# HG changeset patch
# User lecorguille
# Date 1554826217 14400
# Node ID b6ef94529e5091971490d7dce4e49fb8b0941feb
# Parent  d7a7ef786fbec09f483c5d293e6473c93a94e558
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 8ed93601e09e1db2fbaef5af29d58464b639f2a8

diff -r d7a7ef786fbe -r b6ef94529e50 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Tue Apr 09 12:10:17 2019 -0400
@@ -0,0 +1,11 @@
+
+Changelog/News
+--------------
+
+**Version 2.8.2.0 - 08/04/2019**
+
+- UPGRADE: upgrade the MSnbase version from 2.4.0 to 2.8.2 (see MSnbase News_). Almost all the new features may not concern our usage of MSnbase.
+
+**Version 2.4.0.0 - 29/03/2018**
+
+- NEW: a new dedicated tool to read the raw data. This function was previously included in xcms.findChromPeaks. This way, you will now be able to display TICs and BPCs before xcms.findChromPeaks.
diff -r d7a7ef786fbe -r b6ef94529e50 macros_msnbase.xml
--- a/macros_msnbase.xml	Tue Mar 12 10:58:41 2019 -0400
+++ b/macros_msnbase.xml	Tue Apr 09 12:10:17 2019 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@WRAPPER_VERSION@">2.4.0</token>
+    <token name="@WRAPPER_VERSION@">2.8.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-msnbase</requirement>
diff -r d7a7ef786fbe -r b6ef94529e50 msnbase_readmsdata.r
--- a/msnbase_readmsdata.r	Tue Mar 12 10:58:41 2019 -0400
+++ b/msnbase_readmsdata.r	Tue Apr 09 12:10:17 2019 -0400
@@ -91,7 +91,7 @@
 cat("\n\n")
 
 #saving R data in .Rdata file to save the variables used in the present tool
-objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList", "chromTIC", "chromBPI")
+objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI")
 save(list=objects2save[objects2save %in% ls()], file="readmsdata.RData")
 
 
diff -r d7a7ef786fbe -r b6ef94529e50 msnbase_readmsdata.xml
--- a/msnbase_readmsdata.xml	Tue Mar 12 10:58:41 2019 -0400
+++ b/msnbase_readmsdata.xml	Tue Apr 09 12:10:17 2019 -0400
@@ -42,7 +42,7 @@
                 <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" />
                 <has_text text="faahKO_reduce/WT/wt15.CDF faahKO_reduce/WT/wt16.CDF" />
                 <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" />
-                <has_text text="fvarLabels: fileIdx spIdx ... spectrum (27 total)" />
+                <has_text text="fvarLabels: fileIdx spIdx ... spectrum (28 total)" />
                 <has_text text="faahKO_reduce/KO/ko15.CDF        ko15           KO" />
                 <has_text text="faahKO_reduce/KO/ko16.CDF        ko16           KO" />
                 <has_text text="faahKO_reduce/WT/wt15.CDF        wt15           WT" />
@@ -56,7 +56,7 @@
                 <has_text text="rowNames: ./ko15.CDF" />
                 <has_text text="ko15.CDF" />
                 <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" />
-                <has_text text="fvarLabels: fileIdx spIdx ... spectrum (27 total)" />
+                <has_text text="fvarLabels: fileIdx spIdx ... spectrum (28 total)" />
                 <has_text text="./ko15.CDF        ko15            ." />
             </assert_stdout>
         </test>
@@ -230,6 +230,11 @@
 Changelog/News
 --------------
 
+.. _News: https://bioconductor.org/packages/release/bioc/news/MSnbase/NEWS
+
+**Version 2.8.2.0 - 08/04/2019**
+
+- UPGRADE: upgrade the MSnbase version from 2.4.0 to 2.8.2 (see MSnbase News_). Almost all the new features may not concern our usage of MSnbase.
 
 **Version 2.4.0.0 - 29/03/2018**