xcms_summary: xcms_summary.r annotate

annotate 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

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
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	16 source_local <- function(fname) {
018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	17 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/"))
018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	18 }
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	19 source_local("lib.r")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	20
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	21 pkgs <- c("CAMERA", "batch")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	22 loadAndDisplayPackages(pkgs)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	23 cat("\n\n");
0 930478b22633 planemo upload lecorguille parents: diff changeset	24
930478b22633 planemo upload lecorguille parents: diff changeset	25
930478b22633 planemo upload lecorguille parents: diff changeset	26 # ----- FUNCTION -----
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	27 writehtml <- function(...) {
018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	28 cat(..., "\n", file = htmlOutput, append = TRUE, sep = "")
018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	29 }
018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	30 writeraw <- function(htmlOutput, object, open = "at") {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	31 log_file <- file(htmlOutput, open = open)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	32 sink(log_file)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	33 sink(log_file, type = "output")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	34 print(object)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	35 sink()
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	36 close(log_file)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	37 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	38 getSampleNames <- function(xobject) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	39 if (class(xobject) == "xcmsSet")
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	40 return(sampnames(xobject))
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	41 if (class(xobject) == "XCMSnExp")
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	42 return(xobject@phenoData@data$sample_name)
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	43 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	44 getFilePaths <- function(xobject) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	45 if (class(xobject) == "xcmsSet")
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	46 return(xobject@filepaths)
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	47 if (class(xobject) == "XCMSnExp")
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	48 return(fileNames(xobject))
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	49 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	50 equalParams <- function(param1, param2) {
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	51 writeraw("param1.txt", param1, open = "wt")
018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	52 writeraw("param2.txt", param2, open = "wt")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	53 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	54 }
0 930478b22633 planemo upload lecorguille parents: diff changeset	55
930478b22633 planemo upload lecorguille parents: diff changeset	56
930478b22633 planemo upload lecorguille parents: diff changeset	57 # ----- ARGUMENTS -----
930478b22633 planemo upload lecorguille parents: diff changeset	58
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	59 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	60
930478b22633 planemo upload lecorguille parents: diff changeset	61
930478b22633 planemo upload lecorguille parents: diff changeset	62 # ----- ARGUMENTS PROCESSING -----
930478b22633 planemo upload lecorguille parents: diff changeset	63
930478b22633 planemo upload lecorguille parents: diff changeset	64 #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	65 load(args$image);
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 htmlOutput <- "summary.html"
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	68 if (!is.null(args$htmlOutput)) htmlOutput <- args$htmlOutput;
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 user_email <- NULL
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	71 if (!is.null(args$user_email)) user_email <- args$user_email;
0 930478b22633 planemo upload lecorguille parents: diff changeset	72
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	73 # 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	74 if (exists("xset")) {
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	75 xobject <- xset
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	76 # retrocompatability
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	77 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(sampnames(xobject)))
26 db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	78 }
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	79 # if the RData come from CAMERA
27 bed23aa27b4b "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 50478425b4773ebcb393c0e31f1e622b7406dcbb" workflow4metabolomics parents: 26 diff changeset	80 if (exists("xa")) {
bed23aa27b4b "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 50478425b4773ebcb393c0e31f1e622b7406dcbb" workflow4metabolomics parents: 26 diff changeset	81 xobject <- xa@xcmsSet
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	82 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xa@xcmsSet@phenoData$sample_name))
27 bed23aa27b4b "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 50478425b4773ebcb393c0e31f1e622b7406dcbb" workflow4metabolomics parents: 26 diff changeset	83 }
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	84 # if the RData come from XCMS 3.x
26 db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	85 if (exists("xdata")) {
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	86 xobject <- xdata
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	87 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xdata@phenoData@data$sample_name))
26 db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8" workflow4metabolomics parents: 20 diff changeset	88 }
0 930478b22633 planemo upload lecorguille parents: diff changeset	89
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	90 if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.")
