xcms_summary: xcms_summary.r annotate

annotate xcms_summary.r @ 15:97ca0321931b draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857

author	lecorguille
date	Tue, 18 Sep 2018 16:14:05 -0400
parents	a5347d57899f
children	46be2c523a7f

rev	line source
6 ca7c9a6da2c6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 4 diff changeset	1 #!/usr/bin/env Rscript
0 930478b22633 planemo upload lecorguille parents: diff changeset	2
930478b22633 planemo upload lecorguille parents: diff changeset	3
930478b22633 planemo upload lecorguille parents: diff changeset	4
930478b22633 planemo upload lecorguille parents: diff changeset	5 # ----- ARGUMENTS BLACKLIST -----
930478b22633 planemo upload lecorguille parents: diff changeset	6 #xcms.r
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	7 argBlacklist <- c("zipfile", "singlefile_galaxyPath", "singlefile_sampleName", "xfunction", "xsetRdataOutput", "sampleMetadataOutput", "ticspdf", "bicspdf", "rplotspdf")
0 930478b22633 planemo upload lecorguille parents: diff changeset	8 #CAMERA.r
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	9 argBlacklist <- c(argBlacklist, "dataMatrixOutput", "variableMetadataOutput", "new_file_path")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	10
0 930478b22633 planemo upload lecorguille parents: diff changeset	11
930478b22633 planemo upload lecorguille parents: diff changeset	12 # ----- PACKAGE -----
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	13 cat("\tSESSION INFO\n")
0 930478b22633 planemo upload lecorguille parents: diff changeset	14
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	15 #Import the different functions
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	16 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	17 source_local("lib.r")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	18 source_local("lib-xcms3.x.x.r")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	19
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	20 pkgs <- c("CAMERA","batch")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	21 loadAndDisplayPackages(pkgs)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	22 cat("\n\n");
0 930478b22633 planemo upload lecorguille parents: diff changeset	23
930478b22633 planemo upload lecorguille parents: diff changeset	24
930478b22633 planemo upload lecorguille parents: diff changeset	25 # ----- FUNCTION -----
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	26 writehtml <- function(...) { cat(...,"\n", file=htmlOutput,append = TRUE,sep="") }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	27 writeraw <- function(htmlOutput, object, open="at") {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	28 log_file <- file(htmlOutput, open = open)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	29 sink(log_file)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	30 sink(log_file, type = "output")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	31 print(object)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	32 sink()
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	33 close(log_file)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	34 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	35 getSampleNames <- function(xobject) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	36 if (class(xobject) == "xcmsSet")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	37 return (sampnames(xobject))
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	38 if (class(xobject) == "XCMSnExp")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	39 return (xobject@phenoData@data$sample_name)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	40 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	41 getFilePaths <- function(xobject) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	42 if (class(xobject) == "xcmsSet")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	43 return (xobject@filepaths)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	44 if (class(xobject) == "XCMSnExp")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	45 return (fileNames(xobject))
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	46 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	47 equalParams <- function(param1, param2) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	48 writeraw("param1.txt", param1, open="wt")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	49 writeraw("param2.txt", param2, open="wt")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	50 return(tools::md5sum("param1.txt") == tools::md5sum("param2.txt"))
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	51 }
0 930478b22633 planemo upload lecorguille parents: diff changeset	52
930478b22633 planemo upload lecorguille parents: diff changeset	53
930478b22633 planemo upload lecorguille parents: diff changeset	54 # ----- ARGUMENTS -----
930478b22633 planemo upload lecorguille parents: diff changeset	55
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	56 args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
0 930478b22633 planemo upload lecorguille parents: diff changeset	57
930478b22633 planemo upload lecorguille parents: diff changeset	58
930478b22633 planemo upload lecorguille parents: diff changeset	59 # ----- ARGUMENTS PROCESSING -----
930478b22633 planemo upload lecorguille parents: diff changeset	60
930478b22633 planemo upload lecorguille parents: diff changeset	61 #image is an .RData file necessary to use xset variable given by previous tools
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	62 load(args$image);
0 930478b22633 planemo upload lecorguille parents: diff changeset	63
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	64 htmlOutput <- "summary.html"
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	65 if (!is.null(args$htmlOutput)) htmlOutput = args$htmlOutput;
0 930478b22633 planemo upload lecorguille parents: diff changeset	66
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	67 user_email <- NULL
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	68 if (!is.null(args$user_email)) user_email = args$user_email;
0 930478b22633 planemo upload lecorguille parents: diff changeset	69
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	70 # if the RData come from XCMS 1.x
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	71 if (exists("xset")) xobject <- xset
0 930478b22633 planemo upload lecorguille parents: diff changeset	72 # retrocompatability
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	73 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject)))
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	74 # if the RData come from CAMERA
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	75 if (exists("xa")) xobject <- xa@xcmsSet
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	76 # if the RData come from XCMS 3.x
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	77 if (exists("xdata")) xobject <- xdata
0 930478b22633 planemo upload lecorguille parents: diff changeset	78
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	79 if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.")
