xcms_summary: xcms_summary.r annotate

annotate xcms_summary.r @ 26:db6549f27ad1 draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8"

author	workflow4metabolomics
date	Tue, 12 May 2020 16:39:28 -0400
parents	46be2c523a7f
children	bed23aa27b4b

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
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	19 pkgs <- c("CAMERA","batch")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	20 loadAndDisplayPackages(pkgs)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	21 cat("\n\n");
0 930478b22633 planemo upload lecorguille parents: diff changeset	22
930478b22633 planemo upload lecorguille parents: diff changeset	23
930478b22633 planemo upload lecorguille parents: diff changeset	24 # ----- FUNCTION -----
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	25 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	26 writeraw <- function(htmlOutput, object, open="at") {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	27 log_file <- file(htmlOutput, open = open)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	28 sink(log_file)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	29 sink(log_file, type = "output")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	30 print(object)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	31 sink()
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	32 close(log_file)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	33 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	34 getSampleNames <- function(xobject) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	35 if (class(xobject) == "xcmsSet")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	36 return (sampnames(xobject))
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	37 if (class(xobject) == "XCMSnExp")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	38 return (xobject@phenoData@data$sample_name)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	39 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	40 getFilePaths <- function(xobject) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	41 if (class(xobject) == "xcmsSet")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	42 return (xobject@filepaths)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	43 if (class(xobject) == "XCMSnExp")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	44 return (fileNames(xobject))
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	45 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	46 equalParams <- function(param1, param2) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	47 writeraw("param1.txt", param1, open="wt")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	48 writeraw("param2.txt", param2, open="wt")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	49 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	50 }
0 930478b22633 planemo upload lecorguille parents: diff changeset	51
930478b22633 planemo upload lecorguille parents: diff changeset	52
930478b22633 planemo upload lecorguille parents: diff changeset	53 # ----- ARGUMENTS -----
930478b22633 planemo upload lecorguille parents: diff changeset	54
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	55 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	56
930478b22633 planemo upload lecorguille parents: diff changeset	57
930478b22633 planemo upload lecorguille parents: diff changeset	58 # ----- ARGUMENTS PROCESSING -----
930478b22633 planemo upload lecorguille parents: diff changeset	59
930478b22633 planemo upload lecorguille parents: diff changeset	60 #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	61 load(args$image);
0 930478b22633 planemo upload lecorguille parents: diff changeset	62
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	63 htmlOutput <- "summary.html"
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	64 if (!is.null(args$htmlOutput)) htmlOutput = args$htmlOutput;
0 930478b22633 planemo upload lecorguille parents: diff changeset	65
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	66 user_email <- NULL
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	67 if (!is.null(args$user_email)) user_email = args$user_email;
0 930478b22633 planemo upload lecorguille parents: diff changeset	68
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	69 # if the RData come from XCMS 1.x
26 db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	70 if (exists("xset")) {
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	71 xobject <- xset
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	72 # retrocompatability
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	73 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject)))
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	74 }
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	75 # if the RData come from CAMERA
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	76 if (exists("xa")) xobject <- xa@xcmsSet
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	77 # if the RData come from XCMS 3.x
26 db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	78 if (exists("xdata")) {
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	79 xobject <- xdata
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	80 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(xdata@phenoData@data$sample_name))
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	81 }
0 930478b22633 planemo upload lecorguille parents: diff changeset	82
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	83 if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.")
0 930478b22633 planemo upload lecorguille parents: diff changeset	84
930478b22633 planemo upload lecorguille parents: diff changeset	85
930478b22633 planemo upload lecorguille parents: diff changeset	86 # ----- MAIN PROCESSING INFO -----
930478b22633 planemo upload lecorguille parents: diff changeset	87 writehtml("<!DOCTYPE html>")
930478b22633 planemo upload lecorguille parents: diff changeset	88 writehtml("<HTML lang='en'>")
930478b22633 planemo upload lecorguille parents: diff changeset	89
