diff macros_xcms.xml @ 38:67ee46ce9781 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513

--- a/macros_xcms.xml	Wed Sep 05 05:59:21 2018 -0400
+++ b/macros_xcms.xml	Mon Sep 17 08:46:01 2018 -0400
@@ -29,7 +29,7 @@
     <xml name="input_file_load">
         <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
             <conditional name="file_load_conditional">
-                <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
+                <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message saying that your original dataset or zip file have been deleted on the server." >
                     <option value="no" >no need</option>
                     <option value="yes" >yes</option>
                 </param>
@@ -85,6 +85,7 @@
             numDigitsMZ $peaklist.numDigitsMZ
             numDigitsRT $peaklist.numDigitsRT
             intval $peaklist.intval
+            naTOzero $peaklist.naTOzero
         #end if
     </token>
 
@@ -100,6 +101,7 @@
                   <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"/>
             </when>
             <when value="false" />
         </conditional>
@@ -225,7 +227,7 @@
 
     <token name="@HELP_XCMS_MANUAL@">
 
-For details and explanations for all the parameters and the workflow of xcms_ package, see its manual_ and this example_
+For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_
 
 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf