--- a/BlastParser_and_hits.xml	Fri Jun 19 13:17:32 2015 -0400
+++ b/BlastParser_and_hits.xml	Mon Jun 29 06:06:11 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.1.0">
+<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.2.0">
 <description>for virus discovery</description>
 <requirements></requirements>
 <command interpreter="python">
@@ -9,6 +9,13 @@
 	--fastaOutput $fastaOutput
 	--flanking $flanking
 	--mode $mode
+	## Additional parameters.
+    #if $additional_filters.use_filters == "yes":
+        --filter_relativeCov $additional_filters.filter_relativeCov
+        --filter_maxScore $additional_filters.filter_maxScore
+        --filter_meanScore $additional_filters.filter_meanScore
+    #end if
+
 </command>
 <inputs>
 	<param name="sequences" type="data" format="fasta"  label="fasta sequences that have been blasted" />
@@ -18,6 +25,19 @@
 	    <option value="verbose" default="true">verbose</option>
 	    <option value="short">do not report oases contigs</option>
 	</param>
+    <conditional name="additional_filters">
+            <param name="use_filters" type="select" label="Use Additional Filters?">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no">
+            </when>
+            <when value="yes">            
+                <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/>
+                <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/>
+                <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/>
+            </when>
+    </conditional>
 </inputs>
 <outputs>
 	<data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>