# HG changeset patch
# User lecorguille
# Date 1539074380 14400
# Node ID 95e689b7f27f7b3873fb6dc44067b5233e357608
# Parent  6a4d8753a3308a004ec277729f66262fb90ee2fe
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 878be1bfbe93af0a140df76fa47f0a82a48189e3

diff -r 6a4d8753a330 -r 95e689b7f27f abims_xcms_group.xml
--- a/abims_xcms_group.xml	Thu Oct 04 10:37:03 2018 -0400
+++ b/abims_xcms_group.xml	Tue Oct 09 04:39:40 2018 -0400
@@ -73,7 +73,7 @@
             </when>
         </conditional>
 
-        <expand macro="input_peaklist"/>
+        <expand macro="input_peaklist_conditional"/>
 
         <expand macro="input_file_load"/>
     </inputs>
diff -r 6a4d8753a330 -r 95e689b7f27f macros_xcms.xml
--- a/macros_xcms.xml	Thu Oct 04 10:37:03 2018 -0400
+++ b/macros_xcms.xml	Tue Oct 09 04:39:40 2018 -0400
@@ -90,9 +90,6 @@
     </token>
 
     <xml name="input_peaklist">
-        <conditional name="peaklist">
-            <param name="peaklistBool" type="boolean" label="Get a Peak List" />
-            <when value="true">
               <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
               <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
               <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
@@ -102,6 +99,20 @@
                   <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"/>
+    </xml>
+
+    <xml name="input_peaklist_section">
+        <section name="peaklist" title="Peak List" expanded="True">
+            <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" />
+            <expand macro="input_peaklist"/>
+        </section>
+    </xml>
+
+    <xml name="input_peaklist_conditional">
+        <conditional name="peaklist">
+            <param name="peaklistBool" type="boolean" label="Get the Peak List" />
+            <when value="true">
+              <expand macro="input_peaklist"/>
             </when>
             <when value="false" />
         </conditional>