--- a/dunovo.xml	Fri Feb 24 03:18:01 2017 -0500
+++ b/dunovo.xml	Thu Aug 24 02:13:33 2017 -0400
@@ -1,14 +1,21 @@
 <?xml version="1.0"?>
-<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.7">
+<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.7.6">
   <description>from duplex sequencing alignments</description>
   <requirements>
-    <requirement type="package" version="0.7.1">dunovo</requirement>
+    <requirement type="package" version="0.7.6">dunovo</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
-  <command detect_errors="exit_code">dunovo.sh -r $min_reads -q $qual_thres -F $qual_format '$input' '$dcs1' '$dcs2'
+  <command detect_errors="exit_code"><![CDATA[
+    dunovo.py --galaxy $phone -r $min_reads -q $qual_thres -F $qual_format '$input'
     #if $keep_sscs:
-      '$sscs1' '$sscs2'
+      --sscs-file sscs.fa
     #end if
+    > duplex.fa
+    && outconv.py duplex.fa -1 '$dcs1' -2 '$dcs2'
+    #if $keep_sscs:
+      && outconv.py sscs.fa -1 '$sscs1' -2 '$sscs2'
+    #end if
+  ]]>
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Aligned input reads" />
@@ -19,6 +26,7 @@
       <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
     </param>
     <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" />
+    <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send anonymous usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the time taken to process it, and the IP address of the machine running it. No parameters or filenames are sent."/>
   </inputs>
   <outputs>
     <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/>