# HG changeset patch
# User iracooke
# Date 1395182796 14400
# Node ID e5b29190a4a0a7ef64fe4f955095cb45d525d15e
# Parent  ef9e2ec522368e1b619a9dfbe8a939bb35a7ebb3
Uploaded

diff -r ef9e2ec52236 -r e5b29190a4a0 tandem.xml
--- a/tandem.xml	Wed Mar 12 23:10:29 2014 -0400
+++ b/tandem.xml	Tue Mar 18 18:46:36 2014 -0400
@@ -28,7 +28,23 @@
 		#end for
 		'
 
-		$input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol $allow_multi_isotope_search --keep-params-files
+		$input_file -o $output -r 
+
+		--enzyme=$enzyme 
+
+		--precursor-ion-tol-units=$precursor_tolu 
+
+		-v $missed_cleavages 
+
+		-f $fragment_ion_tol 
+
+		-p $precursor_ion_tol 
+
+		$allow_multi_isotope_search 
+
+		--keep-params-files
+
+		$cleavage_semi
 		
 	</command>
 
@@ -90,6 +106,8 @@
 			<option value="1">1</option>
 			<option value="2">2</option>
 		</param>
+
+		<param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="" falsevalue="--no-cleavage-semi" />
 		
 		<param name="enzyme" type="select" format="text">
 		    <label>Enzyme</label>