930478b22633 planemo upload lecorguille parents: diff changeset	90 writehtml("<HEAD>")
930478b22633 planemo upload lecorguille parents: diff changeset	91 writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />")
930478b22633 planemo upload lecorguille parents: diff changeset	92
930478b22633 planemo upload lecorguille parents: diff changeset	93 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	94
0 930478b22633 planemo upload lecorguille parents: diff changeset	95 writehtml("<style>")
930478b22633 planemo upload lecorguille parents: diff changeset	96 writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }")
930478b22633 planemo upload lecorguille parents: diff changeset	97 writehtml("td,th { padding: 5px; padding-right: 12px; }")
930478b22633 planemo upload lecorguille parents: diff changeset	98 writehtml("th { background: #898989; text-align:left;color: white;}")
930478b22633 planemo upload lecorguille parents: diff changeset	99 writehtml("h2 { color: #FFA212; }")
930478b22633 planemo upload lecorguille parents: diff changeset	100 writehtml("ul li { margin-bottom:10px; }")
930478b22633 planemo upload lecorguille parents: diff changeset	101 writehtml("</style>")
930478b22633 planemo upload lecorguille parents: diff changeset	102 writehtml("</HEAD>")
930478b22633 planemo upload lecorguille parents: diff changeset	103
930478b22633 planemo upload lecorguille parents: diff changeset	104 writehtml("<BODY>")
930478b22633 planemo upload lecorguille parents: diff changeset	105 writehtml("<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>")
930478b22633 planemo upload lecorguille parents: diff changeset	106 # to pass the planemo shed_test
930478b22633 planemo upload lecorguille parents: diff changeset	107 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	108 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	109 writehtml("Date: ", format(Sys.time(), "%y%m%d-%H:%M:%S"))
0 930478b22633 planemo upload lecorguille parents: diff changeset	110 }
930478b22633 planemo upload lecorguille parents: diff changeset	111 writehtml("</div>")
930478b22633 planemo upload lecorguille parents: diff changeset	112
930478b22633 planemo upload lecorguille parents: diff changeset	113 writehtml("<h2>Samples used:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	114 writehtml("<div><table>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	115 if (all(getSampleNames(xobject) == sampleNamesList$sampleNamesMakeNames)) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	116 sampleNameHeaderHtml <- paste0("<th>sample</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>")
0 930478b22633 planemo upload lecorguille parents: diff changeset	118 } else {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	119 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	120 sampleNameHtml <- paste0("<td>",getSampleNames(xobject),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>")
12 27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	121 }
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	122
0 930478b22633 planemo upload lecorguille parents: diff changeset	123 if (!exists("md5sumList")) {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	124 md5sumHeaderHtml <- ""
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	125 md5sumHtml <- ""
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	126 md5sumLegend <- ""
2 234df22cd722 planemo upload lecorguille parents: 1 diff changeset	127 } else if (is.null(md5sumList$removalBadCharacters)) {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	128 md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	129 md5sumHtml <- paste0("<td>",md5sumList$origin,"</td>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	130 md5sumLegend <- "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process."
0 930478b22633 planemo upload lecorguille parents: diff changeset	131 } else {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	132 md5sumHeaderHtml <- paste0("<th>md5sum<sup></sup></th><th>md5sum<sup>*</sup> after bad characters removal</th>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	133 md5sumHtml <- paste0("<td>",md5sumList$origin,"</td><td>",md5sumList$removalBadCharacters,"</td>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	134 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	135 }
a5347d57899f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	136
0 930478b22633 planemo upload lecorguille parents: diff changeset	137 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	138 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	139
0 930478b22633 planemo upload lecorguille parents: diff changeset	140 writehtml("</table>")
930478b22633 planemo upload lecorguille parents: diff changeset	141 writehtml(md5sumLegend)
930478b22633 planemo upload lecorguille parents: diff changeset	142 writehtml("</div>")
930478b22633 planemo upload lecorguille parents: diff changeset	143
930478b22633 planemo upload lecorguille parents: diff changeset	144 writehtml("<h2>Function launched:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	145 writehtml("<div><table>")
930478b22633 planemo upload lecorguille parents: diff changeset	146 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	147 # XCMS 3.x
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	148 if (class(xobject) == "XCMSnExp") {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	149 xcmsFunction <- NULL
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	150 params <- NULL
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	151 for (processHistoryItem in processHistory(xobject)) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	152 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	153 next
