>", sampleNameHeaderHtml, "<th>filename</th>", md5sumHeaderHtml, "</tr>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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151 writehtml(paste0("<tr>", sampleNameHtml, "<td>", getFilePaths(xobject), "</td>", md5sumHtml, "</tr>"))
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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152
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153 writehtml("</table>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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154 writehtml(md5sumLegend)
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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155 writehtml("</div>")
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156
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157 writehtml("<h2>Function launched:</h2>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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158 writehtml("<div><table>")
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159 writehtml("<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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160 # XCMS 3.x
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161 if (class(xobject) == "XCMSnExp") {
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162 xcmsFunction <- NULL
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163 params <- NULL
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164 for (processHistoryItem in processHistory(xobject)) {
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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165 if ((xcmsFunction == processType(processHistoryItem)) && equalParams(params, processParam(processHistoryItem))) {
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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166 next
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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167 }
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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168 timestamp <- processDate(processHistoryItem)
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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169 xcmsFunction <- processType(processHistoryItem)
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170 params <- processParam(processHistoryItem)
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171 writehtml("<tr><td>", timestamp, "</td><td>", xcmsFunction, "</td><td colspan='2'><pre>")
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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172 writeraw(htmlOutput, params)
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173 writehtml("</pre></td></tr>")
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174 }
29
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175 }
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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176 # CAMERA and retrocompatability XCMS 1.x
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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177 if (exists("listOFlistArguments")) {
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178 for (tool in names(listOFlistArguments)) {
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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179 listOFlistArgumentsDisplay <- listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]
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180
31
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181 timestamp <- strsplit(tool, "_")[[1]][1]
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182 xcmsFunction <- strsplit(tool, "_")[[1]][2]
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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183 writehtml("<tr><td rowspan='", length(listOFlistArgumentsDisplay), "'>", timestamp, "</td><td rowspan='", length(listOFlistArgumentsDisplay), "'>", xcmsFunction, "</td>")
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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184 line_begin <- ""
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185 for (arg in names(listOFlistArgumentsDisplay)) {
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186 writehtml(line_begin, "<td>", arg, "</td><td>", unlist(listOFlistArgumentsDisplay[arg][1]), "</td></tr>")
1ae878634ab3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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187 line_begin <- "<tr>"
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188 }
15
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189 }
29
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190 }
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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191 writehtml("</table>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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192 writehtml("<br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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193 writehtml("</div>")
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194
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195 if (class(xobject) == "XCMSnExp") {
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196 writehtml("<h2>Informations about the XCMSnExp object:</h2>")
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197 writehtml("<div><pre>")
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198 writeraw(htmlOutput, xobject)
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199 writehtml("</pre></div>")
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200 }
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201
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202 writehtml("<h2>Informations about the xcmsSet object:</h2>")
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203
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204 writehtml("<div><pre>")
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205 # Get the legacy xcmsSet object
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206 xset <- getxcmsSetObject(xobject)
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207 writeraw(htmlOutput, xset)
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208 writehtml("</pre></div>")
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209
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210 # CAMERA
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211 if (exists("xa")) {
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212 writehtml("<h2>Informations about the CAMERA object:</h2>")
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213 writehtml("<div>")
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214 writehtml("Number of pcgroup: ", length(xa@pspectra))
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215 writehtml("</div>")
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216 }
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217
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218 writehtml("<h2>Citations:</h2>")
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219 writehtml("<div><ul>")
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220 writehtml("<li>To cite the <b>XCMS</b> package in publications use:")
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221 writehtml("<ul>")
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222 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>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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223 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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224 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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225 writehtml("</ul>")
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226 writehtml("</li>")
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227
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228 writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")
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229 writehtml("<ul>")
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230 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>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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231 writehtml("</ul>")
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232 writehtml("</li>")
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233
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234 writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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235 writehtml("<ul>")
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236 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>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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237 writehtml("</ul>")
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238 writehtml("</li>")
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239 writehtml("</ul></div>")
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240
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241 writehtml("</BODY>")
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242
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243 writehtml("</HTML>")