<tool id="clusterizeBySlidingWindows" name="clusterize By SlidingWindows">
	<description>Produces a GFF3 file that clusters a list of transcripts using a sliding window. Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks.</description>
	<command interpreter="python">
		../Java/Python/clusterizeBySlidingWindows.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
		#elif $formatType.FormatInputFileName == 'sam':
			-f sam
		#elif $formatType.FormatInputFileName == 'gtf':
			-f gtf
		#end if
		-s $size
		-e $overlap
		-o $outputFileGff 
		$normalize
		$strands
		
		#if $OptionTag.tag == "Yes":
			-g $OptionTag.value
		#end if	

		#if $OptionsOperation.operation == "Yes":
			-r $OptionsOperation.value
		#end if
		
		#if $OptionWriteTag.writeTag == "Yes":
			-w $OptionWriteTag.value
		#end if	
		
		$strand
		$plot $plotPng
		$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>
				<option value="sam">sam</option>
				<option value="gtf">gtf</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>
			<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>


		<param name="size" type="text" value="50000" label="Size option" help="Size of the regions."/>
		<param name="overlap" type="text" value="50" label="Overlap option" help="Overlap between two consecutive regions."/>	
		<param name="normalize" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Normalize option for only GFF3 file format" help="This option normalizes (Warning!! Only for GFF3 file!)"/>
		<param name="strands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="strands option" help="Consider the two strands separately."/>

		<conditional name="OptionTag">
			<param name="tag" type="select" label="use a given tag as input (instead of summing number of features)">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="value" type="text" value="None" label="tag option" help="write a tag name you want to observe."/>
			</when>
			<when value="No">
			</when>
		</conditional>


		<conditional name="OptionsOperation">
			<param name="operation" type="select" label="combine tag value with given operation [choice (sum, avg, med, min, max)]">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="value" type="text" value="None" label="operation option" help="You can ONLY choose one of fowlling operation : sum, avg, med, min, max."/>
			</when>
			<when value="No">
			</when>
		</conditional>

		
		<conditional name="OptionWriteTag">
			<param name="writeTag" type="select" label="write a new tag in output file">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="value" type="text" value="nbElements" label="write tag option" help="print the result in the given tag (default usually is 'nbElements')"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<param name="strand" type="boolean" truevalue="-2" falsevalue="" checked="false" label="strand option" help="This option considers the two strands separately."/>
		<param name="plot" type="boolean" truevalue="-p" falsevalue="" checked="false" label="plot option" help="This option creates a png file."/>
		<param name="excel" type="boolean" truevalue="-x" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/>

	</inputs>

	<outputs>
		<data name="outputFileGff" format="gff3"/>
		<data name="excelOutput" format="csv">
			<filter>excel</filter>
		</data>	
		<data name="plotPng" format="png">
			<filter>plot</filter>
		</data>	
	</outputs> 
</tool>