# HG changeset patch
# User lecorguille
# Date 1539074542 14400
# Node ID 34fe699200ce0758e1eb61ef54677d25cbcb2a11
# Parent  1b60d8eb704aee0c7afd929c6c952e8d0e6d7265
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 878be1bfbe93af0a140df76fa47f0a82a48189e3

diff -r 1b60d8eb704a -r 34fe699200ce README.rst
--- a/README.rst	Thu Oct 04 10:38:22 2018 -0400
+++ b/README.rst	Tue Oct 09 04:42:22 2018 -0400
@@ -2,6 +2,11 @@
 Changelog/News
 --------------
 
+**Version 3.0.0.1 - 09/10/2018**
+
+- IMPROVEMENT: the export of the PeakList is now mandatory
+
+
 **Version 3.0.0.0 - 08/03/2018**
 
 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
diff -r 1b60d8eb704a -r 34fe699200ce abims_xcms_fillPeaks.xml
--- a/abims_xcms_fillPeaks.xml	Thu Oct 04 10:38:22 2018 -0400
+++ b/abims_xcms_fillPeaks.xml	Tue Oct 09 04:42:22 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@WRAPPER_VERSION@.0">
+<tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@WRAPPER_VERSION@.1">
 
     <description>Integrate areas of missing peaks</description>
 
@@ -37,7 +37,7 @@
             <param argument="ppm" type="integer" value="0" label="Specifying a ppm by which the mz width of the peak region should be expanded" help="For peaks with an mz width smaller than ‘mean(c(mzmin, mzmax)) * ppm / 1e6’, the ‘mzmin’ will be replaced by ‘mean(c(mzmin, mzmax)) - (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’ and ‘mzmax’ by ‘mean(c(mzmin, mzmax)) + (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’. This is applied before eventually expanding the mz width using the ‘expandMz’ parameter." />
         </section>
 
-        <expand macro="input_peaklist"/>
+        <expand macro="input_peaklist_section"/>
 
         <expand macro="input_file_load"/>
 
@@ -130,12 +130,12 @@
         </test>-->
         <test>
             <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData" ftype="rdata"/>
-            <conditional name="peaklist">
+            <section name="peaklist">
                 <param name="peaklistBool" value="true" />
                 <param name="convertRTMinute" value="false" />
                 <param name="numDigitsMZ" value="4" />
                 <param name="numDigitsRT" value="1" />
-            </conditional>
+            </section>
             <expand macro="test_file_load_single"/>
             <assert_stdout>
                 <has_text text="expandMz: 0" />
@@ -230,6 +230,11 @@
 Changelog/News
 --------------
 
+**Version 3.0.0.1 - 09/10/2018**
+
+- IMPROVEMENT: the export of the PeakList is now mandatory
+
+
 **Version 3.0.0.0 - 08/03/2018**
 
 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
diff -r 1b60d8eb704a -r 34fe699200ce macros_xcms.xml
--- a/macros_xcms.xml	Thu Oct 04 10:38:22 2018 -0400
+++ b/macros_xcms.xml	Tue Oct 09 04:42:22 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>