0
+ − 1 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
+ − 2 # version="0.1.0"
+ − 3 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABIMS TEAM
+ − 4
+ − 5
+ − 6
+ − 7 # ----- ARGUMENTS BLACKLIST -----
+ − 8 #xcms.r
+ − 9 argBlacklist=c("zipfile","xfunction","xsetRdataOutput","sampleMetadataOutput","ticspdf","bicspdf","rplotspdf")
+ − 10 #CAMERA.r
+ − 11 argBlacklist=c(argBlacklist,"dataMatrixOutput","variableMetadataOutput","new_file_path")
+ − 12
+ − 13 # ----- PACKAGE -----
+ − 14
+ − 15 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "tcltk","igraph", "xcms","snow","CAMERA","multtest","batch")
+ − 16 for(pkg in pkgs) {
+ − 17 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
+ − 18 }
+ − 19
+ − 20
+ − 21 # ----- FUNCTION -----
+ − 22 writehtml = function(...) { cat(...,"\n", file=htmlOutput,append = TRUE,sep="") }
+ − 23
+ − 24
+ − 25 # ----- ARGUMENTS -----
+ − 26
+ − 27 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
+ − 28
+ − 29
+ − 30 # ----- ARGUMENTS PROCESSING -----
+ − 31
+ − 32 #image is an .RData file necessary to use xset variable given by previous tools
+ − 33 load(listArguments[["image"]]);
+ − 34
+ − 35 htmlOutput = "summary.html"
+ − 36 if (!is.null(listArguments[["htmlOutput"]])) htmlOutput = listArguments[["htmlOutput"]];
+ − 37
+ − 38 user_email = NULL
+ − 39 if (!is.null(listArguments[["user_email"]])) user_email = listArguments[["user_email"]];
+ − 40
+ − 41 # if the RData come from CAMERA
+ − 42 if (!exists("xset") & exists("xa")) xset=xa@xcmsSet
+ − 43
+ − 44 # retrocompatability
1
+ − 45 if (!exists("sampleNamesList")) sampleNamesList=list("sampleNamesMakeNames"=make.names(sampnames(xset)))
0
+ − 46
+ − 47 if (!exists("xset")) stop("You need at least a xset or a xa object.")
+ − 48
+ − 49
+ − 50
+ − 51 # ----- MAIN PROCESSING INFO -----
+ − 52 writehtml("<!DOCTYPE html>")
+ − 53 writehtml("<HTML lang='en'>")
+ − 54
+ − 55 writehtml("<HEAD>")
+ − 56 writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />")
+ − 57
+ − 58 writehtml("<title>[W4M] XCMS analysis summary</title>")
+ − 59
+ − 60 writehtml("<style>")
+ − 61 writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }")
+ − 62 writehtml("td,th { padding: 5px; padding-right: 12px; }")
+ − 63 writehtml("th { background: #898989; text-align:left;color: white;}")
+ − 64 writehtml("h2 { color: #FFA212; }")
+ − 65 writehtml("ul li { margin-bottom:10px; }")
+ − 66 writehtml("</style>")
+ − 67 writehtml("</HEAD>")
+ − 68
+ − 69 writehtml("<BODY>")
+ − 70 writehtml("<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>")
+ − 71 # to pass the planemo shed_test
+ − 72 if (user_email != "test@bx.psu.edu") {
+ − 73 if (!is.null(user_email)) writehtml("By: ",user_email," - ")
+ − 74 writehtml("Date: ",format(Sys.time(), "%y%m%d-%H:%M:%S"))
+ − 75 }
+ − 76 writehtml("</div>")
+ − 77
+ − 78 writehtml("<h2>Samples used:</h2>")
+ − 79 writehtml("<div><table>")
+ − 80 if (all(sampnames(xset) != sampleNamesList$sampleNamesMakeNames)) {
+ − 81 sampleNameHeaderHtml = paste("<th>sample</th>")
+ − 82 sampleNameHtml = paste("<td>",sampnames(xset),"</td>")
+ − 83 } else {
+ − 84 sampleNameHeaderHtml = paste("<th>sample</th><th>sample renamed</th>")
+ − 85 sampleNameHtml = paste("<td>",sampnames(xset),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>")
+ − 86 }
+ − 87
+ − 88 if (!exists("md5sumList")) {
+ − 89 md5sumHeaderHtml = ""
+ − 90 md5sumHtml = ""
+ − 91 md5sumLegend=""
+ − 92 } else if (!is.null(md5sumList$removalBadCharacters)) {
+ − 93 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>")
+ − 94 md5sumHtml = paste("<td>",md5sumList$origin,"</td>")
+ − 95 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 chancged during the process."
