# HG changeset patch
# User workflow4metabolomics
# Date 1595337447 14400
# Node ID 0d05d0458376f6be94eadae32afa68de4f19034c
# Parent  a066b8581b97e4b40f494c88a7a58fec395f1bde
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065"

diff -r a066b8581b97 -r 0d05d0458376 abims_xcms_group.xml
--- a/abims_xcms_group.xml	Tue Apr 28 09:34:27 2020 -0400
+++ b/abims_xcms_group.xml	Tue Jul 21 09:17:27 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy1">
+<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy2">
 
     <description>Perform the correspondence, the grouping of chromatographic peaks within and between samples.</description>
 
diff -r a066b8581b97 -r 0d05d0458376 lib.r
--- a/lib.r	Tue Apr 28 09:34:27 2020 -0400
+++ b/lib.r	Tue Jul 21 09:17:27 2020 -0400
@@ -149,7 +149,11 @@
 
     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]}
@@ -172,7 +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])
@@ -241,7 +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")