# HG changeset patch
# User workflow4metabolomics
# Date 1595337474 14400
# Node ID 37d31fd64eb4077bc753285b97a2c19a5d89879e
# Parent  dbd877060ac306636cea4fe7c2d4b96633dc720f
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065"

diff -r dbd877060ac3 -r 37d31fd64eb4 lib.r
--- a/lib.r	Wed Feb 12 08:30:06 2020 -0500
+++ b/lib.r	Tue Jul 21 09:17:54 2020 -0400
@@ -149,14 +149,20 @@
 
     par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
 
-    group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    if(length(unique(xdata$sample_group))<10){
+        group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    }else{
+        group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette="Dark 3")
+    }
     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)
     }
 
@@ -170,7 +176,11 @@
     pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
 
     # Color by group
-    group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    if(length(unique(xdata$sample_group))<10){
+        group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    }else{
+        group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette="Dark 3")
+    }
     if (length(group_colors) > 1) {
         names(group_colors) <- unique(xdata$sample_group)
         plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
@@ -239,7 +249,11 @@
     pdf(pdfname, width=16, height=10)
 
     # Color by group
-    group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    if(length(unique(xdata$sample_group))<10){
+        group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    }else{
+        group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette="Dark 3")
+    }
     if (length(group_colors) > 1) {
         names(group_colors) <- unique(xdata$sample_group)
         plot(chrom, col = group_colors[as.factor(chrom$sample_group)], main=main, peakType = "none")
diff -r dbd877060ac3 -r 37d31fd64eb4 macros_xcms.xml
--- a/macros_xcms.xml	Wed Feb 12 08:30:06 2020 -0500
+++ b/macros_xcms.xml	Tue Jul 21 09:17:54 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" >
diff -r dbd877060ac3 -r 37d31fd64eb4 xcms_plot_chromatogram.xml
--- a/xcms_plot_chromatogram.xml	Wed Feb 12 08:30:06 2020 -0500
+++ b/xcms_plot_chromatogram.xml	Tue Jul 21 09:17:54 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@TOOL_VERSION@.0">
+<tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@TOOL_VERSION@+galaxy1">
     <description>Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s)</description>
 
     <macros>