diff macros_xcms.xml @ 25:26d77e9ceb49 draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"

--- a/macros_xcms.xml	Wed Feb 12 08:28:33 2020 -0500
+++ b/macros_xcms.xml	Wed Apr 07 10:34:07 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
 
-    <token name="@TOOL_VERSION@">3.6.1</token>
+    <token name="@TOOL_VERSION@">3.12.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
@@ -98,7 +98,7 @@
                   <option value="maxo">maxo</option>
                   <option value="intb">intb</option>
               </param>
-              <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Replace the remain NA by 0 in the dataMatrix" help="Rather mandatory for some downstream statistical steps"/>
+              <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="If NA values remain, replace them by 0 in the dataMatrix" help="Mandatory for some of the downstream tools (data processing, statistics) that do not accept NA values"/>
     </xml>
 
     <xml name="input_peaklist_section">
@@ -193,7 +193,7 @@
             <option value="wMean">intensity weighted mean of the peak's m/z values</option>
             <option value="mean">mean of the peak's m/z values</option>
             <option value="apex">use the m/z value at the peak apex</option>
-            <option value="wMeanApex3">ntensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>
+            <option value="wMeanApex3">intensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>
             <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option>
         </param>
         <param argument="integrate" type="select" label="Integration method" >
@@ -243,6 +243,7 @@
 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html
+.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
     </token>
 
@@ -256,6 +257,11 @@
 
 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
     </token>
+    <token name="@HELP_XCMS_NEWVERSION_31200@">
+**Version 3.12.0+galaxy* - 03/03/2020**
+
+- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_)
+    </token>
 
     <xml name="citation">
         <citations>