--- a/SMART/galaxy/CompareOverlappingSmallRef.xml	Mon Feb 10 03:39:09 2014 -0500
+++ b/SMART/galaxy/CompareOverlappingSmallRef.xml	Fri Feb 21 08:32:36 2014 -0500
@@ -1,63 +1,24 @@
 <tool id="CompareOverlappingSmallRef" name="compare overlapping small reference">
-	<description>Provide the queries that overlap with a reference, when the reference dataset is small.</description>  
+	<description>Provide the queries that overlap with a reference, when the query data set is small.</description>  
 	<requirements>
 		<requirement type="set_environment">PYTHONPATH</requirement>
 	</requirements>
 	<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 == 'bam':
-			-f bam
-		#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 == 'bam':
-			-g bam
-		#elif $formatType2.FormatInputFileName2 == 'gtf':
-		    -g gtf
-		#end if
-		-o $outputFileGff 
+		../Java/Python/CompareOverlappingSmallRef.py -i $formatType.inputFileName1 -f $formatType.FormatInputFileName1 -j $formatType2.inputFileName2 -g $formatType2.FormatInputFileName2 -o $outputFileGff $InvertMatch $NotOverlapping $OptionInclusionQuery $OptionInclusionRef -m $OptionMinOverlap
 		#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':
+		#if $OptionCA == 'Collinear':
 			-c 
-		#elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens':
+		#elif $OptionCA == 'AntiSense':
 			-a
 		#end if	
-		$InvertMatch
-		$NotOverlapping
-		$OptionInclusionQuery
-		$OptionInclusionRef
 	</command>
 
 	<inputs>
@@ -91,7 +52,7 @@
 			</when>
 			<when value="gtf">
 				<param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
-								                        </when>
+			</when>
 		</conditional>
 
 		<conditional name="formatType2">
@@ -137,24 +98,14 @@
 			<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>
+		<param name="OptionMinOverlap" type="integer" value="1" label="Min. # of overlapping nt. to declare an overlap."/>
 		<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"/>
+				<param name="minOverlap" type="integer" value="100"/>
 			</when>
 			<when value="No">
 			</when>
@@ -165,26 +116,18 @@
 				<option value="No" selected="true">No</option>
 			</param>
 			<when value="Yes">
-				<param name="minOverlap" type="integer" value="0"/>
+				<param name="minOverlap" type="integer" value="100"/>
 			</when>
 			<when value="No">
 			</when>
 		</conditional>
-		<param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must be nested in a query"/>
+		<param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must be nested in a reference"/>
 		<param name="OptionInclusionRef" type="boolean" truevalue="-K" falsevalue="" checked="false" label="The reference must be 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="OptionCA" type="select" label="Collinear or anti-sense only">
+			<option value="Collinear">Collinear</option>
+			<option value="AntiSense">AntiSense</option>
+			<option value="All" selected="true">All</option>
+		</param>
 		<param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match: the output file will contain all query elements which do NOT overlap"/>
 		<param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Also report the query data which do not overlap, with the nbOverlaps tag set to 0."/>
 	</inputs>