diff msnbase_readmsdata.xml @ 10:84533814b1d5 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01

--- a/msnbase_readmsdata.xml	Fri Feb 08 09:55:50 2019 -0500
+++ b/msnbase_readmsdata.xml	Mon Apr 29 06:07:14 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" />
@@ -56,12 +56,12 @@
                 <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>
         <!-- DISABLE FOR TRAVIS
-        Useful to generate test-data for the further steps-->
+        Useful to generate test-data for the further steps
         <test>
             <param name="input" value="ko16.CDF"  ftype="netcdf" />
             <assert_stdout>
@@ -86,7 +86,7 @@
                 <has_text text="./wt16.CDF        wt16            ." />
             </assert_stdout>
         </test>
-        <!-- -->
+        -->
     </tests>
 
     <help><![CDATA[
@@ -132,7 +132,7 @@
 xcms.findChromPeaks         ``*``.raw.RData      rdata.msnbase.raw
 =========================== ==================== ====================
 
- 
+
 
 **Example of a metabolomic workflow**
 
@@ -158,7 +158,7 @@
 
 You have two methods for your inputs:
 
-    | Single file (recommended): You can put a single file as input. That way, you will be able to launch several readMSData and findChromPeaks in parallel and use "findChromPeaks Merger" before groupChromPeaks. 
+    | Single file (recommended): You can put a single file as input. That way, you will be able to launch several readMSData and findChromPeaks in parallel and use "findChromPeaks Merger" before groupChromPeaks.
     | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
 
 Zip file: Steps for creating the zip file
@@ -223,13 +223,18 @@
 
     | Tabular file that contains for each sample its associated class and polarity (positive,negative and mixed).
     | This file is necessary in further steps of the workflow, as the Anova and PCA steps for example.
-    | You get a sampleMetadata.tsv only if you use a zip. Otherwise, you have to provide one for the findChromPeaks Merger step. 
+    | You get a sampleMetadata.tsv only if you use a zip. Otherwise, you have to provide one for the findChromPeaks Merger step.
 
 ---------------------------------------------------
 
 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**