<tool id="getDistribution" name="get distribution">
	<description>Get Distribution: Get the distribution of the genomic coordinates along 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="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="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 points">
				<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="optionChrom">
			<param name="chrom" type="select" label="if you wish to plot only one chromosome, mention the chromosome name">
				<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="optionStart">
			<param name="start" type="select" label="if you wish to plot only one locus, mention its start position">
				<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="if you wish to plot only one locus, mention its end position">
				<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 figure">
				<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 figure">
				<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="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 the number of element per bin (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 panel sizes are different)"/>
	</inputs>

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

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

Print a density profile of the data for each chromosome, see Figure~\ref{fig:getDistribution}. You have to provide the reference genome, to know the sizes of the chromosomes. You can also provide the number of points (called *bins*) you want per chromosome.

By default, only one curve is plotted per chromosome, but you can plot one curve per strand and per chromosome (the minus strand will be plotted with non-positive values on the *y*-axis).

If you want, you can also plot a specific region, by mentionning the chromosome, the start and the end positions of the region.
    </help>	
</tool>