# HG changeset patch
# User jjohnson
# Date 1598040441 14400
# Node ID 61692bb2c78f2b70ab26f1034219324d42e779f4
# Parent  aeda6093dd4052f163cf98d0ef7485b5c0b73cfd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"

diff -r aeda6093dd40 -r 61692bb2c78f encyclopedia_encyclopedia.xml
--- a/encyclopedia_encyclopedia.xml	Wed Aug 19 08:35:54 2020 -0400
+++ b/encyclopedia_encyclopedia.xml	Fri Aug 21 16:07:21 2020 -0400
@@ -35,7 +35,7 @@
             <option value="final_delta_rt_pdf" selected="false">encyclopedia.txt.final.delta_rt.pdf</option>
             <option value="final_rt_fit_pdf" selected="false">encyclopedia.txt.final.rt_fit.pdf</option>
             <option value="final_rt_fit_txt" selected="false">encyclopedia.txt.final.rt_fit.txt</option>
-            <option value="features" selected="true">features.txt</option>
+            <option value="features" selected="false">features.txt</option>
             <option value="encyclopedia" selected="true">encyclopedia.txt</option>
             <option value="encyclopedia_decoy" selected="false">encyclopedia.decoy.txt</option>
         </param>
@@ -95,6 +95,7 @@
             <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" values="log,features,encyclopedia"/>
             <output name="features" ftype="tabular">
                 <assert_contents>
                     <has_text text="ESYDDVSSFR"/>
@@ -118,7 +119,6 @@
 
 **Inputs**
 
-
   - A spectrum file in mzML format
   - A chromatogram library that can be generated by SearchToLib 
   - A protein data base in fasta format
@@ -129,8 +129,17 @@
 **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 aeda6093dd40 -r 61692bb2c78f macros.xml
--- a/macros.xml	Wed Aug 19 08:35:54 2020 -0400
+++ b/macros.xml	Fri Aug 21 16:07:21 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:
 
     ::