<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': 
	 	-f sam
	  #elif $inputFormatType.FormatInputFileName == 'gtf': 
	 	-f gtf
          #end if
	  
	 -g $outputFormatType.outFormat
  	  #if $optionSequence.choose == 'Yes':
	  	-s $optionSequence.value
		#end if 
	
	  
	  -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="gff2">GFF2</option> 
			  <option value="bam">BAM</option> 
			  <option value="sam">SAM</option> 
			  <option value="gtf">GTF</option> 
		  </param>
		  <when value="gff3">  
			  <param name="inputFileName" format="gff3" type="data" label="Input File"/>
		  </when>
		  <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>
		  <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>
		</conditional>    
  
  
 	  <conditional name="outputFormatType">
		  <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> 
			  <option value="gtf">GTF</option> 
		  </param> 
  		  <when value="gff3">  
		  </when>
		  <when value="bed">  
		  </when>
  		  <when value="gff2">  
		  </when>
		  <when value="wig">  
		  </when>
  		  <when value="sam">  
		  </when>
		  <when value="csv">  
		  </when>
		  <when value="gtf">  
		  </when>
 		</conditional>  
 		
 		<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>

  <outputs>
  		<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="wig" format="wig" />
			<when input="outputFormatType.outFormat" value="sam" format="sam" />
			<when input="outputFormatType.outFormat" value="csv" format="csv" />
			<when input="outputFormatType.outFormat" value="gtf" format="gtf" />
			</change_format> 
		</data>
  </outputs>

  <help>
  </help>
</tool>