0 930478b22633 planemo upload lecorguille parents: diff changeset	80
930478b22633 planemo upload lecorguille parents: diff changeset	81
930478b22633 planemo upload lecorguille parents: diff changeset	82
930478b22633 planemo upload lecorguille parents: diff changeset	83 # ----- MAIN PROCESSING INFO -----
930478b22633 planemo upload lecorguille parents: diff changeset	84 writehtml("<!DOCTYPE html>")
930478b22633 planemo upload lecorguille parents: diff changeset	85 writehtml("<HTML lang='en'>")
930478b22633 planemo upload lecorguille parents: diff changeset	86
930478b22633 planemo upload lecorguille parents: diff changeset	87 writehtml("<HEAD>")
930478b22633 planemo upload lecorguille parents: diff changeset	88 writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />")
930478b22633 planemo upload lecorguille parents: diff changeset	89
930478b22633 planemo upload lecorguille parents: diff changeset	90 writehtml("<title>[W4M] XCMS analysis summary</title>")
12 27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	91
0 930478b22633 planemo upload lecorguille parents: diff changeset	92 writehtml("<style>")
930478b22633 planemo upload lecorguille parents: diff changeset	93 writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }")
930478b22633 planemo upload lecorguille parents: diff changeset	94 writehtml("td,th { padding: 5px; padding-right: 12px; }")
930478b22633 planemo upload lecorguille parents: diff changeset	95 writehtml("th { background: #898989; text-align:left;color: white;}")
930478b22633 planemo upload lecorguille parents: diff changeset	96 writehtml("h2 { color: #FFA212; }")
930478b22633 planemo upload lecorguille parents: diff changeset	97 writehtml("ul li { margin-bottom:10px; }")
930478b22633 planemo upload lecorguille parents: diff changeset	98 writehtml("</style>")
930478b22633 planemo upload lecorguille parents: diff changeset	99 writehtml("</HEAD>")
930478b22633 planemo upload lecorguille parents: diff changeset	100
930478b22633 planemo upload lecorguille parents: diff changeset	101 writehtml("<BODY>")
930478b22633 planemo upload lecorguille parents: diff changeset	102 writehtml("<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>")
930478b22633 planemo upload lecorguille parents: diff changeset	103 # to pass the planemo shed_test
930478b22633 planemo upload lecorguille parents: diff changeset	104 if (user_email != "test@bx.psu.edu") {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	105 if (!is.null(user_email)) writehtml("By: ", user_email," - ")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	106 writehtml("Date: ", format(Sys.time(), "%y%m%d-%H:%M:%S"))
0 930478b22633 planemo upload lecorguille parents: diff changeset	107 }
930478b22633 planemo upload lecorguille parents: diff changeset	108 writehtml("</div>")
930478b22633 planemo upload lecorguille parents: diff changeset	109
930478b22633 planemo upload lecorguille parents: diff changeset	110 writehtml("<h2>Samples used:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	111 writehtml("<div><table>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	112 if (all(getSampleNames(xobject) == sampleNamesList$sampleNamesMakeNames)) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	113 sampleNameHeaderHtml <- paste0("<th>sample</th>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	114 sampleNameHtml <- paste0("<td>",getSampleNames(xobject),"</td>")
0 930478b22633 planemo upload lecorguille parents: diff changeset	115 } else {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	116 sampleNameHeaderHtml <- paste0("<th>sample</th><th>sample renamed</th>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	117 sampleNameHtml <- paste0("<td>",getSampleNames(xobject),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>")
12 27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	118 }
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	119
0 930478b22633 planemo upload lecorguille parents: diff changeset	120 if (!exists("md5sumList")) {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	121 md5sumHeaderHtml <- ""
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	122 md5sumHtml <- ""
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	123 md5sumLegend <- ""
2 234df22cd722 planemo upload lecorguille parents: 1 diff changeset	124 } else if (is.null(md5sumList$removalBadCharacters)) {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	125 md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	126 md5sumHtml <- paste0("<td>",md5sumList$origin,"</td>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	127 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."
