# HG changeset patch
# User lecorguille
# Date 1456386212 18000
# Node ID 11df21afc204851782930d69f388968123081e6f
# Parent  1245c04eebded21f15abf277a8b2ddb17f03efeb
planemo upload

diff -r 1245c04eebde -r 11df21afc204 xcms_summary.r
--- a/xcms_summary.r	Mon Feb 22 17:07:53 2016 -0500
+++ b/xcms_summary.r	Thu Feb 25 02:43:32 2016 -0500
@@ -42,7 +42,7 @@
 if (!exists("xset") & exists("xa")) xset=xa@xcmsSet
 
 # retrocompatability
-if (!exists("sampleNamesList")) sampleNamesList=List("sampleNamesMakeNames"=make.names(sampnames(xset)))
+if (!exists("sampleNamesList")) sampleNamesList=list("sampleNamesMakeNames"=make.names(sampnames(xset)))
 
 if (!exists("xset")) stop("You need at least a xset or a xa object.")
 
@@ -77,7 +77,7 @@
 
     writehtml("<h2>Samples used:</h2>")
     writehtml("<div><table>")
-        if (all(sampnames(xset) != sampleNamesList$sampleNamesMakeNames)) {
+        if (all(sampnames(xset) == sampleNamesList$sampleNamesMakeNames)) {
             sampleNameHeaderHtml = paste("<th>sample</th>")
             sampleNameHtml = paste("<td>",sampnames(xset),"</td>")
         } else {
@@ -89,7 +89,7 @@
             md5sumHeaderHtml = ""
             md5sumHtml = ""
             md5sumLegend=""
-        } else if (!is.null(md5sumList$removalBadCharacters)) {
+        } else if (is.null(md5sumList$removalBadCharacters)) {
             md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>")
             md5sumHtml = paste("<td>",md5sumList$origin,"</td>")
             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."
@@ -139,7 +139,7 @@
         writehtml("<h2>Informations about the CAMERA object:</h2>")
 
         writehtml("<div>")
-            writehtml("Number of pcgroup:",length(xa@pspectra))
+            writehtml("Number of pcgroup: ",length(xa@pspectra))
         writehtml("</div>")
     }