Mercurial > repos > lecorguille > xcms_summary
diff xcms_summary.r @ 29:2a2850fdf29e draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
| author | workflow4metabolomics |
|---|---|
| date | Mon, 11 Sep 2023 09:23:36 +0000 |
| parents | 018a9771de28 |
| children |
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--- a/xcms_summary.r Wed Apr 07 16:46:50 2021 +0000 +++ b/xcms_summary.r Mon Sep 11 09:23:36 2023 +0000 @@ -14,13 +14,15 @@ #Import the different functions source_local <- function(fname) { - argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/")) + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep = "/")) } source_local("lib.r") pkgs <- c("CAMERA", "batch") loadAndDisplayPackages(pkgs) -cat("\n\n"); +cat("\n\n") # ----- FUNCTION ----- @@ -28,29 +30,29 @@ cat(..., "\n", file = htmlOutput, append = TRUE, sep = "") } writeraw <- function(htmlOutput, object, open = "at") { - log_file <- file(htmlOutput, open = open) - sink(log_file) - sink(log_file, type = "output") - print(object) - sink() - close(log_file) + log_file <- file(htmlOutput, open = open) + sink(log_file) + sink(log_file, type = "output") + print(object) + sink() + close(log_file) } getSampleNames <- function(xobject) { - if (class(xobject) == "xcmsSet") - return(sampnames(xobject)) - if (class(xobject) == "XCMSnExp") - return(xobject@phenoData@data$sample_name) + if (class(xobject) == "xcmsSet") + return(sampnames(xobject)) + if (class(xobject) == "XCMSnExp") + return(xobject@phenoData@data$sample_name) } getFilePaths <- function(xobject) { - if (class(xobject) == "xcmsSet") - return(xobject@filepaths) - if (class(xobject) == "XCMSnExp") - return(fileNames(xobject)) + if (class(xobject) == "xcmsSet") + return(xobject@filepaths) + if (class(xobject) == "XCMSnExp") + return(fileNames(xobject)) } equalParams <- function(param1, param2) { - writeraw("param1.txt", param1, open = "wt") - writeraw("param2.txt", param2, open = "wt") - return(tools::md5sum("param1.txt") == tools::md5sum("param2.txt")) + writeraw("param1.txt", param1, open = "wt") + writeraw("param2.txt", param2, open = "wt") + return(tools::md5sum("param1.txt") == tools::md5sum("param2.txt")) } @@ -62,29 +64,29 @@ # ----- ARGUMENTS PROCESSING ----- #image is an .RData file necessary to use xset variable given by previous tools -load(args$image); +load(args$image) htmlOutput <- "summary.html" -if (!is.null(args$htmlOutput)) htmlOutput <- args$htmlOutput; +if (!is.null(args$htmlOutput)) htmlOutput <- args$htmlOutput user_email <- NULL -if (!is.null(args$user_email)) user_email <- args$user_email; +if (!is.null(args$user_email)) user_email <- args$user_email # if the RData come from XCMS 1.x if (exists("xset")) { - xobject <- xset - # retrocompatability - if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(sampnames(xobject))) + xobject <- xset + # retrocompatability + if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(sampnames(xobject))) } # if the RData come from CAMERA if (exists("xa")) { - xobject <- xa@xcmsSet - if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xa@xcmsSet@phenoData$sample_name)) + xobject <- xa@xcmsSet + if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xa@xcmsSet@phenoData$sample_name)) } # if the RData come from XCMS 3.x if (exists("xdata")) { - xobject <- xdata - if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xdata@phenoData@data$sample_name)) + xobject <- xdata + if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xdata@phenoData@data$sample_name)) } if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.") @@ -95,143 +97,141 @@ writehtml("<HTML lang='en'>") writehtml("<HEAD>") - writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />") +writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />") - writehtml("<title>[W4M] XCMS analysis summary</title>") +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("<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("<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(getSampleNames(xobject) == sampleNamesList$sampleNamesMakeNames)) { - sampleNameHeaderHtml <- paste0("<th>sample</th>") - sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td>") - } else { - sampleNameHeaderHtml <- paste0("<th>sample</th><th>sample renamed</th>") - sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td><td>", sampleNamesList$sampleNamesMakeNames, "</td>") - } +writehtml("<h2>Samples used:</h2>") +writehtml("<div><table>") +if (all(getSampleNames(xobject) == sampleNamesList$sampleNamesMakeNames)) { + sampleNameHeaderHtml <- paste0("<th>sample</th>") + sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td>") +} else { + sampleNameHeaderHtml <- paste0("<th>sample</th><th>sample renamed</th>") + sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td><td>", sampleNamesList$sampleNamesMakeNames, "</td>") +} - if (!exists("md5sumList")) { - md5sumHeaderHtml <- "" - md5sumHtml <- "" - md5sumLegend <- "" - } else if (is.null(md5sumList$removalBadCharacters)) { - md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th>") - md5sumHtml <- paste0("<td>", md5sumList$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 changed during the process." - } else { - md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>") - md5sumHtml <- paste0("<td>", md5sumList$origin, "</td><td>", md5sumList$removalBadCharacters, "</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 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/>" - } - - writehtml("<tr>", sampleNameHeaderHtml, "<th>filename</th>", md5sumHeaderHtml, "</tr>") - writehtml(paste0("<tr>", sampleNameHtml, "<td>", getFilePaths(xobject), "</td>", md5sumHtml, "</tr>")) - - writehtml("</table>") - writehtml(md5sumLegend) - writehtml("</div>") +if (!exists("md5sumList")) { + md5sumHeaderHtml <- "" + md5sumHtml <- "" + md5sumLegend <- "" +} else if (is.null(md5sumList$removalBadCharacters)) { + md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th>") + md5sumHtml <- paste0("<td>", md5sumList$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 changed during the process." +} else { + md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>") + md5sumHtml <- paste0("<td>", md5sumList$origin, "</td><td>", md5sumList$removalBadCharacters, "</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 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/>" +} - 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>") - # XCMS 3.x - if (class(xobject) == "XCMSnExp") { - xcmsFunction <- NULL - params <- NULL - for (processHistoryItem in processHistory(xobject)) { - if ((xcmsFunction == processType(processHistoryItem)) && equalParams(params, processParam(processHistoryItem))) - next - timestamp <- processDate(processHistoryItem) - xcmsFunction <- processType(processHistoryItem) - params <- processParam(processHistoryItem) - writehtml("<tr><td>", timestamp, "</td><td>", xcmsFunction, "</td><td colspan='2'><pre>") - writeraw(htmlOutput, params) - writehtml("</pre></td></tr>") - } - } - # CAMERA and retrocompatability XCMS 1.x - if (exists("listOFlistArguments")) { - for (tool in names(listOFlistArguments)) { - listOFlistArgumentsDisplay <- listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)] +writehtml("<tr>", sampleNameHeaderHtml, "<th>filename</th>", md5sumHeaderHtml, "</tr>") +writehtml(paste0("<tr>", sampleNameHtml, "<td>", getFilePaths(xobject), "</td>", md5sumHtml, "</tr>")) + +writehtml("</table>") +writehtml(md5sumLegend) +writehtml("</div>") - 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: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss") - 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>") +# XCMS 3.x +if (class(xobject) == "XCMSnExp") { + xcmsFunction <- NULL + params <- NULL + for (processHistoryItem in processHistory(xobject)) { + if ((xcmsFunction == processType(processHistoryItem)) && equalParams(params, processParam(processHistoryItem))) + next + timestamp <- processDate(processHistoryItem) + xcmsFunction <- processType(processHistoryItem) + params <- processParam(processHistoryItem) + writehtml("<tr><td>", timestamp, "</td><td>", xcmsFunction, "</td><td colspan='2'><pre>") + writeraw(htmlOutput, params) + writehtml("</pre></td></tr>") + } +} +# CAMERA and retrocompatability XCMS 1.x +if (exists("listOFlistArguments")) { + for (tool in names(listOFlistArguments)) { + listOFlistArgumentsDisplay <- listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)] - if (class(xobject) == "XCMSnExp") { - writehtml("<h2>Informations about the XCMSnExp object:</h2>") - - writehtml("<div><pre>") - writeraw(htmlOutput, xobject) - writehtml("</pre></div>") + 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("<h2>Informations about the xcmsSet object:</h2>") - - writehtml("<div><pre>") - # Get the legacy xcmsSet object - xset <- getxcmsSetObject(xobject) - writeraw(htmlOutput, xset) - writehtml("</pre></div>") + } +} +writehtml("</table>") +writehtml("<br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss") +writehtml("</div>") - # CAMERA - if (exists("xa")) { - writehtml("<h2>Informations about the CAMERA object:</h2>") +if (class(xobject) == "XCMSnExp") { + writehtml("<h2>Informations about the XCMSnExp object:</h2>") + writehtml("<div><pre>") + writeraw(htmlOutput, xobject) + writehtml("</pre></div>") +} + +writehtml("<h2>Informations about the xcmsSet object:</h2>") - writehtml("<div>") - writehtml("Number of pcgroup: ", length(xa@pspectra)) - writehtml("</div>") - } +writehtml("<div><pre>") +# Get the legacy xcmsSet object +xset <- getxcmsSetObject(xobject) +writeraw(htmlOutput, xset) +writehtml("</pre></div>") + +# CAMERA +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("<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>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("<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>")