0 930478b22633 planemo upload lecorguille parents: diff changeset	91
930478b22633 planemo upload lecorguille parents: diff changeset	92
930478b22633 planemo upload lecorguille parents: diff changeset	93 # ----- MAIN PROCESSING INFO -----
930478b22633 planemo upload lecorguille parents: diff changeset	94 writehtml("<!DOCTYPE html>")
930478b22633 planemo upload lecorguille parents: diff changeset	95 writehtml("<HTML lang='en'>")
930478b22633 planemo upload lecorguille parents: diff changeset	96
930478b22633 planemo upload lecorguille parents: diff changeset	97 writehtml("<HEAD>")
930478b22633 planemo upload lecorguille parents: diff changeset	98 writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />")
930478b22633 planemo upload lecorguille parents: diff changeset	99
930478b22633 planemo upload lecorguille parents: diff changeset	100 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	101
0 930478b22633 planemo upload lecorguille parents: diff changeset	102 writehtml("<style>")
930478b22633 planemo upload lecorguille parents: diff changeset	103 writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }")
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	104 writehtml("td, th { padding: 5px; padding-right: 12px; }")
0 930478b22633 planemo upload lecorguille parents: diff changeset	105 writehtml("th { background: #898989; text-align:left;color: white;}")
930478b22633 planemo upload lecorguille parents: diff changeset	106 writehtml("h2 { color: #FFA212; }")
930478b22633 planemo upload lecorguille parents: diff changeset	107 writehtml("ul li { margin-bottom:10px; }")
930478b22633 planemo upload lecorguille parents: diff changeset	108 writehtml("</style>")
930478b22633 planemo upload lecorguille parents: diff changeset	109 writehtml("</HEAD>")
930478b22633 planemo upload lecorguille parents: diff changeset	110
930478b22633 planemo upload lecorguille parents: diff changeset	111 writehtml("<BODY>")
930478b22633 planemo upload lecorguille parents: diff changeset	112 writehtml("<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>")
930478b22633 planemo upload lecorguille parents: diff changeset	113 # to pass the planemo shed_test
930478b22633 planemo upload lecorguille parents: diff changeset	114 if (user_email != "test@bx.psu.edu") {
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	115 if (!is.null(user_email)) writehtml("By: ", user_email, " - ")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	116 writehtml("Date: ", format(Sys.time(), "%y%m%d-%H:%M:%S"))
0 930478b22633 planemo upload lecorguille parents: diff changeset	117 }
930478b22633 planemo upload lecorguille parents: diff changeset	118 writehtml("</div>")
930478b22633 planemo upload lecorguille parents: diff changeset	119
930478b22633 planemo upload lecorguille parents: diff changeset	120 writehtml("<h2>Samples used:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	121 writehtml("<div><table>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	122 if (all(getSampleNames(xobject) == sampleNamesList$sampleNamesMakeNames)) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	123 sampleNameHeaderHtml <- paste0("<th>sample</th>")
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	124 sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td>")
0 930478b22633 planemo upload lecorguille parents: diff changeset	125 } else {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	126 sampleNameHeaderHtml <- paste0("<th>sample</th><th>sample renamed</th>")
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	127 sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td><td>", sampleNamesList$sampleNamesMakeNames, "</td>")
12 27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	128 }
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	129
0 930478b22633 planemo upload lecorguille parents: diff changeset	130 if (!exists("md5sumList")) {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	131 md5sumHeaderHtml <- ""
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	132 md5sumHtml <- ""
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	133 md5sumLegend <- ""
2 234df22cd722 planemo upload lecorguille parents: 1 diff changeset	134 } else if (is.null(md5sumList$removalBadCharacters)) {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	135 md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th>")
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	136 md5sumHtml <- paste0("<td>", md5sumList$origin, "</td>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	137 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	138 } else {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	139 md5sumHeaderHtml <- paste0("<th>md5sum<sup></sup></th><th>md5sum<sup>*</sup> after bad characters removal</th>")
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	140 md5sumHtml <- paste0("<td>", md5sumList$origin, "</td><td>", md5sumList$removalBadCharacters, "</td>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	141 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	142 }
a5347d57899f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	143
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	144 writehtml("<tr>", sampleNameHeaderHtml, "<th>filename</th>", md5sumHeaderHtml, "</tr>")
018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	145 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	146
0 930478b22633 planemo upload lecorguille parents: diff changeset	147 writehtml("</table>")
930478b22633 planemo upload lecorguille parents: diff changeset	148 writehtml(md5sumLegend)
930478b22633 planemo upload lecorguille parents: diff changeset	149 writehtml("</div>")
930478b22633 planemo upload lecorguille parents: diff changeset	150
930478b22633 planemo upload lecorguille parents: diff changeset	151 writehtml("<h2>Function launched:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	152 writehtml("<div><table>")
930478b22633 planemo upload lecorguille parents: diff changeset	153 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	154 # XCMS 3.x
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	155 if (class(xobject) == "XCMSnExp") {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	156 xcmsFunction <- NULL
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	157 params <- NULL
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	158 for (processHistoryItem in processHistory(xobject)) {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	159 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	160 next
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	161 timestamp <- processDate(processHistoryItem)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	162 xcmsFunction <- processType(processHistoryItem)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	163 params <- processParam(processHistoryItem)
