diff abims_xcms_fillPeaks.xml @ 19:7b74ec867ad2 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 717c02f887ce343ca55f862c8020aaf49f5581d8

--- a/abims_xcms_fillPeaks.xml	Wed Feb 08 04:36:59 2017 -0500
+++ b/abims_xcms_fillPeaks.xml	Wed Feb 08 05:27:41 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.1">
+<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.0">
 
     <description>Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas</description>
 
@@ -18,7 +18,14 @@
 
         method $method
 
-        @COMMAND_PEAKLIST@
+        #if $peaklist.peaklistBool
+            variableMetadataOutput $variableMetadata
+            dataMatrixOutput $dataMatrix
+            convertRTMinute $peaklist.convertRTMinute
+            numDigitsMZ $peaklist.numDigitsMZ
+            numDigitsRT $peaklist.numDigitsRT
+            intval $peaklist.intval
+        #end if
 
         @COMMAND_FILE_LOAD@
 
@@ -32,16 +39,32 @@
             <option value="chrom" selected="true">chrom</option>
             <option value="MSW" >MSW</option>
         </param>
-
-        <expand macro="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>
         <expand macro="file_load"/>
 
     </inputs>
 
     <outputs>
         <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" />
-        <expand macro="output_peaklist"/>
+        <data name="variableMetadata" format="tabular" label="${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>
         <data name="log" format="txt" label="xset.log.txt"  hidden="true" />
     </outputs>
 
@@ -272,10 +295,6 @@
 Changelog/News
 --------------
 
-**Version 2.1.1 - 07/02/2017**
-
-- IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom)
-
 **Version 2.1.0 - 03/02/2017**
 
 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data
@@ -292,6 +311,7 @@
 
 - TEST: refactoring to pass planemo test using conda dependencies
 
+
 **Version 2.0.5 - 10/02/2016**
 
 - BUGFIX: better management of errors. Datasets remained green although the process failed