--- a/SMART/galaxy/ConvertTranscriptFile.xml	Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/galaxy/ConvertTranscriptFile.xml	Wed Feb 05 11:51:11 2014 -0500
@@ -3,33 +3,14 @@
 	<requirements>
 		<requirement type="set_environment">PYTHONPATH</requirement>
 	</requirements>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName 
-	  #if $inputFormatType.FormatInputFileName == 'gff3':
-	  	-f gff3
-	  #elif $inputFormatType.FormatInputFileName == 'bed': 
-	 	-f bed 
-	  #elif $inputFormatType.FormatInputFileName == 'bam': 
-	 	-f blast
-	  #elif $inputFormatType.FormatInputFileName == 'sam': 
-	 	-f sam
-	  #elif $inputFormatType.FormatInputFileName == 'gtf': 
-	 	-f gtf
-          #end if
-	  
-	 -g $outputFormatType.outFormat
-	  
-	  -n $name
-	  $strand
-	  -o $outputFile
-	 
-  </command>
+  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName -f $inputFormatType.FormatInputFileName -g $outputFormatType.outFormat -n $name $strand -o $outputFile </command>
   <inputs>
 	  <conditional name="inputFormatType">
 		  <param name="FormatInputFileName"  type="select" label="Input File Format">
 			  <option value="gff3">GFF3</option> 
 			  <option value="bed">BED</option> 
+			  <option value="sam">SAM</option> 
 			  <option value="bam">BAM</option> 
-			  <option value="sam">SAM</option> 
 			  <option value="gtf">GTF</option> 
 		  </param>
 		  <when value="gff3">  
@@ -38,12 +19,12 @@
 		  <when value="bed">  
 			  <param name="inputFileName" format="bed" type="data" label="Input File"/>
 		  </when>
+		  <when value="sam">  
+			  <param name="inputFileName" format="sam" type="data" label="Input File"/>
+		  </when>
 		  <when value="bam">  
 			  <param name="inputFileName" format="bam" type="data" label="Input File"/>
 		  </when>
-		  <when value="sam">  
-			  <param name="inputFileName" format="sam" type="data" label="Input File"/>
-		  </when>
 		  <when value="gtf">  
 			  <param name="inputFileName" format="gtf" type="data" label="Input File"/>
 		  </when>