--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/getNb.xml	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,78 @@
+<tool id="getNumber" name="get number">
+	<description>Get the distribution of exons per transcripts, or mapping per read, or transcript per cluster.</description>
+	<command interpreter="python">
+		../Java/Python/getNb.py -i $formatType.inputFileName
+		#if $formatType.FormatInputFileName == 'bed':
+			-f bed
+		#elif $formatType.FormatInputFileName == 'gff':
+			-f gff	
+		#elif $formatType.FormatInputFileName == 'gff2':
+			-f gff2
+		#elif $formatType.FormatInputFileName == 'gff3':
+			-f gff3
+		#elif $formatType.FormatInputFileName == 'sam':
+			-f sam
+		#elif $formatType.FormatInputFileName == 'gtf':
+			-f gtf
+		#end if
+		-o $outputFilePNG
+		-q $query
+		$barPlot
+		#if $optionXMAX.XMAX == 'Yes':
+			-x $optionXMAX.xMaxValue
+		#end if		
+
+	</command>
+
+	<inputs>
+		<conditional name="formatType">
+			<param name="FormatInputFileName" type="select" label="Input 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="inputFileName" format="bed" type="data" label="Input File"/>
+			</when>
+			<when value="gff">
+				<param name="inputFileName" format="gff" type="data" label="Input File"/>
+			</when>
+			<when value="gff2">
+				<param name="inputFileName" format="gff2" type="data" label="Input File"/>
+			</when>
+			<when value="gff3">
+				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
+			</when>
+			<when value="sam">
+				<param name="inputFileName" format="sam" type="data" label="Input File"/>
+			</when>
+			<when value="gtf">
+				<param name="inputFileName" format="gtf" type="data" label="Input File"/>
+			</when>
+		</conditional>
+		
+		<param name="query" type="text" value="None" label="compulsory option, choice (exon, transcript, cluster)" />
+		<param name="barPlot" type="boolean" truevalue="-b" falsevalue="" checked="false" label="use barplot representation"/>
+		
+		<conditional name="optionXMAX">
+			<param name="XMAX" type="select" label="maximum value on the x-axis to plot ">
+					<option value="Yes">Yes</option>
+					<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="xMaxValue" type="integer" value="0" />
+			</when>
+			<when value="No">
+			</when>
+		</conditional>
+		
+	</inputs>
+
+	<outputs>
+		<data name="outputFilePNG" format="png" label="[getNB]out file"/>
+	</outputs> 
+	
+</tool>