# HG changeset patch
# User jjohnson
# Date 1598040780 14400
# Node ID 0172dfa08216ea39d11f6bf7b6a98a6004fcd845
# Parent  4936de9f90247a1b35fdb19684177d092c77d764
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"

diff -r 4936de9f9024 -r 0172dfa08216 encyclopedia_walnut.xml
--- a/encyclopedia_walnut.xml	Wed Aug 19 08:39:11 2020 -0400
+++ b/encyclopedia_walnut.xml	Fri Aug 21 16:13:00 2020 -0400
@@ -30,9 +30,9 @@
         <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>
@@ -65,6 +65,7 @@
         <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" values="log,features,pecan"/>
             <output name="features" ftype="tabular">
                 <assert_contents>
                     <has_text text="LHYNEGLNIK"/>
@@ -73,9 +74,6 @@
         </test>
     </tests>
     <help><![CDATA[
-
-    <help><![CDATA[
-
 **Walnut**
 
 @ENCYCLOPEDIA_WIKI@
@@ -84,20 +82,29 @@
 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.
 
 
+
 **Inputs**
 
-
   - A spectrum file in mzML format
   - A protein data base in fasta format
 
-
 @MSCONVERT_HELP@
 
 **Outputs**
 
   - A log file
-  - The identified features in tabular format 
-  - The identified proteins in tabular format 
+  - 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" />
diff -r 4936de9f9024 -r 0172dfa08216 macros.xml
--- a/macros.xml	Wed Aug 19 08:39:11 2020 -0400
+++ b/macros.xml	Fri Aug 21 16:13:00 2020 -0400
@@ -128,7 +128,7 @@
     <token name="@LINK_LIB_INPUT@"><![CDATA[
     #if $library
     #set $l_name = $ln_name($library)
-    cp '$library' $l_name &&
+    cp '$library' '$l_name' &&
     #else
     #set $l_name = None
     #end if
@@ -494,7 +494,7 @@
     </token>
     <token name="@MSCONVERT_HELP@"><![CDATA[
 
-    The MSConvert command can be used to deconvolute DIA raw files. You need to use these options
+    The MSConvert command can be used to convert and deconvolute DIA raw files to mzML format. You need to use these options:
 
     ::