--- a/ITSx.xml	Thu Jun 04 12:05:10 2015 -0400
+++ b/ITSx.xml	Fri Jun 05 11:10:49 2015 -0400
@@ -5,14 +5,16 @@
   </description>
 
   <command interpreter="perl">
-  ITSx -i $input --detailed_results T --cpu $cpu $preserve $reset 
+  ITSx -i $input --detailed_results T -N $domain_num --cpu ${NSLOTS} $preserve $reset
   </command>
   <requirements>
 	<requirement type="package" version="3.1b1">hmmer</requirement>
   </requirements>
   <inputs>
 	<param name="input" type="data" format="fasta" label="Input Fasta"/>
-	<param name="cpu" type="integer" value="1" label="cpu"/>
+	<param name="domain_num" type="integer" value="2" label="Minimum number of domains"
+    help="The minimum number of domains (different HMM gene profiles) that must match a sequence or it to be included in the output (detected as an ITS sequence). Setting the value lower than two will increase the number of false positives, while increasing it above two will decrease ITSx detection abilities on fragmentary data. "/>
+    <!--  <param name="cpu" type="integer" value="1" label="cpu"/> -->
 	<param name="complement" type="boolean" checked="true" truevalue="--complement T" falsevalue="--complement F" label="Check both DNA strands against the database"/>
 	<param name="heuristics" type="boolean" checked="false" truevalue="--heuristics T" falsevalue="--heuristics F" label="Use HMMER's heuristic filtering"/>
 	<param name="reset" type="boolean" checked="false" truevalue="--reset T" falsevalue="--reset F" label="Re-creates the HMM-database before ITSx is run"/>