diff abims_xcms_fillPeaks.xml @ 11:de0d85537ee3 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797

--- a/abims_xcms_fillPeaks.xml	Tue Feb 07 04:05:02 2017 -0500
+++ b/abims_xcms_fillPeaks.xml	Fri Apr 07 07:37:05 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.8">
+<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>
 
@@ -12,22 +12,15 @@
     <command><![CDATA[
         @COMMAND_XCMS_SCRIPT@
         xfunction fillPeaks
-        image $image
+        image '$image'
 
-        xsetRdataOutput $xsetRData
+        xsetRdataOutput '$xsetRData'
 
         method $method
 
-        #if $peaklist.peaklistBool
-            variableMetadataOutput $variableMetadata
-            dataMatrixOutput $dataMatrix
-            convertRTMinute $peaklist.convertRTMinute
-            numDigitsMZ $peaklist.numDigitsMZ
-            numDigitsRT $peaklist.numDigitsRT
-            intval $peaklist.intval
-        #end if
+        @COMMAND_PEAKLIST@
 
-        @COMMAND_ZIPFILE_LOAD@
+        @COMMAND_FILE_LOAD@
 
         @COMMAND_LOG_EXIT@
 
@@ -39,32 +32,16 @@
             <option value="chrom" selected="true">chrom</option>
             <option value="MSW" >MSW</option>
         </param>
-        <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="zipfile_load"/>
+
+        <expand macro="input_peaklist"/>
+
+        <expand macro="input_file_load"/>
 
     </inputs>
 
     <outputs>
         <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" />
-        <data name="variableMetadata" format="tabular" label="${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>
+        <expand macro="output_peaklist" function="fillpeaks" />
         <data name="log" format="txt" label="xset.log.txt"  hidden="true" />
     </outputs>
 
@@ -93,8 +70,30 @@
                 <param name="numDigitsMZ" value="4" />
                 <param name="numDigitsRT" value="1" />
             </conditional>
-            <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
-            <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip"  ftype="zip" />
+            <expand macro="test_file_load_zip"/>
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 4 samples" />
+                    <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" />
+                    <has_text text="Mass range: 200.1-600 m/z" />
+                    <has_text text="Peaks: 32720 (about 8180 per sample)" />
+                    <has_text text="Peak Groups: 8157" />
+                    <has_text text="Sample classes: KO, WT" />
+                </assert_contents>
+            </output>
+            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
+            <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
+        </test>
+        <test>
+            <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData"/>
+            <param name="method" value="chrom"/>
+            <conditional name="peaklist">
+                <param name="convertRTMinute" value="false" />
+                <param name="peaklistBool" value="true" />
+                <param name="numDigitsMZ" value="4" />
+                <param name="numDigitsRT" value="1" />
+            </conditional>
+            <expand macro="test_file_load_single"/>
             <output name="log">
                 <assert_contents>
                     <has_text text="object with 4 samples" />
@@ -269,6 +268,12 @@
 Changelog/News
 --------------
 
+**Version 2.1.0 - 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)
+
+- IMPROVEMENT: xcms.fillpeaks can deal with merged individual data
+
 **Version 2.0.8 - 22/12/2016**
 
 - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate
@@ -281,7 +286,6 @@
 
 - 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