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	154 timestamp <- processDate(processHistoryItem)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	155 xcmsFunction <- processType(processHistoryItem)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	156 params <- processParam(processHistoryItem)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	157 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	158 writeraw(htmlOutput, params)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	159 writehtml("</pre></td></tr>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	160 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	161 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	162 # CAMERA and retrocompatability XCMS 1.x
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	163 if (exists("listOFlistArguments")) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	164 for(tool in names(listOFlistArguments)) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	165 listOFlistArgumentsDisplay <- listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]
0 930478b22633 planemo upload lecorguille parents: diff changeset	166
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	167 timestamp <- strsplit(tool,"_")[[1]][1]
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	168 xcmsFunction <- strsplit(tool,"_")[[1]][2]
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	169 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	170 line_begin <- ""
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	171 for (arg in names(listOFlistArgumentsDisplay)) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	172 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	173 line_begin <- "<tr>"
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	174 }
0 930478b22633 planemo upload lecorguille parents: diff changeset	175 }
930478b22633 planemo upload lecorguille parents: diff changeset	176 }
930478b22633 planemo upload lecorguille parents: diff changeset	177 writehtml("</table>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	178 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	179 writehtml("</div>")
930478b22633 planemo upload lecorguille parents: diff changeset	180
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	181 if (class(xobject) == "XCMSnExp") {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	182 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	183
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	184 writehtml("<div><pre>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	185 writeraw(htmlOutput, xobject)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	186 writehtml("</pre></div>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	187 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	188
0 930478b22633 planemo upload lecorguille parents: diff changeset	189 writehtml("<h2>Informations about the xcmsSet object:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	190
930478b22633 planemo upload lecorguille parents: diff changeset	191 writehtml("<div><pre>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	192 # Get the legacy xcmsSet object
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	193 xset <- getxcmsSetObject(xobject)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	194 writeraw(htmlOutput, xset)
0 930478b22633 planemo upload lecorguille parents: diff changeset	195 writehtml("</pre></div>")
930478b22633 planemo upload lecorguille parents: diff changeset	196
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	197 # CAMERA
0 930478b22633 planemo upload lecorguille parents: diff changeset	198 if (exists("xa")) {
930478b22633 planemo upload lecorguille parents: diff changeset	199 writehtml("<h2>Informations about the CAMERA object:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	200
930478b22633 planemo upload lecorguille parents: diff changeset	201 writehtml("<div>")
3 f5d7654148bd planemo upload lecorguille parents: 2 diff changeset	202 writehtml("Number of pcgroup: ",length(xa@pspectra))
0 930478b22633 planemo upload lecorguille parents: diff changeset	203 writehtml("</div>")
930478b22633 planemo upload lecorguille parents: diff changeset	204 }
930478b22633 planemo upload lecorguille parents: diff changeset	205
930478b22633 planemo upload lecorguille parents: diff changeset	206 writehtml("<h2>Citations:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	207 writehtml("<div><ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	208 writehtml("<li>To cite the <b>XCMS</b> package in publications use:")
930478b22633 planemo upload lecorguille parents: diff changeset	209 writehtml("<ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	210 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	211 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	212 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	213 writehtml("</ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	214 writehtml("</li>")
930478b22633 planemo upload lecorguille parents: diff changeset	215
930478b22633 planemo upload lecorguille parents: diff changeset	216 writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")
930478b22633 planemo upload lecorguille parents: diff changeset	217 writehtml("<ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	218 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	219 writehtml("</ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	220 writehtml("</li>")
930478b22633 planemo upload lecorguille parents: diff changeset	221
930478b22633 planemo upload lecorguille parents: diff changeset	222 writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")
930478b22633 planemo upload lecorguille parents: diff changeset	223 writehtml("<ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	224 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	225 writehtml("</ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	226 writehtml("</li>")
930478b22633 planemo upload lecorguille parents: diff changeset	227 writehtml("</ul></div>")
930478b22633 planemo upload lecorguille parents: diff changeset	228
930478b22633 planemo upload lecorguille parents: diff changeset	229 writehtml("</BODY>")
930478b22633 planemo upload lecorguille parents: diff changeset	230
930478b22633 planemo upload lecorguille parents: diff changeset	231 writehtml("</HTML>")

Mercurial > repos > lecorguille > xcms_summary

annotate xcms_summary.r @ 26:db6549f27ad1 draft