--- a/snap.xml	Fri Aug 12 15:01:58 2016 -0400
+++ b/snap.xml	Fri Aug 12 18:26:59 2016 -0400
@@ -20,11 +20,10 @@
         $transcripts "$output3"
         #end if
         -gff
+        -quiet
         $organism
-        from gff2Togff3 import Convertor
-        f = Convertor("$output1", "$output4")
-        f.convert()
-        "$input1" > "$output4"
+        $input1
+        | python $__tool_directory__/gff2Togff3.py --output $output1
     ]]></command>
     <inputs>
         <param type="data" name="input1" format="dna.gz" />
@@ -89,7 +88,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output1" format="gff" label="${tool.name} on ${on_string}: GTF/GFF">
+        <data name="output1" format="gff3" label="${tool.name} on ${on_string}: GTF/GFF3">
         </data>
         <data name="output2" format="fasta" label="${tool.name} on ${on_string}: Protein sequence">
             <filter>proteins == "-aa"</filter>
@@ -102,8 +101,7 @@
         <test>
             <param name="input1" value="thale.dna.gz"/>
             <param name="organism" value="At.hmm" />
-            <param name="format" value="-gff" />
-            <output name="output1" file="thale.gff"/>
+            <output name="output1" file="thale.gff3"/>
         </test>
     </tests>
     <help><![CDATA[