Mercurial > repos > lecorguille > xcms_summary
comparison xcms_summary.r @ 4:1245c04eebde draft
planemo upload
author | lecorguille |
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date | Mon, 22 Feb 2016 17:07:53 -0500 |
parents | 89a8b5ff3e44 |
children | 11df21afc204 |
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3:89a8b5ff3e44 | 4:1245c04eebde |
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40 | 40 |
41 # if the RData come from CAMERA | 41 # if the RData come from CAMERA |
42 if (!exists("xset") & exists("xa")) xset=xa@xcmsSet | 42 if (!exists("xset") & exists("xa")) xset=xa@xcmsSet |
43 | 43 |
44 # retrocompatability | 44 # retrocompatability |
45 if (!exists("sampleNamesList")) sampleNamesList=list("sampleNamesMakeNames"=make.names(sampnames(xset))) | 45 if (!exists("sampleNamesList")) sampleNamesList=List("sampleNamesMakeNames"=make.names(sampnames(xset))) |
46 | 46 |
47 if (!exists("xset")) stop("You need at least a xset or a xa object.") | 47 if (!exists("xset")) stop("You need at least a xset or a xa object.") |
48 | 48 |
49 | 49 |
50 | 50 |
75 } | 75 } |
76 writehtml("</div>") | 76 writehtml("</div>") |
77 | 77 |
78 writehtml("<h2>Samples used:</h2>") | 78 writehtml("<h2>Samples used:</h2>") |
79 writehtml("<div><table>") | 79 writehtml("<div><table>") |
80 if (all(sampnames(xset) == sampleNamesList$sampleNamesMakeNames)) { | 80 if (all(sampnames(xset) != sampleNamesList$sampleNamesMakeNames)) { |
81 sampleNameHeaderHtml = paste("<th>sample</th>") | 81 sampleNameHeaderHtml = paste("<th>sample</th>") |
82 sampleNameHtml = paste("<td>",sampnames(xset),"</td>") | 82 sampleNameHtml = paste("<td>",sampnames(xset),"</td>") |
83 } else { | 83 } else { |
84 sampleNameHeaderHtml = paste("<th>sample</th><th>sample renamed</th>") | 84 sampleNameHeaderHtml = paste("<th>sample</th><th>sample renamed</th>") |
85 sampleNameHtml = paste("<td>",sampnames(xset),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>") | 85 sampleNameHtml = paste("<td>",sampnames(xset),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>") |
87 | 87 |
88 if (!exists("md5sumList")) { | 88 if (!exists("md5sumList")) { |
89 md5sumHeaderHtml = "" | 89 md5sumHeaderHtml = "" |
90 md5sumHtml = "" | 90 md5sumHtml = "" |
91 md5sumLegend="" | 91 md5sumLegend="" |
92 } else if (is.null(md5sumList$removalBadCharacters)) { | 92 } else if (!is.null(md5sumList$removalBadCharacters)) { |
93 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>") | 93 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>") |
94 md5sumHtml = paste("<td>",md5sumList$origin,"</td>") | 94 md5sumHtml = paste("<td>",md5sumList$origin,"</td>") |
95 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." | 95 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 } else { | 96 } else { |
97 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>") | 97 md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>") |
98 md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$removalBadCharacters,"</td>") | 98 md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$origin,"</td>") |
99 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/>" | 99 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 } | 100 } |
101 | 101 |
102 writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>") | 102 writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>") |
103 writehtml(paste("<tr>",sampleNameHtml,"<td>",xset@filepaths,"</td>",md5sumHtml,"</tr>")) | 103 writehtml(paste("<tr>",sampleNameHtml,"<td>",xset@filepaths,"</td>",md5sumHtml,"</tr>")) |