0 930478b22633 planemo upload lecorguille parents: diff changeset	128 } else {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	129 md5sumHeaderHtml <- paste0("<th>md5sum<sup></sup></th><th>md5sum<sup>*</sup> after bad characters removal</th>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	130 md5sumHtml <- paste0("<td>",md5sumList$origin,"</td><td>",md5sumList$removalBadCharacters,"</td>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	131 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/>"
13 a5347d57899f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	132 }
a5347d57899f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	133
0 930478b22633 planemo upload lecorguille parents: diff changeset	134 writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	135 writehtml(paste0("<tr>",sampleNameHtml,"<td>",getFilePaths(xobject),"</td>",md5sumHtml,"</tr>"))
12 27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	136
0 930478b22633 planemo upload lecorguille parents: diff changeset	137 writehtml("</table>")
930478b22633 planemo upload lecorguille parents: diff changeset	138 writehtml(md5sumLegend)
930478b22633 planemo upload lecorguille parents: diff changeset	139 writehtml("</div>")
930478b22633 planemo upload lecorguille parents: diff changeset	140
930478b22633 planemo upload lecorguille parents: diff changeset	141 writehtml("<h2>Function launched:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	142 writehtml("<div><table>")
930478b22633 planemo upload lecorguille parents: diff changeset	143 writehtml("<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	144 # XCMS 3.x
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	145 if (class(xobject) == "XCMSnExp") {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	146 xcmsFunction <- NULL
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	147 params <- NULL
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	148 for (processHistoryItem in processHistory(xobject)) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	149 if ((xcmsFunction == processType(processHistoryItem)) && equalParams(params, processParam(processHistoryItem)))
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	150 next
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	151 timestamp <- processDate(processHistoryItem)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	152 xcmsFunction <- processType(processHistoryItem)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	153 params <- processParam(processHistoryItem)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	154 writehtml("<tr><td>",timestamp,"</td><td>",xcmsFunction,"</td><td colspan='2'><pre>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	155 writeraw(htmlOutput, params)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	156 writehtml("</pre></td></tr>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	157 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	158 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	159 # CAMERA and retrocompatability XCMS 1.x
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	160 if (exists("listOFlistArguments")) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	161 for(tool in names(listOFlistArguments)) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	162 listOFlistArgumentsDisplay <- listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]
0 930478b22633 planemo upload lecorguille parents: diff changeset	163
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	164 timestamp <- strsplit(tool,"_")[[1]][1]
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	165 xcmsFunction <- strsplit(tool,"_")[[1]][2]
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	166 writehtml("<tr><td rowspan='",length(listOFlistArgumentsDisplay),"'>",timestamp,"</td><td rowspan='",length(listOFlistArgumentsDisplay),"'>",xcmsFunction,"</td>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	167 line_begin <- ""
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	168 for (arg in names(listOFlistArgumentsDisplay)) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	169 writehtml(line_begin,"<td>",arg,"</td><td>",unlist(listOFlistArgumentsDisplay[arg][1]),"</td></tr>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	170 line_begin <- "<tr>"
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	171 }
0 930478b22633 planemo upload lecorguille parents: diff changeset	172 }
930478b22633 planemo upload lecorguille parents: diff changeset	173 }
930478b22633 planemo upload lecorguille parents: diff changeset	174 writehtml("</table>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	175 writehtml("<br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss")
