diff SMART/galaxy/getWigProfile.xml @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/getWigProfile.xml	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,70 @@
+<tool id="getWigProfile" name="get wig profile">
+	<description>Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description>
+	<command interpreter="python">
+		../Java/Python/getWigProfile.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
+		#end if
+		-w $inputWigFile
+		-p $nbPoints
+		-d $distance
+		$strands
+		-o $outputFilePNG
+		#if $optionSMO.SMO == 'Yes':
+			-m $optionSMO.smoothen
+		#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>
+			</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>
+		</conditional>
+		
+		<param name="inputWigFile" type="data" label="Input Wig File" format="wig"/>
+		<param name="nbPoints" type="integer" value="1000" label="number of points on the x-axis"/>
+		<param name="distance" type="integer" value="0" label="distance around genomic coordinates"/>
+		<param name="strands" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately"/>
+		
+		<conditional name="optionSMO">
+			<param name="SMO" type="select" label="smoothen the curve">
+					<option value="Yes">Yes</option>
+					<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="smoothen" type="integer" value="0"/>
+			</when>
+			<when value="No">
+			</when>
+		</conditional>
+		
+	</inputs>
+
+	<outputs>
+		<data name="outputFilePNG" format="png" label="[getWigProfile]out file"/>
+	</outputs> 
+	
+</tool>