<tool id="getDistribution" name="get distribution">
	<description>Get Distribution: Get the distribution of the genomic coordinates on a genome.</description>
	<command interpreter="python">
		../Java/Python/GetDistribution.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 == 'csv':
			-f csv
		#elif $formatType.FormatInputFileName == 'sam':
			-f sam
		#elif $formatType.FormatInputFileName == 'gtf':
			-f gtf
		#end if
		
		-r $refFile
		
		#if $optionNbBin.Nb == 'Yes':
			-b $optionNbBin.nbBins
		#end if
		
		#if $optionStart.start == 'Yes':
			-s $optionStart.startValue
		#end if	
		
		#if $optionEnd.end == 'Yes':
			-e $optionEnd.endValue
		#end if	
		
		#if $optionHeight.height == 'Yes':
			-H $optionHeight.heightValue
		#end if	
		
		#if $optionWidth.width == 'Yes':
			-W $optionWidth.widthValue
		#end if	
		
		#if $optionYMin.YMin == 'Yes':
			-y $optionYMin.YMinValue
		#end if
		
		#if $optionYMax.YMax == 'Yes':
			-Y $optionYMax.YMaxValue
		#end if
		
		#if $optionChrom.chrom == 'Yes':
			-c $optionChrom.chromValue
		#end if
	
		#if $optionColor.color == 'Yes':
			-l $optionColor.colorValue
		#end if

		$bothStrands
		$average
		$normalize
		$csv $outputCSV
		$gff $outputGFF
		-m
		-o $outputFile

	</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="csv">csv</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="csv">
				<param name="inputFileName" format="csv" 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="refFile" format="fasta" type="data" label="reference genome file"/>
		
		<conditional name="optionNbBin">
			<param name="Nb" type="select" label="number of bins">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="nbBins" type="integer" value="1000" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionStart">
			<param name="start" type="select" label="start from a given region">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="startValue" type="integer" value="0" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionEnd">
			<param name="end" type="select" label="end from a given region">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="endValue" type="integer" value="0" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionHeight">
			<param name="height" type="select" label="height of the graphics">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="heightValue" type="integer" value="300" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionWidth">
			<param name="width" type="select" label="width of the graphics">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="widthValue" type="integer" value="1000" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionYMin">
			<param name="YMin" type="select" label="minimum value on the y-axis to plot">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="YMinValue" type="integer" value="1000" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionYMax">
			<param name="YMax" type="select" label="maximum value on the y-axis to plot">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="YMaxValue" type="integer" value="1000" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionChrom">
			<param name="chrom" type="select" label="plot only one given chromosome">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="chromValue" type="text" value="chromName" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionColor">
			<param name="color" type="select" label="color of the lines (separated by commas and no space)">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="colorValue" type="text" value="red,blue" />
			</when>
			<when value="No">
			</when>
		</conditional>


		<param name="bothStrands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="plot one curve per strand"/>
		<param name="average" type="boolean" truevalue="-a" falsevalue="" checked="false" label="plot plot average (instead of sum)"/>

		<conditional name="optionNames">
			<param name="names" type="select" label="name for the tags (separated by commas and no space)">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="namesValue" type="text" value="nbElements" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panels are different)"/>
		<param name="csv" type="boolean" truevalue="-x" falsevalue="" checked="false" label="write a .csv file."/>
		<param name="gff" type="boolean" truevalue="-g" falsevalue="" checked="false" label="write a .gff file."/>
	</inputs>

	<outputs>
		<data name="outputFile" format="png" label="[getDistribution] out png file"/>
		<data name="outputCSV" format="csv" label="[getDistribution] output csv file">
			<filter>csv</filter>
		</data>

		<data name="outputGFF" format="gff" label="[getDistribution] output gff file">
			<filter>gff</filter>
		</data>
	</outputs> 

    <help>
        This script gives a .tar out file, if you want to take look at the results, you have to download it.
    </help>	
</tool>