# HG changeset patch
# User workflow4metabolomics
# Date 1600934930 0
# Node ID 0cab69429e1e3f67723cc6c616b81f9bed16ac3c
# Parent  37d31fd64eb4077bc753285b97a2c19a5d89879e
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 50478425b4773ebcb393c0e31f1e622b7406dcbb"

diff -r 37d31fd64eb4 -r 0cab69429e1e lib.r
--- a/lib.r	Tue Jul 21 09:17:54 2020 -0400
+++ b/lib.r	Thu Sep 24 08:08:50 2020 +0000
@@ -256,7 +256,7 @@
     }
     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")
+        plot(chrom, col = group_colors[chrom$sample_group], main=main, peakType = "none")
         legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
     }
 
diff -r 37d31fd64eb4 -r 0cab69429e1e repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Jul 21 09:17:54 2020 -0400
+++ b/repository_dependencies.xml	Thu Sep 24 08:08:50 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" ?>
 <repositories>
-    <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/>
-    <repository changeset_revision="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    <repository name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="7800ba9a4c1e"/>
+    <repository name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="544f6d2329ac"/>
 </repositories>
\ No newline at end of file
diff -r 37d31fd64eb4 -r 0cab69429e1e xcms_plot_chromatogram.xml
--- a/xcms_plot_chromatogram.xml	Tue Jul 21 09:17:54 2020 -0400
+++ b/xcms_plot_chromatogram.xml	Thu Sep 24 08:08:50 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@TOOL_VERSION@+galaxy1">
+<tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@TOOL_VERSION@+galaxy2">
     <description>Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s)</description>
 
     <macros>
@@ -102,6 +102,10 @@
 Changelog/News
 --------------
 
+**Galaxy Version 3.6.1+galaxy2 - 23/09/2020**
+
+- BUGFIX: sample group colours did not match group labels.
+
 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
 @HELP_XCMS_NEWVERSION_3610@