0 930478b22633 planemo upload lecorguille parents: diff changeset	176 writehtml("</div>")
930478b22633 planemo upload lecorguille parents: diff changeset	177
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	178 if (class(xobject) == "XCMSnExp") {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	179 writehtml("<h2>Informations about the XCMSnExp object:</h2>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	180
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	181 writehtml("<div><pre>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	182 writeraw(htmlOutput, xobject)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	183 writehtml("</pre></div>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	184 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	185
0 930478b22633 planemo upload lecorguille parents: diff changeset	186 writehtml("<h2>Informations about the xcmsSet object:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	187
930478b22633 planemo upload lecorguille parents: diff changeset	188 writehtml("<div><pre>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	189 # Get the legacy xcmsSet object
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	190 xset <- getxcmsSetObject(xobject)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	191 writeraw(htmlOutput, xset)
0 930478b22633 planemo upload lecorguille parents: diff changeset	192 writehtml("</pre></div>")
930478b22633 planemo upload lecorguille parents: diff changeset	193
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	194 # CAMERA
0 930478b22633 planemo upload lecorguille parents: diff changeset	195 if (exists("xa")) {
930478b22633 planemo upload lecorguille parents: diff changeset	196 writehtml("<h2>Informations about the CAMERA object:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	197
930478b22633 planemo upload lecorguille parents: diff changeset	198 writehtml("<div>")
3 f5d7654148bd planemo upload lecorguille parents: 2 diff changeset	199 writehtml("Number of pcgroup: ",length(xa@pspectra))
0 930478b22633 planemo upload lecorguille parents: diff changeset	200 writehtml("</div>")
930478b22633 planemo upload lecorguille parents: diff changeset	201 }
930478b22633 planemo upload lecorguille parents: diff changeset	202
930478b22633 planemo upload lecorguille parents: diff changeset	203 writehtml("<h2>Citations:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	204 writehtml("<div><ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	205 writehtml("<li>To cite the <b>XCMS</b> package in publications use:")
930478b22633 planemo upload lecorguille parents: diff changeset	206 writehtml("<ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	207 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>")
930478b22633 planemo upload lecorguille parents: diff changeset	208 writehtml("<li>","Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)","</li>")
930478b22633 planemo upload lecorguille parents: diff changeset	209 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>")
930478b22633 planemo upload lecorguille parents: diff changeset	210 writehtml("</ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	211 writehtml("</li>")
930478b22633 planemo upload lecorguille parents: diff changeset	212
930478b22633 planemo upload lecorguille parents: diff changeset	213 writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")
930478b22633 planemo upload lecorguille parents: diff changeset	214 writehtml("<ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	215 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>")
930478b22633 planemo upload lecorguille parents: diff changeset	216 writehtml("</ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	217 writehtml("</li>")
930478b22633 planemo upload lecorguille parents: diff changeset	218
930478b22633 planemo upload lecorguille parents: diff changeset	219 writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")
930478b22633 planemo upload lecorguille parents: diff changeset	220 writehtml("<ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	221 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>")
930478b22633 planemo upload lecorguille parents: diff changeset	222 writehtml("</ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	223 writehtml("</li>")
930478b22633 planemo upload lecorguille parents: diff changeset	224 writehtml("</ul></div>")
930478b22633 planemo upload lecorguille parents: diff changeset	225
930478b22633 planemo upload lecorguille parents: diff changeset	226 writehtml("</BODY>")
930478b22633 planemo upload lecorguille parents: diff changeset	227
930478b22633 planemo upload lecorguille parents: diff changeset	228 writehtml("</HTML>")

Mercurial > repos > lecorguille > xcms_summary

annotate xcms_summary.r @ 15:97ca0321931b draft