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	164 writehtml("<tr><td>", timestamp, "</td><td>", xcmsFunction, "</td><td colspan='2'><pre>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	165 writeraw(htmlOutput, params)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	166 writehtml("</pre></td></tr>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	167 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	168 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	169 # CAMERA and retrocompatability XCMS 1.x
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	170 if (exists("listOFlistArguments")) {
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	171 for (tool in names(listOFlistArguments)) {
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	172 listOFlistArgumentsDisplay <- listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]
0 930478b22633 planemo upload lecorguille parents: diff changeset	173
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	174 timestamp <- strsplit(tool, "_")[[1]][1]
018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	175 xcmsFunction <- strsplit(tool, "_")[[1]][2]
018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	176 writehtml("<tr><td rowspan='", length(listOFlistArgumentsDisplay), "'>", timestamp, "</td><td rowspan='", length(listOFlistArgumentsDisplay), "'>", xcmsFunction, "</td>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	177 line_begin <- ""
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	178 for (arg in names(listOFlistArgumentsDisplay)) {
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	179 writehtml(line_begin, "<td>", arg, "</td><td>", unlist(listOFlistArgumentsDisplay[arg][1]), "</td></tr>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	180 line_begin <- "<tr>"
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	181 }
0 930478b22633 planemo upload lecorguille parents: diff changeset	182 }
930478b22633 planemo upload lecorguille parents: diff changeset	183 }
930478b22633 planemo upload lecorguille parents: diff changeset	184 writehtml("</table>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	185 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	186 writehtml("</div>")
930478b22633 planemo upload lecorguille parents: diff changeset	187
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	188 if (class(xobject) == "XCMSnExp") {
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	189 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	190
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	191 writehtml("<div><pre>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	192 writeraw(htmlOutput, xobject)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	193 writehtml("</pre></div>")
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	194 }
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	195
0 930478b22633 planemo upload lecorguille parents: diff changeset	196 writehtml("<h2>Informations about the xcmsSet object:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	197
930478b22633 planemo upload lecorguille parents: diff changeset	198 writehtml("<div><pre>")
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	199 # Get the legacy xcmsSet object
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	200 xset <- getxcmsSetObject(xobject)
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	201 writeraw(htmlOutput, xset)
0 930478b22633 planemo upload lecorguille parents: diff changeset	202 writehtml("</pre></div>")
930478b22633 planemo upload lecorguille parents: diff changeset	203
15 97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	204 # CAMERA
0 930478b22633 planemo upload lecorguille parents: diff changeset	205 if (exists("xa")) {
930478b22633 planemo upload lecorguille parents: diff changeset	206 writehtml("<h2>Informations about the CAMERA object:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	207
930478b22633 planemo upload lecorguille parents: diff changeset	208 writehtml("<div>")
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	209 writehtml("Number of pcgroup: ", length(xa@pspectra))
0 930478b22633 planemo upload lecorguille parents: diff changeset	210 writehtml("</div>")
930478b22633 planemo upload lecorguille parents: diff changeset	211 }
930478b22633 planemo upload lecorguille parents: diff changeset	212
930478b22633 planemo upload lecorguille parents: diff changeset	213 writehtml("<h2>Citations:</h2>")
930478b22633 planemo upload lecorguille parents: diff changeset	214 writehtml("<div><ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	215 writehtml("<li>To cite the <b>XCMS</b> package in publications use:")
930478b22633 planemo upload lecorguille parents: diff changeset	216 writehtml("<ul>")
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	217 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>")
018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	218 writehtml("<li>", "Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)", "</li>")
018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	219 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>")
0 930478b22633 planemo upload lecorguille parents: diff changeset	220 writehtml("</ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	221 writehtml("</li>")
930478b22633 planemo upload lecorguille parents: diff changeset	222
930478b22633 planemo upload lecorguille parents: diff changeset	223 writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")
930478b22633 planemo upload lecorguille parents: diff changeset	224 writehtml("<ul>")
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	225 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>")
0 930478b22633 planemo upload lecorguille parents: diff changeset	226 writehtml("</ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	227 writehtml("</li>")
930478b22633 planemo upload lecorguille parents: diff changeset	228
930478b22633 planemo upload lecorguille parents: diff changeset	229 writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")
930478b22633 planemo upload lecorguille parents: diff changeset	230 writehtml("<ul>")
28 018a9771de28 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 27 diff changeset	231 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>")
0 930478b22633 planemo upload lecorguille parents: diff changeset	232 writehtml("</ul>")
930478b22633 planemo upload lecorguille parents: diff changeset	233 writehtml("</li>")
930478b22633 planemo upload lecorguille parents: diff changeset	234 writehtml("</ul></div>")
930478b22633 planemo upload lecorguille parents: diff changeset	235
930478b22633 planemo upload lecorguille parents: diff changeset	236 writehtml("</BODY>")
930478b22633 planemo upload lecorguille parents: diff changeset	237
930478b22633 planemo upload lecorguille parents: diff changeset	238 writehtml("</HTML>")

Mercurial > repos > lecorguille > xcms_summary

annotate xcms_summary.r @ 28:018a9771de28 draft