<tool id="GetDifferentialExpression" name="get differential expression">
	<description>Get the differential expression between 2 conditions using Fisher's exact test, on regions defined by a third file.</description>
	<command interpreter="python">
		../Java/Python/GetDifferentialExpression.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
			
		-k $formatTypeRef.inputFileNameRef
		#if $formatTypeRef.FormatInputFileNameRef == 'bed':
			-l bed
		#elif $formatTypeRef.FormatInputFileNameRef == 'gff':
			-l gff	
		#elif $formatTypeRef.FormatInputFileNameRef == 'gff2':
			-l gff2
		#elif $formatTypeRef.FormatInputFileNameRef == 'gff3':
			-l gff3
		#elif $formatTypeRef.FormatInputFileNameRef == 'sam':
			-l sam
		#elif $formatTypeRef.FormatInputFileNameRef == 'gtf':
			-l gtf
		#end if
		
		-o $outputFileGff 
		
		$simple
		$adjusted


		#if $optionSimplePara.simplePara == 'Yes':
			-S $optionSimplePara.paraValue
		#end if		
		
		#if $optionFixedSizeFactor.FSF == 'Yes':
			-x $optionFixedSizeFactor.FSFValue
		#end if
		
		#if $optionFDR.FDR == 'Yes':
			-d $optionFDR.FDRValue
		#end if
		$plot $outputFilePNG
	</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>

		<conditional name="formatTypeRef">
			<param name="FormatInputFileNameRef" type="select" label="Input Ref 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="inputFileNameRef" format="bed" type="data" label="Input Ref File"/>
			</when>
			<when value="gff">
				<param name="inputFileNameRef" format="gff" type="data" label="Input Ref File"/>
			</when>
			<when value="gff2">
				<param name="inputFileNameRef" format="gff2" type="data" label="Input Ref File"/>
			</when>
			<when value="gff3">
				<param name="inputFileNameRef" format="gff3" type="data" label="Input Ref File"/>
			</when>
			<when value="sam">
				<param name="inputFileNameRef" format="sam" type="data" label="Input Ref File"/>
			</when>
			<when value="gtf">
				<param name="inputFileNameRef" format="gtf" type="data" label="Input Ref File"/>
			</when>
		</conditional>

		<param name="simple" type="boolean" truevalue="-s" falsevalue="" checked="false" label="normalize using the number of reads in each condition"/>
		<param name="adjusted" type="boolean" truevalue="-a" falsevalue="" checked="false" label="normalize using the number of reads of 'mean' regions"/>
		
		<conditional name="optionSimplePara">
			<param name="simplePara" 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="paraValue" type="text" value="None" label="provide the number of reads" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionFixedSizeFactor">
			<param name="FSF" type="select" label="give the magnification factor for the normalization using fixed size sliding windows in reference regions (leave empty for no such normalization)">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="FSFValue" type="integer" value="0" />
			</when>
			<when value="No">
			</when>
		</conditional>
		
		<conditional name="optionFDR">
			<param name="FDR" type="select" label="use FDR">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="FDRValue" type="float" value="0.0"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		
		<param name="plot" type="boolean" truevalue="-p" falsevalue="" checked="false" label="plot option" help="plot cloud plot"/>

	</inputs>

	<outputs>
		<data name="outputFileGff" format="gff3" label="[GetDifferentialExpression]out file"/>
		<data name="outputFilePNG" format="PNG" label="[GetDifferentialExpression]PNG file">
			<filter>plot</filter>
		</data>
	</outputs> 
	
	<help>
		example: python GetDifferentialExpression.py -i input1 -f gff3 -j input2 -g gff3 -k ref -l gff3 -o output.gff3
	</help>
</tool>