--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/mergeTranscriptLists.xml	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,153 @@
+<tool id="mergeTranscriptLists" name="merge transcript lists">
+	<description>Merge the elements of two lists of genomic coordinates.</description>
+	<requirements>
+		<requirement type="set_environment">PYTHONPATH</requirement>
+	</requirements>
+	<command interpreter="python">
+		../Java/Python/mergeTranscriptLists.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
+			
+		$all
+		$normalize
+				
+		#if $OptionDistance.dis == 'Yes':
+			-d $OptionDistance.disVal
+		#end if	
+		
+		#if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
+			-c 
+		#elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
+			-a
+		#end if	
+		
+		-o $outputFileGff 
+	</command>
+
+	<inputs>
+		<conditional name="formatType">
+			<param name="FormatInputFileName1" type="select" label="Input File Format 1">
+				<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 File Format 2">
+				<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>
+
+
+		<param name="all" type="boolean" truevalue="-k" falsevalue="" checked="false" label="print all the transcripts, not only those overlapping"/>
+		<param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize the number of reads per cluster by the number of mappings per read "/>
+		
+		<conditional name="OptionDistance">
+			<param name="dis" type="select" label="provide the number of reads" >
+					<option value="Yes">Yes</option>
+					<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="disVal" type="integer" value="0" label="max. distance between two transcripts" />
+			</when>
+			<when value="No">
+			</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>
+
+	</inputs>
+
+	<outputs>
+		<data name="outputFileGff" format="gff3" label="[merge transcript lists] output file"/>
+	</outputs> 
+	
+	<help>
+The script is similar to *compare overlapping*, except that when data of two different sets overlap, they are merged. You can use the same parameters as *compare overlapping* and use them to look for transcription on both strands, for example.
+
+Optionally, you can also add to the output all the elements from the first set which do not overlap with the second set.
+	</help>
+</tool>