--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/GetFlanking.xml	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,179 @@
+<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>