# HG changeset patch
# User lecorguille
# Date 1486549679 18000
# Node ID 4992ecc91c969b8043d6c3b1b139af49c417e55d
# Parent  d9e7403f16f38f636c290d3927b40e41c7fc2cd6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 717c02f887ce343ca55f862c8020aaf49f5581d8

diff -r d9e7403f16f3 -r 4992ecc91c96 macros.xml
--- a/macros.xml	Wed Feb 08 04:37:18 2017 -0500
+++ b/macros.xml	Wed Feb 08 05:27:59 2017 -0500
@@ -70,42 +70,7 @@
         </conditional>
     </xml>
 
-    <token name="@COMMAND_PEAKLIST@">
-        #if $peaklist.peaklistBool
-            variableMetadataOutput $variableMetadata
-            dataMatrixOutput $dataMatrix
-            convertRTMinute $peaklist.convertRTMinute
-            numDigitsMZ $peaklist.numDigitsMZ
-            numDigitsRT $peaklist.numDigitsRT
-            intval $peaklist.intval
-        #end if
-    </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" />
-              <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
-                  <option value="into" selected="true">into</option>
-                  <option value="maxo">maxo</option>
-                  <option value="intb">intb</option>
-              </param>
-            </when>
-            <when value="false" />
-        </conditional>
-    </xml>
-
-    <xml name="output_peaklist">
-        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.fillPeaks.variableMetadata.tsv">
-            <filter>(peaklist['peaklistBool'])</filter>
-        </data>
-        <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.fillPeaks.dataMatrix.tsv" >
-            <filter>(peaklist['peaklistBool'])</filter>
-        </data>
-    </xml>
 
     <token name="@HELP_AUTHORS@">
 .. class:: infomark