--- a/encyclopedia_encyclopedia.xml	Fri Jun 19 14:02:41 2020 +0000
+++ b/encyclopedia_encyclopedia.xml	Mon Sep 14 16:57:41 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_LIB_INPUT@
-        EncyclopeDIA -Djava.awt.headless=true
+        EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US
+            -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g
+            -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
         @SCAN_INPUT@
         @FASTA_INPUT@
         @LIB_INPUT@
@@ -24,25 +26,20 @@
     <inputs>
         <expand macro="scan_input"/>
         <expand macro="fasta_input"/>
-        <expand macro="lib_input" token_optional="false" token_help="Chromatogram elib from SearchToLib"/>
-        <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="lib_input" optional="false" libhelp="Chromatogram elib from SearchToLib on pooled samples"/>
+        <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="first_delta_rt_pdf" selected="true">encyclopedia.txt.first.delta_rt.pdf</option>
-            <option value="first_rt_fit_pdf" selected="true">encyclopedia.txt.first.rt_fit.pdf</option>
-            <option value="first_rt_fit_txt" selected="true">encyclopedia.txt.first.rt_fit.txt</option>
-            <option value="final_delta_rt_pdf" selected="true">encyclopedia.txt.final.delta_rt.pdf</option>
-            <option value="final_rt_fit_pdf" selected="true">encyclopedia.txt.final.rt_fit.pdf</option>
-            <option value="final_rt_fit_txt" selected="true">encyclopedia.txt.final.rt_fit.txt</option>
-            <option value="features" selected="true">features.txt</option>
-            <option value="encyclopedia" selected="true">encyclopedia.txt</option>
-            <option value="encyclopedia_decoy" selected="true">encyclopedia.decoy.txt</option>
+            <option value="first_delta_rt_pdf" selected="false">Initial Delta Retention Time Plot</option>
+            <option value="first_rt_fit_pdf" selected="false">Initial Fitted Retention Time Plot</option>
+            <option value="first_rt_fit_txt" selected="false">Initial Fitted Retention Time Table</option>
+            <option value="final_delta_rt_pdf" selected="false">Final Delta Retention Time Plot</option>
+            <option value="final_rt_fit_pdf" selected="false">Final Fitted Retention Time Plot</option>
+            <option value="final_rt_fit_txt" selected="false">Final Fitted Retention Time Table</option>
+            <option value="features" selected="false">features</option>
+            <option value="encyclopedia" selected="true">encyclopedia results</option>
+            <option value="encyclopedia_decoy" selected="false">encyclopedia decoy results</option>
         </param>
     </inputs>
     <outputs>
@@ -95,45 +92,56 @@
             </actions>
         </data>
     </outputs>
-    <help><![CDATA[
-EncyclopeDIA is a library search engine for DIA data.
-You should prefix your arguments with a high memory setting, e.g. "-Xmx8g" for 8gb
+    <tests>
+        <test>
+            <param name="scan_input" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML"/>
+            <param name="library" ftype="elib" value="BCS_hela.elib"/>
+            <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/>
+            <param name="select_outputs" value="log,features,encyclopedia"/>
+            <output name="features" ftype="tabular">
+                <assert_contents>
+                    <has_text text="ESYDDVSSFR"/>
+                </assert_contents>
+            </output>
+            <output name="encyclopedia" ftype="tabular">
+                <assert_contents>
+                    <has_text text="ESYDDVSSFR"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
 
-Required Parameters:
-	-i	input .DIA or .MZML file
-	-f	protein .FASTA database
-	-l	library .ELIB file
+    <help><![CDATA[
+**EncyclopeDIA**
+
+@ENCYCLOPEDIA_WIKI@
 
-Other Parameters:
-	-o	output report file (default: [input file].encyclopedia.txt)
-	-acquisition                          (default: Non-Overlapping DIA)
-	-enzyme                               (default: trypsin)
-	-expectedPeakWidth                    (default: 25)
-	-filterPeaklists                      (default: false)
-	-fixed                                (default: C=57.0214635)
-	-foffset                              (default: 0)
-	-frag                                 (default: CID)
-	-ftol                                 (default: 10)
-	-ftolunits                            (default: ppm)
-	-lftol                                (default: 10)
-	-lftolunits                           (default: ppm)
-	-localizationModification             (default: none)
-	-minIntensity                         (default: -1.0)
-	-minNumOfQuantitativePeaks            (default: 3)
-	-minQuantitativeIonNumber             (default: 3)
-	-numberOfExtraDecoyLibrariesSearched  (default: 0.0)
-	-numberOfQuantitativePeaks            (default: 5)
-	-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)
-	-rtWindowInMin                        (default: -1.0)
-	-scoringBreadthType                   (default: window)
-	-verifyModificationIons               (default: true)
+EncyclopeDIA extracts peptide fragmentation chromatograms from MZML files, matches them to spectra in libraries, and calculates various scoring features. These features are interpreted by Percolator to identify peptides.
+
+
+**Inputs**
+
+  - A spectrum file in mzML format
+  - A chromatogram library that can be generated by SearchToLib 
+  - A protein data base in fasta format
+
+
+@MSCONVERT_HELP@
+
+**Outputs**
+
+  - 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" />