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1 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
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2 # version="0.1.0"
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3 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABIMS TEAM
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4
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5
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6
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7 # ----- ARGUMENTS BLACKLIST -----
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8 #xcms.r
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9 argBlacklist=c("zipfile","xfunction","xsetRdataOutput","sampleMetadataOutput","ticspdf","bicspdf","rplotspdf")
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10 #CAMERA.r
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11 argBlacklist=c(argBlacklist,"dataMatrixOutput","variableMetadataOutput","new_file_path")
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12
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13 # ----- PACKAGE -----
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14
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15 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")
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16 for(pkg in pkgs) {
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17 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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18 }
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19
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20
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21 # ----- FUNCTION -----
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22 writehtml = function(...) { cat(...,"\n", file=htmlOutput,append = TRUE,sep="") }
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23
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24
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25 # ----- ARGUMENTS -----
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26
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27 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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28
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29
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30 # ----- ARGUMENTS PROCESSING -----
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31
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32 #image is an .RData file necessary to use xset variable given by previous tools
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33 load(listArguments[["image"]]);
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34
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35 htmlOutput = "report.html"
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36 if (!is.null(listArguments[["htmlOutput"]])){
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37 htmlOutput = listArguments[["htmlOutput"]];
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38 }
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39
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40 user_email = NULL
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41 if (!is.null(listArguments[["user_email"]])){
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42 user_email = listArguments[["user_email"]];
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43 }
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44
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45
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46 # ----- MAIN PROCESSING INFO -----
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47 writehtml("<!DOCTYPE html>")
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48 writehtml("<HTML lang='en'>")
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49
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50 writehtml("<HEAD>")
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51 writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />")
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52
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53 writehtml("<title>[W4M] XCMS analysis report</title>")
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54
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55 writehtml("<style>")
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56 writehtml("table { min-width: 500px; border:1px solid #D6B161; border-collapse:collapse;}")
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57 writehtml("th { background: #898989; text-align:left;}")
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58 writehtml("tr { border: 1px solid #000000 }")
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59 writehtml("h2 { color: #FFA212; }")
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60 writehtml("ul li { margin-bottom:10px; }")
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61 writehtml("</style>")
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62 writehtml("</HEAD>")
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63
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64 writehtml("<BODY>")
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65 writehtml("<h1>___ XCMS analysis report using Workflow4Metabolomics ___</h1>")
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66 # to pass the planemo shed_test
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67 if (user_email != "test@bx.psu.edu") {
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68 if (!is.null(user_email)) writehtml("By: ",user_email," - ")
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69 writehtml("Date: ",format(Sys.time(), "%y%m%d-%H:%M:%S"))
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70 }
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71
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72
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73 writehtml("<h2>Samples used:</h2>")
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74 writehtml("<table")
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75 writehtml("<tr><th>sample</th><th>filename</th></tr>")
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76 writehtml(paste("<tr><td>",sampnames(xset),"</td><td>",xset@filepaths,"</td></tr>"))
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77 writehtml("</table>")
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78
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79 writehtml("<h2>Function launched:</h2>")
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80 writehtml("<table>")
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81 writehtml("<tr><th>timestamp<br />(ymd-h:m:s)</th><th>function</th><th>argument</th><th>value</th></tr>")
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82 for(tool in names(listOFlistArguments)) {
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83 listOFlistArgumentsDisplay=listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]
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84
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85 timestamp = strsplit(tool,"_")[[1]][1]
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86 xcmsFunction = strsplit(tool,"_")[[1]][2]
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87 writehtml("<tr><td rowspan='",length(listOFlistArgumentsDisplay),"'>",timestamp,"</td><td rowspan='",length(listOFlistArgumentsDisplay),"'>",xcmsFunction,"</td>")
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88 line_begin=""
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89 for (arg in names(listOFlistArgumentsDisplay)) {
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90 writehtml(line_begin,"<td>",arg,"</td><td>",unlist(listOFlistArgumentsDisplay[arg][1]),"</td></tr>")
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91 line_begin="<tr>"
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92 }
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93 }
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94 writehtml("</table>")
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95
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96 writehtml("<h2>Information about the xcmsSet object:</h2>")
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97
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98 log_file=file(htmlOutput, open = "at")
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99 writehtml("<pre>")
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100 sink(log_file)
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101 sink(log_file, type = "output")
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102 xset
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103 sink()
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104 writehtml("</pre>")
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105
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106 writehtml("<h2>Citations:</h2>")
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107 writehtml("<ul>")
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108 writehtml("<li>To cite the <b>XCMS</b> package in publications use:")
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109 writehtml("<ul>")
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110 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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111 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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112 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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113 writehtml("</ul>")
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114 writehtml("</li>")
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115
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116 writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")
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117 writehtml("<ul>")
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118 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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119 writehtml("</ul>")
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120 writehtml("</li>")
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121
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122 writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")
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123 writehtml("<ul>")
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124 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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125 writehtml("</ul>")
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126 writehtml("</li>")
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127 writehtml("</ul>")
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128
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129 writehtml("</BODY>")
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130
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131 writehtml("</HTML>")
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132
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