# HG changeset patch
# User workflow4metabolomics
# Date 1581594161 0
# Node ID 32c1cbdbdd3b48f9bf5b504415d842bad1c9a32e
# Parent  1986c48d86cee7cea9d599199b7b12e55dddafa3
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"

diff -r 1986c48d86ce -r 32c1cbdbdd3b README.rst
--- a/README.rst	Wed Feb 12 13:26:47 2020 +0000
+++ b/README.rst	Thu Feb 13 11:42:41 2020 +0000
@@ -4,6 +4,10 @@
 
 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
+**Version 3.6.1+galaxy1 - 13/02/2020**
+
+- NEW: if a retention time ajustment have already been applied to your data. The function applyAdjustedRtime will replace raw retention times with adjusted retention times and so alloww to cumulate the ajustments.
+
 **Version 3.6.1.0 - 03/09/2019**
 
 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
diff -r 1986c48d86ce -r 32c1cbdbdd3b abims_xcms_retcor.xml
--- a/abims_xcms_retcor.xml	Wed Feb 12 13:26:47 2020 +0000
+++ b/abims_xcms_retcor.xml	Thu Feb 13 11:42:41 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_retcor" name="xcms adjustRtime (retcor)" version="@TOOL_VERSION@+galaxy0">
+<tool id="abims_xcms_retcor" name="xcms adjustRtime (retcor)" version="@TOOL_VERSION@+galaxy1">
 
     <description>Retention Time Correction</description>
 
@@ -290,6 +290,9 @@
 .. _PeakGroups_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-peakGroups.html#heading-2
 .. _Obiwarp_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-obiwarp.html
 
+WARNING: if a retention time ajustment have already been applied to your data.
+The function applyAdjustedRtime will replace raw retention times with adjusted retention times and so alloww to cumulate the ajustments.
+
 @HELP_XCMS_MANUAL@
 
 ------------
@@ -308,6 +311,10 @@
 
 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
+**Version 3.6.1+galaxy1 - 13/02/2020**
+
+- NEW: if a retention time ajustment have already been applied to your data. The function applyAdjustedRtime will replace raw retention times with adjusted retention times and so alloww to cumulate the ajustments.
+
 @HELP_XCMS_NEWVERSION_3610@
 
 **Version 3.4.4.1 - 30/04/2019**
diff -r 1986c48d86ce -r 32c1cbdbdd3b xcms_retcor.r
--- a/xcms_retcor.r	Wed Feb 12 13:26:47 2020 +0000
+++ b/xcms_retcor.r	Thu Feb 13 11:42:41 2020 +0000
@@ -63,6 +63,12 @@
 
 adjustRtimeParam <- do.call(paste0(method,"Param"), args)
 print(adjustRtimeParam)
+
+if (hasAdjustedRtime(xdata)) {
+  cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment")
+  cat("Replace raw retention times with adjusted retention times.\n")
+  xdata <- applyAdjustedRtime(xdata)
+}
 xdata <- adjustRtime(xdata, param=adjustRtimeParam)
 
 #cat("\t\t\tCompute and Store TIC and BPI\n")