# HG changeset patch
# User okorol
# Date 1433517049 14400
# Node ID c711ca9a7f4c940ee84893e72b0cf52220f0baa7
# Parent  2986d8c4db111fa2d8a4053824984b985f2de154
Uploaded

diff -r 2986d8c4db11 -r c711ca9a7f4c ITSx.xml
--- 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"/>