# HG changeset patch
# User lecorguille
# Date 1486553803 18000
# Node ID d743af7feaad4b19e813a7ad0dd51420fb62fabf
# Parent  4992ecc91c969b8043d6c3b1b139af49c417e55d
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty

diff -r 4992ecc91c96 -r d743af7feaad macros.xml
--- a/macros.xml	Wed Feb 08 05:27:59 2017 -0500
+++ b/macros.xml	Wed Feb 08 06:36:43 2017 -0500
@@ -70,7 +70,42 @@
         </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