--- a/encyclopedia_walnut.xml	Fri Jun 19 14:04:16 2020 +0000
+++ b/encyclopedia_walnut.xml	Mon Sep 14 16:58:35 2020 +0000
@@ -4,12 +4,14 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command detect_errors="exit_code"><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         @CMD_IMPORTS@
         @LINK_SCAN_INPUT@
         @LINK_FASTA_INPUT@
         @LINK_TARGET_FASTA@
-        EncyclopeDIA -Djava.awt.headless=true -Xmx12g -walnut
+        EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US
+            -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -walnut
+            -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
         @SCAN_INPUT@
         @FASTA_INPUT@
         @TARGET_FASTA@
@@ -26,19 +28,13 @@
         <expand macro="scan_input"/>
         <expand macro="fasta_input"/>
         <expand macro="target_fasta"/>
-        <expand macro="common_options"/>
-        <expand macro="mass_library_tolerance"/>
-        <expand macro="percolator_options"/>
-        <expand macro="peak_options"/>
-        <expand macro="window_options"/>
-        <expand macro="modification_options"/>
-        <expand macro="search_options"/>
+        <expand macro="options_section"/>
         <param name="select_outputs" type="select" label="Select outputs" multiple="true">
             <option value="log" selected="true">log</option>
             <option value="elib" selected="true">elib</option>
-            <option value="features" selected="true">features.txt</option>
+            <option value="features" selected="false">features.txt</option>
             <option value="pecan" selected="true">pecan.txt</option>
-            <option value="pecan_decoy" selected="true">pecan.decoy.txt</option>
+            <option value="pecan_decoy" selected="false">pecan.decoy.txt</option>
         </param>
     </inputs>
     <outputs>
@@ -67,52 +63,50 @@
             </actions>
         </data>
     </outputs>
+    <tests>
+        <test>
+            <param name="scan_input" ftype="mzml" value="BCS_hela_narrow_3_1.mzML"/>
+            <param name="fasta" ftype="fasta" value="uniprot_tiny_human.fasta"/>
+            <param name="select_outputs" value="log,features,pecan"/>
+            <output name="features" ftype="tabular">
+                <assert_contents>
+                    <has_text text="LHYNEGLNIK"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help><![CDATA[
+**Walnut**
+
+@ENCYCLOPEDIA_WIKI@
+
 Walnut is a FASTA database search engine for Data-Independent Acquisition (DIA) MS/MS data.
 Walnut uses PeCAn-style scoring to extract peptide fragmentation chromatograms from MZML files, assign peaks, and calculate various peak features. These features are interpreted by Percolator to identify peptides.
 
-Required Parameters: 
-	-i	input .DIA or .MZML file
-	-f	background FASTA file
+
+
+**Inputs**
+
+  - A spectrum file in mzML format
+  - A protein data base in fasta format
+
+@MSCONVERT_HELP@
+
+**Outputs**
 
-Other Parameters: 
-	-t	target FASTA file (default: background FASTA file)
-	-tp	true/false target FASTA file contains peptides (default: false)
-	-o	output report file (default: [input file].pecan.txt)
-	-acquisition                          (default: overlapping dia)
-	-addDecoysToBackground                (default: false)
-	-alpha                                (default: 1.8)
-	-beta                                 (default: 0.4)
-	-dontRunDecoys                        (default: false)
-	-enzyme                               (default: trypsin)
-	-filterPeaklists                      (default: false)
-	-fixed                                (default: C=57.0214635)
-	-foffset                              (default: 0)
-	-frag                                 (default: YONLY)
-	-ftol                                 (default: 10)
-	-ftolunits                            (default: ppm)
-	-maxCharge                            (default: 3)
-	-maxLength                            (default: 100)
-	-maxMissedCleavage                    (default: 1)
-	-minCharge                            (default: 2)
-	-minEluteTime                         (default: 12)
-	-minIntensity                         (default: -1.0)
-	-minLength                            (default: 5)
-	-minNumOfQuantitativePeaks            (default: 3)
-	-minQuantitativeIonNumber             (default: 3)
-	-numberOfQuantitativePeaks            (default: 5)
-	-numberOfReportedPeaks                (default: 1)
-	-numberOfThreadsUsed                  (default: 12)
-	-percolatorProteinThreshold           (default: 0.01)
-	-percolatorThreshold                  (default: 0.01)
-	-percolatorVersionNumber              (default: 3)
-	-poffset                              (default: 0)
-	-precursorIsolationMargin             (default: 0)
-	-precursorWindowSize                  (default: -1)
-	-ptol                                 (default: 10)
-	-ptolunits                            (default: ppm)
-	-requireVariableMods                  (default: false)
-	-variable                             (default: -)
+  - A log file
+  - A Chromatogram Library (.elib)
+  - The identified features in tabular format
+    Feature values of scans that are used by percolator to determine matches.
+  - The identified Peptide Spectral Match results in tabular format
+    Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
+  - The identified peptides in tabular format
+    Per peptide: the normalized intensity for each scan file.
+    Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ...
+  - The identified proteins in tabular format
+    Per protein: the normalized intensity for each scan file.
+    Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ...
+
 
     ]]></help>
     <expand macro="citations" />