Mercurial > repos > lecorguille > xcms_summary

comparison xcms_summary.r @ 12:27e7da5f6848 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author lecorguille
date Fri, 07 Apr 2017 07:37:23 -0400
parents ed8d80fc927c
children a5347d57899f
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11:cb599006715f 12:27e7da5f6848
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6 6
7 # ----- ARGUMENTS BLACKLIST ----- 7 # ----- ARGUMENTS BLACKLIST -----
8 #xcms.r 8 #xcms.r
9 argBlacklist=c("zipfile","xfunction","xsetRdataOutput","sampleMetadataOutput","ticspdf","bicspdf","rplotspdf") 9 argBlacklist=c("zipfile","singlefile_galaxyPath","singlefile_sampleName","xfunction","xsetRdataOutput","sampleMetadataOutput","ticspdf","bicspdf","rplotspdf")
10 #CAMERA.r 10 #CAMERA.r
11 argBlacklist=c(argBlacklist,"dataMatrixOutput","variableMetadataOutput","new_file_path") 11 argBlacklist=c(argBlacklist,"dataMatrixOutput","variableMetadataOutput","new_file_path")
12 12
13 # ----- PACKAGE ----- 13 # ----- PACKAGE -----
14 14
55 55
56 writehtml("<HEAD>") 56 writehtml("<HEAD>")
57 writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />") 57 writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />")
58 58
59 writehtml("<title>[W4M] XCMS analysis summary</title>") 59 writehtml("<title>[W4M] XCMS analysis summary</title>")
60 60
61 writehtml("<style>") 61 writehtml("<style>")
62 writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }") 62 writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }")
63 writehtml("td,th { padding: 5px; padding-right: 12px; }") 63 writehtml("td,th { padding: 5px; padding-right: 12px; }")
64 writehtml("th { background: #898989; text-align:left;color: white;}") 64 writehtml("th { background: #898989; text-align:left;color: white;}")
65 writehtml("h2 { color: #FFA212; }") 65 writehtml("h2 { color: #FFA212; }")
82 sampleNameHeaderHtml = paste("<th>sample</th>") 82 sampleNameHeaderHtml = paste("<th>sample</th>")
83 sampleNameHtml = paste("<td>",sampnames(xset),"</td>") 83 sampleNameHtml = paste("<td>",sampnames(xset),"</td>")
84 } else { 84 } else {
85 sampleNameHeaderHtml = paste("<th>sample</th><th>sample renamed</th>") 85 sampleNameHeaderHtml = paste("<th>sample</th><th>sample renamed</th>")
86 sampleNameHtml = paste("<td>",sampnames(xset),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>") 86 sampleNameHtml = paste("<td>",sampnames(xset),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>")
87 } 87 }
88 88
89 if (!exists("md5sumList")) { 89 if (!exists("md5sumList")) {
90 md5sumHeaderHtml = "" 90 md5sumHeaderHtml = ""
91 md5sumHtml = "" 91 md5sumHtml = ""
92 md5sumLegend="" 92 md5sumLegend=""
93 } else if (is.null(md5sumList$removalBadCharacters)) { 93 } else if (is.null(md5sumList$removalBadCharacters)) {
94 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>") 94 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>")
95 md5sumHtml = paste("<td>",md5sumList$origin,"</td>") 95 md5sumHtml = paste("<td>",md5sumList$origin,"</td>")
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 chancged during the process." 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."
97 } else { 97 } else {
98 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>") 98 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>")
99 md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$removalBadCharacters,"</td>") 99 md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$removalBadCharacters,"</td>")
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 chancged during the process.<br/><sup>**</sup>Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>" 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/>"
101 } 101 }
102 102
103 writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>") 103 writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>")
104 writehtml(paste("<tr>",sampleNameHtml,"<td>",xset@filepaths,"</td>",md5sumHtml,"</tr>")) 104 writehtml(paste("<tr>",sampleNameHtml,"<td>",xset@filepaths,"</td>",md5sumHtml,"</tr>"))
105 105
106 writehtml("</table>") 106 writehtml("</table>")
107 writehtml(md5sumLegend) 107 writehtml(md5sumLegend)
108 writehtml("</div>") 108 writehtml("</div>")
109 109
110 writehtml("<h2>Function launched:</h2>") 110 writehtml("<h2>Function launched:</h2>")
168 writehtml("</ul></div>") 168 writehtml("</ul></div>")
169 169
170 writehtml("</BODY>") 170 writehtml("</BODY>")
171 171
172 writehtml("</HTML>") 172 writehtml("</HTML>")
173