Mercurial > repos > lecorguille > xcms_summary
diff xcms_summary.r @ 0:930478b22633 draft
planemo upload
| author | lecorguille |
|---|---|
| date | Mon, 22 Feb 2016 16:44:04 -0500 |
| parents | |
| children | 457a68338c2f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xcms_summary.r Mon Feb 22 16:44:04 2016 -0500 @@ -0,0 +1,172 @@ +#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file +# version="0.1.0" +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABIMS TEAM + + + +# ----- ARGUMENTS BLACKLIST ----- +#xcms.r +argBlacklist=c("zipfile","xfunction","xsetRdataOutput","sampleMetadataOutput","ticspdf","bicspdf","rplotspdf") +#CAMERA.r +argBlacklist=c(argBlacklist,"dataMatrixOutput","variableMetadataOutput","new_file_path") + +# ----- PACKAGE ----- + +pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "tcltk","igraph", "xcms","snow","CAMERA","multtest","batch") +for(pkg in pkgs) { + suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) +} + + +# ----- FUNCTION ----- +writehtml = function(...) { cat(...,"\n", file=htmlOutput,append = TRUE,sep="") } + + +# ----- ARGUMENTS ----- + +listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects + + +# ----- ARGUMENTS PROCESSING ----- + +#image is an .RData file necessary to use xset variable given by previous tools +load(listArguments[["image"]]); + +htmlOutput = "summary.html" +if (!is.null(listArguments[["htmlOutput"]])) htmlOutput = listArguments[["htmlOutput"]]; + +user_email = NULL +if (!is.null(listArguments[["user_email"]])) user_email = listArguments[["user_email"]]; + +# if the RData come from CAMERA +if (!exists("xset") & exists("xa")) xset=xa@xcmsSet + +# retrocompatability +if (!exists("sampleNamesList")) sampleNamesList=List("sampleNamesMakeNames"=make.names(sampnames(xset))) + +if (!exists("xset")) stop("You need at least a xset or a xa object.") + + + +# ----- MAIN PROCESSING INFO ----- +writehtml("<!DOCTYPE html>") +writehtml("<HTML lang='en'>") + +writehtml("<HEAD>") + writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />") + + writehtml("<title>[W4M] XCMS analysis summary</title>") + + writehtml("<style>") + writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }") + writehtml("td,th { padding: 5px; padding-right: 12px; }") + writehtml("th { background: #898989; text-align:left;color: white;}") + writehtml("h2 { color: #FFA212; }") + writehtml("ul li { margin-bottom:10px; }") + writehtml("</style>") +writehtml("</HEAD>") + +writehtml("<BODY>") + writehtml("<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>") + # to pass the planemo shed_test + if (user_email != "test@bx.psu.edu") { + if (!is.null(user_email)) writehtml("By: ",user_email," - ") + writehtml("Date: ",format(Sys.time(), "%y%m%d-%H:%M:%S")) + } + writehtml("</div>") + + writehtml("<h2>Samples used:</h2>") + writehtml("<div><table>") + if (all(sampnames(xset) != sampleNamesList$sampleNamesMakeNames)) { + sampleNameHeaderHtml = paste("<th>sample</th>") + sampleNameHtml = paste("<td>",sampnames(xset),"</td>") + } else { + sampleNameHeaderHtml = paste("<th>sample</th><th>sample renamed</th>") + sampleNameHtml = paste("<td>",sampnames(xset),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>") + } + + if (!exists("md5sumList")) { + md5sumHeaderHtml = "" + md5sumHtml = "" + md5sumLegend="" + } else if (!is.null(md5sumList$removalBadCharacters)) { + md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>") + md5sumHtml = paste("<td>",md5sumList$origin,"</td>") + 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." + } else { + md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>") + md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$origin,"</td>") + 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/>" + } + + writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>") + writehtml(paste("<tr>",sampleNameHtml,"<td>",xset@filepaths,"</td>",md5sumHtml,"</tr>")) + + writehtml("</table>") + writehtml(md5sumLegend) + writehtml("</div>") + + writehtml("<h2>Function launched:</h2>") + writehtml("<div><table>") + writehtml("<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>") + for(tool in names(listOFlistArguments)) { + listOFlistArgumentsDisplay=listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)] + + timestamp = strsplit(tool,"_")[[1]][1] + xcmsFunction = strsplit(tool,"_")[[1]][2] + writehtml("<tr><td rowspan='",length(listOFlistArgumentsDisplay),"'>",timestamp,"</td><td rowspan='",length(listOFlistArgumentsDisplay),"'>",xcmsFunction,"</td>") + line_begin="" + for (arg in names(listOFlistArgumentsDisplay)) { + writehtml(line_begin,"<td>",arg,"</td><td>",unlist(listOFlistArgumentsDisplay[arg][1]),"</td></tr>") + line_begin="<tr>" + } + } + writehtml("</table>") + writehtml("<br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss") + writehtml("</div>") + + writehtml("<h2>Informations about the xcmsSet object:</h2>") + + writehtml("<div><pre>") + log_file=file(htmlOutput, open = "at") + sink(log_file) + sink(log_file, type = "output") + xset + sink() + writehtml("</pre></div>") + + if (exists("xa")) { + writehtml("<h2>Informations about the CAMERA object:</h2>") + + writehtml("<div>") + writehtml("Number of pcgroup:",length(xa@pspectra)) + writehtml("</div>") + } + + writehtml("<h2>Citations:</h2>") + writehtml("<div><ul>") + writehtml("<li>To cite the <b>XCMS</b> package in publications use:") + writehtml("<ul>") + 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>") + writehtml("<li>","Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)","</li>") + 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>") + writehtml("</ul>") + writehtml("</li>") + + writehtml("<li>To cite the <b>CAMERA</b> package in publications use:") + writehtml("<ul>") + 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>") + writehtml("</ul>") + writehtml("</li>") + + writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:") + writehtml("<ul>") + 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>") + writehtml("</ul>") + writehtml("</li>") + writehtml("</ul></div>") + +writehtml("</BODY>") + +writehtml("</HTML>") +