--- a/macro.xml	Sat Jan 13 09:02:58 2018 -0500
+++ b/macro.xml	Tue Apr 02 11:57:05 2019 -0400
@@ -2,10 +2,9 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.5.6">mykrobe</requirement>
+      <requirement type="package" version="0.6.1">mykrobe</requirement>
     </requirements>    
   </xml>
-
   <token name="@select_inputs@">
     <![CDATA[
          #set $name='sample'
@@ -39,6 +38,57 @@
     ]]>
   </token>
 
+  <token name="@shared_options@">
+    <![CDATA[
+        #if $kmer:
+          --kmer '${kmer}'
+        #end if
+        #if $expected_depth:
+          --expected_depth '${expected_depth}'
+        #end if
+
+        $ont
+
+        $report_all_calls
+
+        #if $expected_error_rate:
+          --expected_error_rate '${expected_error_rate}'
+        #end if
+
+        #if $min_variant_conf:
+          --min_variant_conf '${min_variant_conf}'
+        #end if
+
+        #if $min_gene_conf:
+          --min_gene_conf '${min_gene_conf}'
+        #end if
+
+        #if $min_proportion_expected_depth:
+          --min_proportion_expected_depth '${min_proportion_expected_depth}'
+        #end if
+
+        #if $min_gene_percent_covg_threshold:
+          --min_gene_percent_covg_threshold  '${min_gene_percent_covg_threshold}'
+        #end if
+
+        $guess_sequence_method
+
+        $ignore_minor_calls
+
+        #if $ignore_filtered:
+          --ignore_filtered '${ignore_filtered}'
+        #end if
+
+        #if $model:
+          --model '${model}'
+        #end if
+
+        #if $ploidy:
+          --ploidy '${ploidy}'
+        #end if
+    ]]>
+  </token>
+
   <xml name="inputs">
     <conditional name="data_type">
       <param name="type" type="select" label="Specify the read type.">
@@ -59,6 +109,26 @@
     </conditional>
   </xml>
 
+  <xml name="options">
+    <param argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
+    <param argument="--expected_error_rate" optional="True" type="float" label="Expected error rate"  help="Expected sequencing error rate. Set to 0.15 for ONT genotyping"/>
+    <param argument="--expected_depth" optional="True" type="integer" min="0" label="Expected depth"  help=""/>
+    <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data"  help=""/>
+    <param argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping"  help=""/>      
+    <param argument="--min_gene_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for gene genotyping"  help=""/>
+    <param argument="--min_gene_percent_covg_threshold" optional="True" type="integer" min="0" label="Minimum gene predict coverage"  help="all genes alleles found above this percent coverage will be reported (default 100 (only best alleles reported))"/>      
+    <param argument="--min_proportion_expected_depth" optional="True" type="float" label="Minimum depth required on the sum of both alleles" help="Default 0.3 (30%)"/>
+    <param argument="--model" optional="True" type="data" format="txt" label="Genotype model used" help="default kmer_count. Options kmer_count, median_depth"/>
+    <param argument="--ploidy" optional="True" type="select" label="Diploid or Haploid" help="Use a diploid (includes 0/1 calls) or haploid genotyping model">
+      <option value="diploid">diploid</option>
+      <option value="haploid">haploid</option>
+    </param>
+    <param argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="Report all calls"  help=""/>
+    <param argument="--ignore_minor_calls" type="boolean" truevalue="--ignore_minor_calls" falsevalue="" label="Ignore minor calls"  help="Ignore minor calls when running resistance prediction"/>
+    <param argument="--ignore_filtered" type="data" format="txt" label="Ignore filtered" optional="True" help="Don't include filtered genotypes"/>
+    <param argument="--guess_sequence_method" type="boolean" truevalue="--guess_sequence_method" falsevalue="" label="Guess sequence method"  help="Guess if ONT or Illumia based on error rate. If error rate is > 10%, ploidy is set to haploid and a confidence threshold is used"/>
+  </xml>
+
   <token name="@ATTRIBUTION@">
     <![CDATA[
              

--- 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"/>