# HG changeset patch
# User galaxyp
# Date 1463767615 14400
# Node ID 70dade9fb8e38a6e360c526879e57f914640805f
# Parent  3ef5a7dd1a36e868e42910bf0dbbe88c147cb559
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9cae80c2ab1d6c933382cd8584e2d51f3c3d305b-dirty

diff -r 3ef5a7dd1a36 -r 70dade9fb8e3 macros.xml
--- a/macros.xml	Tue May 10 06:33:08 2016 -0400
+++ b/macros.xml	Fri May 20 14:06:55 2016 -0400
@@ -41,10 +41,8 @@
             help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
             <option value="Trypsin">Trypsin</option>
             <option value="Arg-C">Arg-C</option>
-            <option value="Semi-Arg-C">Semi-Arg-C</option>
             <option value="CNBr">CNBr</option>
             <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
-            <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
             <option value="Formic Acid">Formic Acid</option>
             <option value="Lys-C">Lys-C</option>
             <option value="Lys-C, no P rule">Lys-C, no P rule</option>
@@ -52,13 +50,13 @@
             <option value="Trypsin + CNBr">Trypsin + CNBr</option>
             <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
             <option value="Trypsin, no P rule">Trypsin, no P rule</option>
-            <option value="whole protein">whole protein</option>
+            <option value="Whole Protein">Whole Protein</option> 
             <option value="Asp-N">Asp-N</option>
             <option value="Glu-C">Glu-C</option>
             <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
             <option value="Top-Down">Top-Down</option>
             <option value="Semi-Tryptic">Semi-Tryptic</option>
-            <option value="No enzyme">No enzyme</option>
+            <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! -->
             <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
             <option value="Asp-N (DE)">Asp-N (DE)</option>
             <option value="Glu-C (DE)">Glu-C (DE)</option>
@@ -66,6 +64,13 @@
             <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
             <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
             <option value="Semi-Glu-C">Semi-Glu-C</option>
+            <option value="LysargiNase">LysargiNase</option>
+            <option value="Semi-LysargiNase">Semi-LysargiNase</option>
+            <option value="Trypsin + Glu-C">Trypsin + Glu-C</option>
+            <option value="Semi-Arg-C">Semi-Arg-C</option>
+            <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option>
+            <option value="Arg-N">Arg-N</option>
+            <option value="Semi-Arg-N">Semi-Arg-N</option>
         </param>
         <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
             help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>