<tool id="GetFlanking" name="get flanking">
	<description>Get the flanking regions of a set of reference.</description>
	<command interpreter="python">
		../Java/Python/GetFlanking.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

  		#if $OptionUpDownStream.OptionUD == 'UpStream':
			-5 
		#elif $OptionUpDownStream.OptionUD == 'DownStream':
			-3
		#end if	


  		#if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
			-c 
		#elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
			-a
		#end if	
		
		#if $OptionMax.maximum == "Yes":
			-D $OptionMax.max
		#end if		
		#if $OptionMin.minimum == "Yes":
			-d $OptionMin.min
		#end if	
  		
  		-o $outputFile  

		
		
	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName1" type="select" label="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="Refence 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="OptionUpDownStream">
			<param name="OptionUD" type="select" label="UpStream or DownStream">
				<option value="UpStream">UpStream</option>
				<option value="DownStream">DownStream</option>
				<option value="NONE" selected="true">NONE</option>
			</param>
			<when value="UpStream">
			</when>
			<when value="DownStream">
			</when>
			<when value="NONE">
			</when>
		</conditional>
				
		<conditional name="OptionColinearOrAntiSens">
			<param name="OptionCA" type="select" label="Colinear or anti-sens">
				<option value="Colinear">Colinear</option>
				<option value="AntiSens">AntiSens</option>
				<option value="NONE" selected="true">NONE</option>
			</param>
			<when value="Colinear">
			</when>
			<when value="AntiSens">
			</when>
			<when value="NONE">
			</when>
		</conditional>
		
		<conditional name="OptionMax">
			<param name="maximum" type="select" label="maximum distance between 2 elements">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="max" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		
		<conditional name="OptionMin">
			<param name="minimum" type="select" label="minimum distance between 2 elements">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="min" type="integer" value="0" />
			</when>
			<when value="No">
			</when>
		</conditional>	
		
	</inputs>


  	<outputs>
   		<data format="gff3" name="outputFile" label="[GetFlanking] Output File"/>
  	</outputs>
	
	
</tool>