+ − 96 } else {
+ − 97 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>")
+ − 98 md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$origin,"</td>")
+ − 99 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 chancged during the process.<br/><sup>**</sup>Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>"
+ − 100 }
+ − 101
+ − 102 writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>")
+ − 103 writehtml(paste("<tr>",sampleNameHtml,"<td>",xset@filepaths,"</td>",md5sumHtml,"</tr>"))
+ − 104
+ − 105 writehtml("</table>")
+ − 106 writehtml(md5sumLegend)
+ − 107 writehtml("</div>")
+ − 108
+ − 109 writehtml("<h2>Function launched:</h2>")
+ − 110 writehtml("<div><table>")
+ − 111 writehtml("<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>")
+ − 112 for(tool in names(listOFlistArguments)) {
+ − 113 listOFlistArgumentsDisplay=listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]
+ − 114
+ − 115 timestamp = strsplit(tool,"_")[[1]][1]
+ − 116 xcmsFunction = strsplit(tool,"_")[[1]][2]
+ − 117 writehtml("<tr><td rowspan='",length(listOFlistArgumentsDisplay),"'>",timestamp,"</td><td rowspan='",length(listOFlistArgumentsDisplay),"'>",xcmsFunction,"</td>")
+ − 118 line_begin=""
+ − 119 for (arg in names(listOFlistArgumentsDisplay)) {
+ − 120 writehtml(line_begin,"<td>",arg,"</td><td>",unlist(listOFlistArgumentsDisplay[arg][1]),"</td></tr>")
+ − 121 line_begin="<tr>"
+ − 122 }
+ − 123 }
+ − 124 writehtml("</table>")
+ − 125 writehtml("<br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss")
+ − 126 writehtml("</div>")
+ − 127
+ − 128 writehtml("<h2>Informations about the xcmsSet object:</h2>")
+ − 129
+ − 130 writehtml("<div><pre>")
+ − 131 log_file=file(htmlOutput, open = "at")
+ − 132 sink(log_file)
+ − 133 sink(log_file, type = "output")
+ − 134 xset
+ − 135 sink()
+ − 136 writehtml("</pre></div>")
+ − 137
+ − 138 if (exists("xa")) {
+ − 139 writehtml("<h2>Informations about the CAMERA object:</h2>")
+ − 140
+ − 141 writehtml("<div>")
+ − 142 writehtml("Number of pcgroup:",length(xa@pspectra))
+ − 143 writehtml("</div>")
+ − 144 }
+ − 145
+ − 146 writehtml("<h2>Citations:</h2>")
+ − 147 writehtml("<div><ul>")
+ − 148 writehtml("<li>To cite the <b>XCMS</b> package in publications use:")
+ − 149 writehtml("<ul>")
+ − 150 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>")
+ − 151 writehtml("<li>","Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)","</li>")
+ − 152 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>")
+ − 153 writehtml("</ul>")
+ − 154 writehtml("</li>")
+ − 155
+ − 156 writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")
+ − 157 writehtml("<ul>")
+ − 158 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>")
+ − 159 writehtml("</ul>")
+ − 160 writehtml("</li>")
+ − 161
+ − 162 writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")
+ − 163 writehtml("<ul>")
+ − 164 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>")
+ − 165 writehtml("</ul>")
+ − 166 writehtml("</li>")
+ − 167 writehtml("</ul></div>")
+ − 168
+ − 169 writehtml("</BODY>")
+ − 170
+ − 171 writehtml("</HTML>")
+ − 172
