# HG changeset patch
# User workflow4metabolomics
# Date 1588080867 14400
# Node ID a066b8581b97e4b40f494c88a7a58fec395f1bde
# Parent  761913919c2105c45159a511192993d55412b3e1
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"

diff -r 761913919c21 -r a066b8581b97 abims_xcms_group.xml
--- a/abims_xcms_group.xml	Wed Feb 12 08:29:15 2020 -0500
+++ b/abims_xcms_group.xml	Tue Apr 28 09:34:27 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy0">
+<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy1">
 
     <description>Perform the correspondence, the grouping of chromatographic peaks within and between samples.</description>
 
@@ -357,6 +357,10 @@
 
 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
+**Version 3.6.1+galaxy1 - 22/04/2020**
+
+- BUGFIX: sample group colours were not displayed in plots.
+
 @HELP_XCMS_NEWVERSION_3610@
 
 @HELP_XCMS_NEWVERSION_3440@
diff -r 761913919c21 -r a066b8581b97 lib.r
--- a/lib.r	Wed Feb 12 08:29:15 2020 -0500
+++ b/lib.r	Tue Apr 28 09:34:27 2020 -0400
@@ -151,12 +151,14 @@
 
     group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
     names(group_colors) <- unique(xdata$sample_group)
+    col_per_samp <- as.character(xdata$sample_group)
+    for(i in 1:length(group_colors)){col_per_samp[col_per_samp==(names(group_colors)[i])]<-group_colors[i]}
 
     xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
     for (i in 1:nrow(featureDefinitions(xdata))) {
         mzmin = featureDefinitions(xdata)[i,]$mzmin
         mzmax = featureDefinitions(xdata)[i,]$mzmax
-        plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
+        plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=col_per_samp, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
         legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
     }
 
diff -r 761913919c21 -r a066b8581b97 macros_xcms.xml
--- a/macros_xcms.xml	Wed Feb 12 08:29:15 2020 -0500
+++ b/macros_xcms.xml	Tue Apr 28 09:34:27 2020 -0400
@@ -98,7 +98,7 @@
                   <option value="maxo">maxo</option>
                   <option value="intb">intb</option>
               </param>
-              <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Replace the remain NA by 0 in the dataMatrix" help="Rather mandatory for some downstream statistical steps"/>
+              <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="If NA values remain, replace them by 0 in the dataMatrix" help="Mandatory for some of the downstream tools (data processing, statistics) that do not accept NA values"/>
     </xml>
 
     <xml name="input_peaklist_section">
@@ -193,7 +193,7 @@
             <option value="wMean">intensity weighted mean of the peak's m/z values</option>
             <option value="mean">mean of the peak's m/z values</option>
             <option value="apex">use the m/z value at the peak apex</option>
-            <option value="wMeanApex3">ntensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>
+            <option value="wMeanApex3">intensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>
             <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option>
         </param>
         <param argument="integrate" type="select" label="Integration method" >