--- a/pilon.xml	Sat Aug 13 04:48:25 2016 -0400
+++ b/pilon.xml	Tue Apr 04 11:18:22 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="pilon" name="pilon" version="0.1">
+<tool id="pilon" name="pilon" version="1.20.1">
     <description>An automated genome assembly improvement and variant detection tool</description>
     <requirements>
-      <requirement type="package" version="1.18">pilon</requirement>
+      <requirement type="package" version="1.20">pilon</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       #if $auto_selection.auto_enabled == "yes"
@@ -70,8 +70,8 @@
           $options.duplicates
           $options.iupac
           $options.nonpf
-          #if len($options.targetlist.strip()) > 0
-            --targetlist $options.targetlist
+          #if len($options.targets.strip()) > 0
+            --targets $options.targets
           #end if
           --fix $options.fixes
           $options.verbose
@@ -95,7 +95,7 @@
           <option value="builtin">Use a built-in genome"</option>
         </param>
         <when value="history">
-          <param format="fasta" type="data" metadata_name="dbkey" name="history_item" />
+          <param format="fasta" type="data" name="history_item" label="Select a reference genome"/>
         </when>
         <when value="builtin">
           <param label="Select a reference genome" name="builtin" type="select">
@@ -168,6 +168,7 @@
             <option value="amb">Fix ambigious bases in FASTA output (experimental)</option>
             <option value="breaks">Allow local reassembly to open new gaps (experimental, requires local assembly fixing to be selected)</option>
             <option value="novel">Assemble novel sequence from unaligned non-jump reads (experimental)</option>
+            <!-- TODO: enable this when documented in pilon <option value="circle">Trim long reads for circular continuity(experimental, requires unpaired reads)</option>-->
           </param>
           <param argument="diploid" label="Organism is diploid" type="boolean" checked="false"
             help="Sample is from diploid organism; will eventually affect calling of heterozygous SNPs"
@@ -181,9 +182,9 @@
           <param argument="nonpf" label="Use low quality reads" type="boolean" checked="false"
             help="Use reads which failed sequencer quality filtering"
             truevalue="--nonpf" falsevalue="" />
-          <param argument="targetlist" label="List of targets to process (leave blank for all)" default="" type="text" length="40"
+          <param argument="targets" label="List of targets to process (leave blank for all)" type="text"
             help="Only process the specified target(s).  Targets are comma-separated, and each target is a fasta element name optionally followed by a base range." />
-          <param argument="verbose" label="Verbose output (in tool log)" type="boolean" check="false"
+          <param argument="verbose" label="Verbose output (in tool log)" type="boolean" checked="false"
             truevalue="--verbose" falsevalue="" />
           <param argument="defaultqual" label="Default base quality" type="integer" min="1" value="15"
             help="Assumes bases are of this quality if quals are no present in input BAMs" />