diff encyclopedia_encyclopedia.xml @ 1:b4f1a49ff3b5 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"

--- a/encyclopedia_encyclopedia.xml	Fri Jun 19 10:13:10 2020 -0400
+++ b/encyclopedia_encyclopedia.xml	Tue Jun 30 11:39:02 2020 -0400
@@ -24,7 +24,7 @@
     <inputs>
         <expand macro="scan_input"/>
         <expand macro="fasta_input"/>
-        <expand macro="lib_input" token_optional="false" token_help="Chromatogram elib from SearchToLib"/>
+        <expand macro="lib_input" optional="false" libhelp="Chromatogram elib from SearchToLib on pooled samples"/>
         <expand macro="common_options"/>
         <expand macro="mass_library_tolerance"/>
         <expand macro="percolator_options"/>
@@ -96,44 +96,27 @@
         </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
+**EncyclopeDIA**
+
+@ENCYCLOPEDIA_WIKI@
 
-Required Parameters:
-	-i	input .DIA or .MZML file
-	-f	protein .FASTA database
-	-l	library .ELIB file
+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**
+
 
-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)
+  - 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
+  - The identified features in tabular format 
 
     ]]></help>
     <expand macro="citations" />