<tool id="macs" name="MACS">
	<description>Model-based Analysis of ChiP-Seq</description>
	
	<command interpreter="python">
	macs_wrapper.py -t $mappedReadsIP -c $mappedReadsControl --name $experimentName --format $inputFormat['formatSelect'] --gsize $genomeSize --tsize $tagLength --bw $bandWidth --pvalue $pValueCutoff --mfold $hcEnrichmentRatio --shiftsize $shiftSize --peaks-xls $peaksXLS --peaks-bed $peaksBED --neg-peaks-xls $negPeaksXLS --neg-peaks-bed $negPeaksBED --R-model $rModel 
	</command>
	
	<inputs>
		<conditional name="inputFormat">
			<param name="formatSelect">
				<option value="BED">BED</option>
				<option value="ELAND" selected="true">ELAND</option>
			</param>
			<when value="BED">
				<param type="data" format="BED" name="mappedReadsIP" label="Mapped reads file from IP"/>
				<param type="data" format="BED" name="mappedReadsControllabel="Mapped reads file from control"/>			
			</when>
			<when value="ELAND">
				<param type="data" format="ELAND" name="mappedReadsIP" label="Mapped reads file from IP"/>
				<param type="data" format="ELAND" name="mappedReadsControl" label="Mapped reads file from control"/>			
			</when>		
		</conditional>
		
		<param type="text" name="experimentName" label="Experiment name" />
	
		<param name="genomeSize" type="integer" label="Genome size"/>
		<param name="tagLength" type="integer" value="25" label="Tag length" />
		<param name="bandWidth" type="integer" value="300" label="Band width" />
		<param name="pValueCutoff" type="float" value=".00001" label="Pvalue cutoff" />
		<param name="hcEnrichmentRatio" type="integer" value="32" label="High-confidence enrichment ratio" />
		<param name="shiftSize" type="integer" value="100" label="Shift size in bp" /> 
	</inputs>
	
	<outputs>
		<data format="xls" name="peaksXLS" label="Called peaks (xls)"/>
		<data format="bed" name="peaksBED" label="Called peaks (bed)"/>
		<data format="xls" name="negPeaksXLS" label="Negative peaks (xls)"/>
		<data format="bed" name="negPeaksBED" label="Negative peaks (bed)"/>
		<data format="text" name="rModel" label="R script for generating model pdf"/>
	</outputs>
</tool>