Mercurial > repos > lecorguille > xcms_summary
diff xcms_summary.r @ 28:018a9771de28 draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
| author | workflow4metabolomics |
|---|---|
| date | Wed, 07 Apr 2021 16:46:50 +0000 |
| parents | bed23aa27b4b |
| children | 2a2850fdf29e |
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--- a/xcms_summary.r Thu Sep 24 08:09:02 2020 +0000 +++ b/xcms_summary.r Wed Apr 07 16:46:50 2021 +0000 @@ -13,17 +13,21 @@ cat("\tSESSION INFO\n") #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="/")) } +source_local <- function(fname) { + 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") +pkgs <- c("CAMERA", "batch") loadAndDisplayPackages(pkgs) cat("\n\n"); # ----- FUNCTION ----- -writehtml <- function(...) { cat(...,"\n", file=htmlOutput,append = TRUE,sep="") } -writeraw <- function(htmlOutput, object, open="at") { +writehtml <- function(...) { + 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") @@ -33,26 +37,26 @@ } getSampleNames <- function(xobject) { if (class(xobject) == "xcmsSet") - return (sampnames(xobject)) + return(sampnames(xobject)) if (class(xobject) == "XCMSnExp") - return (xobject@phenoData@data$sample_name) + return(xobject@phenoData@data$sample_name) } getFilePaths <- function(xobject) { if (class(xobject) == "xcmsSet") - return (xobject@filepaths) + return(xobject@filepaths) if (class(xobject) == "XCMSnExp") - return (fileNames(xobject)) + return(fileNames(xobject)) } equalParams <- function(param1, param2) { - writeraw("param1.txt", param1, open="wt") - writeraw("param2.txt", param2, open="wt") + writeraw("param1.txt", param1, open = "wt") + writeraw("param2.txt", param2, open = "wt") return(tools::md5sum("param1.txt") == tools::md5sum("param2.txt")) } # ----- ARGUMENTS ----- -args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects +args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects # ----- ARGUMENTS PROCESSING ----- @@ -61,26 +65,26 @@ 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$user_email; # if the RData come from XCMS 1.x if (exists("xset")) { xobject <- xset # retrocompatability - if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject))) + if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(sampnames(xobject))) } # if the RData come from CAMERA if (exists("xa")) { xobject <- xa@xcmsSet - if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(xa@xcmsSet@phenoData$sample_name)) + 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)) + if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xdata@phenoData@data$sample_name)) } if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.") @@ -97,7 +101,7 @@ writehtml("<style>") writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }") - writehtml("td,th { padding: 5px; padding-right: 12px; }") + writehtml("td, th { padding: 5px; padding-right: 12px; }") writehtml("th { background: #898989; text-align:left;color: white;}") writehtml("h2 { color: #FFA212; }") writehtml("ul li { margin-bottom:10px; }") @@ -108,7 +112,7 @@ writehtml("<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>") # to pass the planemo shed_test if (user_email != "test@bx.psu.edu") { - if (!is.null(user_email)) writehtml("By: ", user_email," - ") + if (!is.null(user_email)) writehtml("By: ", user_email, " - ") writehtml("Date: ", format(Sys.time(), "%y%m%d-%H:%M:%S")) } writehtml("</div>") @@ -117,10 +121,10 @@ writehtml("<div><table>") if (all(getSampleNames(xobject) == sampleNamesList$sampleNamesMakeNames)) { sampleNameHeaderHtml <- paste0("<th>sample</th>") - sampleNameHtml <- paste0("<td>",getSampleNames(xobject),"</td>") + sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td>") } else { sampleNameHeaderHtml <- paste0("<th>sample</th><th>sample renamed</th>") - sampleNameHtml <- paste0("<td>",getSampleNames(xobject),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>") + sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td><td>", sampleNamesList$sampleNamesMakeNames, "</td>") } if (!exists("md5sumList")) { @@ -129,16 +133,16 @@ md5sumLegend <- "" } else if (is.null(md5sumList$removalBadCharacters)) { md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th>") - md5sumHtml <- paste0("<td>",md5sumList$origin,"</td>") + 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$removalBadCharacters,"</td>") + md5sumHtml <- paste0("<td>", md5sumList$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("<tr>", sampleNameHeaderHtml, "<th>filename</th>", md5sumHeaderHtml, "</tr>") + writehtml(paste0("<tr>", sampleNameHtml, "<td>", getFilePaths(xobject), "</td>", md5sumHtml, "</tr>")) writehtml("</table>") writehtml(md5sumLegend) @@ -157,22 +161,22 @@ timestamp <- processDate(processHistoryItem) xcmsFunction <- processType(processHistoryItem) params <- processParam(processHistoryItem) - writehtml("<tr><td>",timestamp,"</td><td>",xcmsFunction,"</td><td colspan='2'><pre>") + 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)) { + 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>") + 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>") + writehtml(line_begin, "<td>", arg, "</td><td>", unlist(listOFlistArgumentsDisplay[arg][1]), "</td></tr>") line_begin <- "<tr>" } } @@ -202,7 +206,7 @@ writehtml("<h2>Informations about the CAMERA object:</h2>") writehtml("<div>") - writehtml("Number of pcgroup: ",length(xa@pspectra)) + writehtml("Number of pcgroup: ", length(xa@pspectra)) writehtml("</div>") } @@ -210,21 +214,21 @@ 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("<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("<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("<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>")