--- a/SMART/galaxy/ConvertTranscriptFile.xml	Fri Apr 19 10:13:11 2013 -0400
+++ b/SMART/galaxy/ConvertTranscriptFile.xml	Mon Apr 22 11:08:07 2013 -0400
@@ -1,12 +1,10 @@
-<tool id="ConvertTranscriptFile" name="Convert transcript file">
+<tool id="ConvertTranscriptFile" name="convert transcript file">
   <description>Convert a file from a format to another.</description>
   <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 == 'gff2': 
-	 	-f gff2
 	  #elif $inputFormatType.FormatInputFileName == 'bam': 
 	 	-f blast
 	  #elif $inputFormatType.FormatInputFileName == 'sam': 
@@ -16,10 +14,6 @@
           #end if
 	  
 	 -g $outputFormatType.outFormat
-  	  #if $optionSequence.choose == 'Yes':
-	  	-s $optionSequence.value
-		#end if 
-	
 	  
 	  -n $name
 	  $strand
@@ -31,7 +25,6 @@
 		  <param name="FormatInputFileName"  type="select" label="Input File Format">
 			  <option value="gff3">GFF3</option> 
 			  <option value="bed">BED</option> 
-			  <option value="gff2">GFF2</option> 
 			  <option value="bam">BAM</option> 
 			  <option value="sam">SAM</option> 
 			  <option value="gtf">GTF</option> 
@@ -42,9 +35,6 @@
 		  <when value="bed">  
 			  <param name="inputFileName" format="bed" type="data" label="Input File"/>
 		  </when>
-		  <when value="gff2">  
-			  <param name="inputFileName" format="gff2" type="data" label="Input File"/>
-		  </when>
 		  <when value="bam">  
 			  <param name="inputFileName" format="bam" type="data" label="Input File"/>
 		  </when>
@@ -61,7 +51,6 @@
 		  <param name="outFormat"  type="select" label="Please choose the format that you want to convert to (corresponding to your input file format).">
 			  <option value="gff3">GFF3</option> 
 			  <option value="bed">BED</option> 
-			  <option value="gff2">GFF2</option> 
 			  <option value="wig">WIG</option> 
 			  <option value="sam">SAM</option> 
 			  <option value="csv">CSV</option> 
@@ -71,8 +60,6 @@
 		  </when>
 		  <when value="bed">  
 		  </when>
-  		  <when value="gff2">  
-		  </when>
 		  <when value="wig">  
 		  </when>
   		  <when value="sam">  
@@ -85,18 +72,6 @@
  		
  		<param name="name" type="text" value="SMART" label="name for the transcripts"/>
  		
- 		<conditional name="optionSequence">
- 		<param name="choose" type="select" label="give the corresponding Multi-Fasta file (useful for EMBL format)">
-			<option value="Yes">Yes</option>
-			<option value="No" selected="true">No</option>
-		</param>
-		<when value="Yes">
-			 <param name="value" type="data" format="mfa" />
-		</when>
-		<when value="No">
-		</when>
-		</conditional>
- 		 
  		<param name="strand" type="boolean" truevalue="-t" falsevalue="" checked="false" label="consider the 2 strands as different (only useful for writing WIG files)"/>
  		 
   </inputs>
@@ -105,7 +80,7 @@
   		<data name="outputFile" format="gff3" label="$inputFormatType.FormatInputFileName to $outputFormatType.outFormat">
 			<change_format>
 			<when input="outputFormatType.outFormat" value="bed" format="bed" />
-			<when input="outputFormatType.outFormat" value="gff2" format="gff2" />
+			<when input="outputFormatType.outFormat" value="gff" format="gff" />
 			<when input="outputFormatType.outFormat" value="wig" format="wig" />
 			<when input="outputFormatType.outFormat" value="sam" format="sam" />
 			<when input="outputFormatType.outFormat" value="csv" format="csv" />
@@ -115,5 +90,6 @@
   </outputs>
 
   <help>
+Simple conversion tool.
   </help>
 </tool>