<tool id="GetFlanking" name="get flanking">
	<description>Get the flanking regions of a set of reference.</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
	<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="Only provide upstream/dowstream features">
				<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="Only provide collinear/antisens features">
				<option value="Colinear">Collinear</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="[get flanking] output file"/>
  	</outputs>
	
	<help>
This tool prints the elements from the second set of genomic intervals which are closest to (in other words, are flanking) the elements from the first set. You can also play on different parameters:

- restrict the search to downstream or upstream elements, or print downstream and upstream elements,

- only consider collinear flanking elements,

- only consider anti-sense flanking elements,

- only consider elements which are close enough (using some given distance),

- only consider flanking elements which do not overlap with the reference element.

Notice that elements from the second sets may be printed at most once, whether they are the flanking element of several elements from the first or not.
	</help>
	
</tool>