--- a/hammock.xml	Mon Jan 26 06:24:21 2015 -0500
+++ b/hammock.xml	Fri Aug 28 07:38:12 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="hammock_1.0" name="Hammock - cluster peptides">
+<tool id="hammock_1.0" name="Hammock - cluster peptides" version="1.0.2" hidden="false">
 
     <description>Clusters short peptide sequences</description>
 
@@ -15,6 +15,12 @@
 	    #if $advanced_greedy_params.set_greedy_params == "set":
 		-x $advanced_greedy_params.max_shift
 		-p $advanced_greedy_params.shift_penalty
+		-R $advanced_greedy_params.set_order.order
+
+		#if $advanced_greedy_params.set_order.order == "random":
+			-S $advanced_greedy_params.set_order.seed
+		#end if
+	
 		-m \${MATRIX_PATH}${advanced_greedy_params.scoring_matrix}.txt
             	#if $advanced_greedy_params.greedy_params.set_greedy == "set":
                 	-g $advanced_greedy_params.greedy_params.greedy_threshold
@@ -103,6 +109,24 @@
 
          	<param name="shift_penalty" type="integer" value="0" label="Sequence shift penalty" help="Score penalty added to to each alignment score during greedy clustering. This penalty is added for every amino acid aligned towards a (trailing) gap. This value should typically be non-positive (With a positive value, sequences benefit from containing more gaps). See -p, --gap penalty in manual for details."/>
 
+	      <conditional name="set_order">
+
+              		<param name="order" type="select" label="Greedy clustering order" help="Select the order of sequences during the greedy clustering. See -R, --order in manual for details.">
+                  		<option value="size">Size</option>
+                  		<option value="alphabetic">Alphabetic</option>
+                  		<option value="random">Random</option>
+              		</param>
+
+			<when value="size" />
+			<when value="alphabetic" />
+            		<when value="random">
+         			<param name="seed" type="integer" value="42" label="Seed for random number generation" help="Set a seed value for the pseudorandom sequence order. See -S, --seed in manual for details."/>
+			</when>
+
+		</conditional>
+
+		
+
               <param name="scoring_matrix" type="select" label="Substitiution matrix schema." help="Select a substitution matrix to be used to score alignments during glreedy clustering. See -m, --matrix in manual for details.">
                   <option value="blosum62">Blosum 62</option>
                   <option value="blosum30">Blosum 30</option>