--- a/snap.xml	Fri Aug 12 12:03:46 2016 -0400
+++ b/snap.xml	Fri Aug 12 15:01:58 2016 -0400
@@ -1,6 +1,6 @@
-<tool id="snap" name="Semi-HMM-based Nucleic Acid Parser (SNAP)" version="0.1.0">
+<tool id="snap" name="Semi-HMM-based Nucleic Acid Parser (SNAP)" version="1.0">
     <requirements>
-	<requirement type="package" version="0.1.0">snap</requirement>
+        <requirement type="package" version="1.0">snap</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -19,9 +19,12 @@
         #if $transcripts == "-tx":
         $transcripts "$output3"
         #end if
-        $format
+        -gff
         $organism
-        "$input1" > "$output1"
+        from gff2Togff3 import Convertor
+        f = Convertor("$output1", "$output4")
+        f.convert()
+        "$input1" > "$output4"
     ]]></command>
     <inputs>
         <param type="data" name="input1" format="dna.gz" />
@@ -54,10 +57,6 @@
             <option value="O.sativa.hmm">O.sativa</option>
             <option value="Os.hmm">Os</option>
         </param>
-        <param name="format" label="output format setting" type="select" multiple="false" format="text" help="Choose a output format.">
-            <option value="-gff">GFF</option>
-            <option value="-ace">ACE</option>
-        </param>
         <param name="proteins" type="select" label="Create FASTA file of proteins">
             <option value="-aa">Yes</option>
             <option value="">No</option>
@@ -91,13 +90,10 @@
     </inputs>
     <outputs>
         <data name="output1" format="gff" label="${tool.name} on ${on_string}: GTF/GFF">
-            <change_format>
-                <when input="format" value="-ace" format="acedb" />
-            </change_format>
         </data>
         <data name="output2" format="fasta" label="${tool.name} on ${on_string}: Protein sequence">
             <filter>proteins == "-aa"</filter>
-        </data>/Users/yating/Desktop/gonramp/snap-wrapper/thale.gff
+        </data>
         <data name="output3" format="fasta" label="${tool.name} on ${on_string}: Coding sequence">
             <filter>transcripts == "-tx"</filter>
         </data>