--- a/mykrobe_genotype.xml	Sat Jan 13 09:02:58 2018 -0500
+++ b/mykrobe_genotype.xml	Tue Apr 02 11:57:05 2019 -0400
@@ -1,5 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
-<tool id="mykrobe_genotype" name="mkyrobe genotype" version="0.5.6" >
+<tool id="mykrobe_genotype" name="mkyrobe genotype" version="0.6.1" >
   <description>Antibiotic resistance predictions</description>
   <macros>
     <import>macro.xml</import>
@@ -10,17 +9,14 @@
         @select_inputs@
 
         mykrobe genotype 
-        '$name'
-        '$probe_set'
+        '${name}'
+        '${probe_set}'
 
-        #if $kmer:
-          --kmer $kmer
+        #if $filter:
+          --filters '${filter}'
         #end if
 
-        #if $expected_depth:
-          --expected_depth $expected_depth
-        #end if
-
+        @shared_options@
 
         -q
         -t "\${GALAXY_SLOTS:-1}"
@@ -33,14 +29,14 @@
         #else
           *.fasta  
         #end if
-         > $json
+         > '$json'
 ]]>
   </command>
   <inputs>
     <expand macro="inputs" />
-    <param name="probe_set" type="data" format="fasta" label="Probe Set"/>
-    <param name="kmer" argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
-    <param name="expected_depth" argument="--expected_depth" optional="True" type="integer" min="0" label="Expected Depth"  help=""/>
+    <param argument="--probe_set" type="data" format="fasta" label="Probe Set"/>
+    <param argument="--filter" type="data" format="txt,fasta" label="Filter Genotypes" optional="True" help="Don't include filtered genotypes"/>
+    <expand macro="options"/>
   </inputs>
   <outputs>
     <data name="json" format="json" label="JSON prediction"/>