annotate xcms_summary.r @ 14:4c757d1ba7b4 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
author lecorguille
date Tue, 13 Feb 2018 04:51:37 -0500
parents a5347d57899f
children 97ca0321931b
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1 #!/usr/bin/env Rscript
ca7c9a6da2c6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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2 # version="1.0.0"
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3 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABIMS TEAM
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7 # ----- ARGUMENTS BLACKLIST -----
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8 #xcms.r
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9 argBlacklist=c("zipfile","singlefile_galaxyPath","singlefile_sampleName","xfunction","xsetRdataOutput","sampleMetadataOutput","ticspdf","bicspdf","rplotspdf")
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10 #CAMERA.r
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11 argBlacklist=c(argBlacklist,"dataMatrixOutput","variableMetadataOutput","new_file_path")
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13 # ----- PACKAGE -----
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14
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15 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "igraph", "xcms","CAMERA","batch")
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16 for(pkg in pkgs) {
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17 cat(pkg,"\n")
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18 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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19 }
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20
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22 # ----- FUNCTION -----
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23 writehtml = function(...) { cat(...,"\n", file=htmlOutput,append = TRUE,sep="") }
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24
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25
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26 # ----- ARGUMENTS -----
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27
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28 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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29
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31 # ----- ARGUMENTS PROCESSING -----
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32
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33 #image is an .RData file necessary to use xset variable given by previous tools
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34 load(listArguments[["image"]]);
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35
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36 htmlOutput = "summary.html"
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37 if (!is.null(listArguments[["htmlOutput"]])) htmlOutput = listArguments[["htmlOutput"]];
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38
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39 user_email = NULL
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40 if (!is.null(listArguments[["user_email"]])) user_email = listArguments[["user_email"]];
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41
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42 # if the RData come from CAMERA
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43 if (!exists("xset") & exists("xa")) xset=xa@xcmsSet
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44
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45 # retrocompatability
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46 if (!exists("sampleNamesList")) sampleNamesList=list("sampleNamesMakeNames"=make.names(sampnames(xset)))
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47
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48 if (!exists("xset")) stop("You need at least a xset or a xa object.")
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49
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51
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52 # ----- MAIN PROCESSING INFO -----
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53 writehtml("<!DOCTYPE html>")
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54 writehtml("<HTML lang='en'>")
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55
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56 writehtml("<HEAD>")
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57 writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />")
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58
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59 writehtml("<title>[W4M] XCMS analysis summary</title>")
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60
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61 writehtml("<style>")
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62 writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }")
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63 writehtml("td,th { padding: 5px; padding-right: 12px; }")
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64 writehtml("th { background: #898989; text-align:left;color: white;}")
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65 writehtml("h2 { color: #FFA212; }")
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66 writehtml("ul li { margin-bottom:10px; }")
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67 writehtml("</style>")
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68 writehtml("</HEAD>")
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69
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70 writehtml("<BODY>")
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71 writehtml("<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>")
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72 # to pass the planemo shed_test
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73 if (user_email != "test@bx.psu.edu") {
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74 if (!is.null(user_email)) writehtml("By: ",user_email," - ")
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75 writehtml("Date: ",format(Sys.time(), "%y%m%d-%H:%M:%S"))
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76 }
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77 writehtml("</div>")
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78
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79 writehtml("<h2>Samples used:</h2>")
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80 writehtml("<div><table>")
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81 if (all(sampnames(xset) == sampleNamesList$sampleNamesMakeNames)) {
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82 sampleNameHeaderHtml = paste("<th>sample</th>")
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83 sampleNameHtml = paste("<td>",sampnames(xset),"</td>")
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84 } else {
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85 sampleNameHeaderHtml = paste("<th>sample</th><th>sample renamed</th>")
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86 sampleNameHtml = paste("<td>",sampnames(xset),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>")
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87 }
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88
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89 if (!exists("md5sumList")) {
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90 md5sumHeaderHtml = ""
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91 md5sumHtml = ""
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92 md5sumLegend=""
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93 } else if (is.null(md5sumList$removalBadCharacters)) {
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94 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>")
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95 md5sumHtml = paste("<td>",md5sumList$origin,"</td>")
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96 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."
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97 } else {
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98 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>")
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99 md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$removalBadCharacters,"</td>")
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100 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/>"
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101 }
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102
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103 writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>")
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104 writehtml(paste("<tr>",sampleNameHtml,"<td>",xset@filepaths,"</td>",md5sumHtml,"</tr>"))
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105
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106 writehtml("</table>")
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107 writehtml(md5sumLegend)
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108 writehtml("</div>")
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109
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110 writehtml("<h2>Function launched:</h2>")
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111 writehtml("<div><table>")
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112 writehtml("<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>")
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113 for(tool in names(listOFlistArguments)) {
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114 listOFlistArgumentsDisplay=listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]
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115
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116 timestamp = strsplit(tool,"_")[[1]][1]
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117 xcmsFunction = strsplit(tool,"_")[[1]][2]
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118 writehtml("<tr><td rowspan='",length(listOFlistArgumentsDisplay),"'>",timestamp,"</td><td rowspan='",length(listOFlistArgumentsDisplay),"'>",xcmsFunction,"</td>")
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119 line_begin=""
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120 for (arg in names(listOFlistArgumentsDisplay)) {
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121 writehtml(line_begin,"<td>",arg,"</td><td>",unlist(listOFlistArgumentsDisplay[arg][1]),"</td></tr>")
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122 line_begin="<tr>"
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123 }
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124 }
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125 writehtml("</table>")
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126 writehtml("<br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss")
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127 writehtml("</div>")
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128
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129 writehtml("<h2>Informations about the xcmsSet object:</h2>")
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130
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131 writehtml("<div><pre>")
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132 log_file=file(htmlOutput, open = "at")
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133 sink(log_file)
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134 sink(log_file, type = "output")
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135 xset
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136 sink()
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137 writehtml("</pre></div>")
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138
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139 if (exists("xa")) {
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140 writehtml("<h2>Informations about the CAMERA object:</h2>")
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141
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142 writehtml("<div>")
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143 writehtml("Number of pcgroup: ",length(xa@pspectra))
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144 writehtml("</div>")
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145 }
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146
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147 writehtml("<h2>Citations:</h2>")
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148 writehtml("<div><ul>")
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149 writehtml("<li>To cite the <b>XCMS</b> package in publications use:")
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150 writehtml("<ul>")
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151 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>")
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152 writehtml("<li>","Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)","</li>")
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153 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>")
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154 writehtml("</ul>")
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155 writehtml("</li>")
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156
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157 writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")
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158 writehtml("<ul>")
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159 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>")
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160 writehtml("</ul>")
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161 writehtml("</li>")
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162
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163 writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")
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164 writehtml("<ul>")
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165 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>")
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166 writehtml("</ul>")
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167 writehtml("</li>")
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168 writehtml("</ul></div>")
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169
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170 writehtml("</BODY>")
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172 writehtml("</HTML>")