<tool id="findTss" name="findTss">
	<description>Find the transcription start site of a list of transcripts.</description>
	<command interpreter="python">
		../Java/Python/findTss.py -i $formatType.inputFileName
		#if $formatType.FormatInputFileName == 'bed':
			-f bed
		#elif $formatType.FormatInputFileName == 'gff':
			-f gff
		#elif $formatType.FormatInputFileName == 'gff2':
			-f gff2
		#elif $formatType.FormatInputFileName == 'gff3':
			-f gff3
		#end if
			

		-o $outputFileGff 
		$colinear
		$normalize
		-d $distance
		$excel $excelOutput
		
	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName" type="select" label="Input File Format">
				<option value="bed">bed</option>
				<option value="gff">gff</option>
				<option value="gff2">gff2</option>
				<option value="gff3">gff3</option>
			</param>
			<when value="bed">
				<param name="inputFileName" format="bed" type="data" label="Input File"/>
			</when>
			<when value="gff">
				<param name="inputFileName" format="gff" type="data" label="Input File"/>
			</when>
			<when value="gff2">
				<param name="inputFileName" format="gff2" type="data" label="Input File"/>
			</when>
			<when value="gff3">
				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
			</when>
		</conditional>

		<param name="colinear" type="boolean" truevalue="-e" falsevalue="" checked="false" label="colinear option" help="This option clusterizes only the same strand reads"/>
		<param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize option for only GFF3 file format" help="This option normalize (Warning!! Only for GFF3 file!!!!!)"/>
		<param name="distance" type="text" value="10" label="distance option" help="Limit the maximum distance between two reads"/>
		<param name="excel" type="boolean" truevalue="-c" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/>
	</inputs>

	<outputs>
		<data name="outputFileGff" format="gff3" label="[findTss] Output File"/>
		<data name="excelOutput" format="csv" label="[findTss] CSV File">
			<filter>excel</filter>
		</data>	
	</outputs> 
	
</tool>