view smart_toolShed/SMART/galaxy/getWigProfile.xml @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

<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>