<tool id="CompareOverlappingSmallRef" name="Compare Overlapping Small Reference">
	<description>Provide the queries that overlap with a reference, when the reference is small.</description>  
	<command interpreter="python">
		../Java/Python/CompareOverlappingSmallQuery.py -i $formatType.inputFileName1 
		#if $formatType.FormatInputFileName1 == 'bed':  
		-f bed
		#elif $formatType.FormatInputFileName1 == 'gff':
			-f gff	
		#elif $formatType.FormatInputFileName1 == 'gff2':
			-f gff2
		#elif $formatType.FormatInputFileName1 == 'gff3':
			-f gff3
		#elif $formatType.FormatInputFileName1 == 'sam':
			-f sam
		#elif $formatType.FormatInputFileName1 == 'gtf':
			-f gtf
		#end if
		-j $formatType2.inputFileName2
		#if $formatType2.FormatInputFileName2 == 'bed':
			-g bed
		#elif $formatType2.FormatInputFileName2 == 'gff':
			-g gff	
		#elif $formatType2.FormatInputFileName2 == 'gff2':
			-g gff2
		#elif $formatType2.FormatInputFileName2 == 'gff3':
			-g gff3
		#elif $formatType2.FormatInputFileName2 == 'sam':
			-g sam
		#elif $formatType2.FormatInputFileName2 == 'gtf':
		    -g gtf
		#end if
		-o $outputFileGff 
		#if $OptionDistance.Dist == 'Yes':
			-d $OptionDistance.distance
		#end if
		#if $OptionMinOverlap.present == 'Yes':
			-m $OptionMinOverlap.minOverlap
		#end if
		#if $OptionPcOverlapQuery.present == 'Yes':
			-p $OptionPcOverlapQuery.minOverlap
		#end if
		#if $OptionPcOverlapRef.present == 'Yes':
			-P $OptionPcOverlapRef.minOverlap
		#end if
		#if $OptionCollinearOrAntiSens.OptionCA == 'Collinear':
			-c 
		#elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens':
			-a
		#end if	
		$InvertMatch
		$NotOverlapping
		$OptionInclusionQuery
		$OptionInclusionRef
	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName1" type="select" label="Input Query 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="inputFileName1" format="bed" type="data" label="Input File 1"/>
			</when>
			<when value="gff">
				<param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
			</when>
			<when value="gff2">
				<param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
			</when>
			<when value="gff3">
				<param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
			</when>
			<when value="sam">
				<param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
			</when>
			<when value="gtf">
				<param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
								                        </when>
		</conditional>

		<conditional name="formatType2">
			<param name="FormatInputFileName2" type="select" label="Input Reference 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="inputFileName2" format="bed" type="data" label="Input File 2"/>
			</when>
			<when value="gff">
				<param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
			</when>
			<when value="gff2">
				<param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
			</when>
			<when value="gff3">
				<param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
			</when>
			<when value="sam">
				<param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
			</when>
			<when value="gtf">
				<param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
			</when>
		</conditional>
		<conditional name="OptionDistance">
			<param name="Dist" type="select" label="Maximum Distance between two reads">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="distance" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		<conditional name="OptionMinOverlap">
			<param name="present" type="select" label="Minimum number of common nucleotides to declare an overlap">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="minOverlap" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		<conditional name="OptionPcOverlapQuery">
			<param name="present" type="select" label="N% of the query must overlap">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="minOverlap" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		<conditional name="OptionPcOverlapRef">
			<param name="present" type="select" label="N% of the reference must overlap">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="minOverlap" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		<param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must nested in a query"/>
		<param name="OptionInclusionRef" type="boolean" truevalue="-K" falsevalue="" checked="false" label="The reference must nested in a query"/>
		<conditional name="OptionCollinearOrAntiSens">
			<param name="OptionCA" type="select" label="Collinear or anti-sens">
				<option value="Collinear">Collinear</option>
				<option value="AntiSens">AntiSens</option>
				<option value="NONE" selected="true">NONE</option>
			</param>
			<when value="Collinear">
			</when>
			<when value="AntiSens">
			</when>
			<when value="NONE">
			</when>
		</conditional>
		<param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>
		<param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/>
	</inputs>

	<outputs>
		<data name="outputFileGff" format="gff3"/>
	</outputs> 
</tool>