# HG changeset patch
# User iracooke
# Date 1395185251 14400
# Node ID 210d04f6e2c6d74ce7bc72b6051d811d004b512d
# Parent  e5b29190a4a0a7ef64fe4f955095cb45d525d15e
Uploaded

diff -r e5b29190a4a0 -r 210d04f6e2c6 tandem.xml
--- a/tandem.xml	Tue Mar 18 18:46:36 2014 -0400
+++ b/tandem.xml	Tue Mar 18 19:27:31 2014 -0400
@@ -109,9 +109,37 @@
 
 		<param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="" falsevalue="--no-cleavage-semi" />
 		
+
+		<!--W, [2014-03-18T23:22:33.477692 #5258]  WARN -- : Use one of the following cleavage site specifications:
+W, [2014-03-18T23:22:33.477720 #5258]  WARN -- : 	argc - [R]|{P}
+W, [2014-03-18T23:22:33.477744 #5258]  WARN -- : 	aspn - [X]|[D]
+W, [2014-03-18T23:22:33.477768 #5258]  WARN -- : 	chymotrypsin - [FLMWY]|{P}
+W, [2014-03-18T23:22:33.477791 #5258]  WARN -- : 	clostripain - [R]|[X]
+W, [2014-03-18T23:22:33.477814 #5258]  WARN -- : 	cnbr - [M]|{P}
+W, [2014-03-18T23:22:33.477838 #5258]  WARN -- : 	elastase - [AGILV]|{P}
+W, [2014-03-18T23:22:33.477907 #5258]  WARN -- : 	formicacid - [D]|{P}
+W, [2014-03-18T23:22:33.477931 #5258]  WARN -- : 	gluc - [DE]|{P}
+W, [2014-03-18T23:22:33.477954 #5258]  WARN -- : 	gluc_bicarb - [E]|{P}
+W, [2014-03-18T23:22:33.477977 #5258]  WARN -- : 	iodosobenzoate - [W]|[X]
+W, [2014-03-18T23:22:33.478000 #5258]  WARN -- : 	lysc - [K]|{P}
+W, [2014-03-18T23:22:33.478029 #5258]  WARN -- : 	lysc-p - [K]|[X]
+W, [2014-03-18T23:22:33.478112 #5258]  WARN -- : 	lysn - [X]|[K]
+W, [2014-03-18T23:22:33.478138 #5258]  WARN -- : 	lysn_promisc - [X]|[AKRS]
+W, [2014-03-18T23:22:33.478172 #5258]  WARN -- : 	nonspecific - [X]|[X]
+W, [2014-03-18T23:22:33.478196 #5258]  WARN -- : 	pepsina - [FL]|[X]
+W, [2014-03-18T23:22:33.478259 #5258]  WARN -- : 	protein_endopeptidase - [P]|[X]
+W, [2014-03-18T23:22:33.478285 #5258]  WARN -- : 	staph_protease - [E]|[X]
+W, [2014-03-18T23:22:33.478309 #5258]  WARN -- : 	tca - [FMWY]|{P},[KR]|{P},[X]|[D]
+W, [2014-03-18T23:22:33.478333 #5258]  WARN -- : 	trypsin - [KR]|{P}
+W, [2014-03-18T23:22:33.478356 #5258]  WARN -- : 	trypsin/chymotrypsin - [FKLMRWY]|{P}
+W, [2014-03-18T23:22:33.478380 #5258]  WARN -- : 	trypsin/cnbr - [KR]|{P},[M]|{P}
+W, [2014-03-18T23:22:33.478403 #5258]  WARN -- : 	trypsin_gluc - [DEKR]|{P}-->
+
+
 		<param name="enzyme" type="select" format="text">
 		    <label>Enzyme</label>
-		    <option value="Trypsin">Trypsin</option>
+		    <option value="trypsin">Trypsin - [KR]|{P}</option>
+		    <option value="argc">argc - [R]|{P}</option>
 		</param>
 		
 		<param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>