<tool id="GetSizes" name="get sizes">
	<description>Get the sizes of a set of genomic coordinates.</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
	<command interpreter="python">
		../Java/Python/getSizes.py -i $formatType.inputFileName $formatType.FormatInputFileName
	
		#if $OptionQuery.OptionQ == 'NONE':
			-q size
		#else:
			$OptionQuery.OptionQ
		#end if

		-o $outputFile

		#if $OptionXMax.xMax == "Yes":
			-x $OptionXMax.maxValue
		#end if
		#if $OptionX.xLab == "Yes":
		        -a $OptionX.xLabValue
		#end if
                #if $OptionY.yLab == "Yes":
		        -b $OptionY.yLabValue
		#end if
		$barPlot
	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName" type="select" label="Input File Format">
				<option value="-f bed">bed</option>
				<option value="-f gff">gff</option>
				<option value="-f gff2">gff2</option>
				<option value="-f gff3">gff3</option>
				<option value="-f sam">sam</option>
				<option value="-f gtf">gtf</option>
				<option value="-f fasta">fasta</option>
				<option value="-f fastq">fastq</option>
			</param>
			<when value="-f bed">
				<param name="inputFileName" format="bed" type="data" label="Input File"/>
			</when>
			<when value="-f gff">
				<param name="inputFileName" format="gff" type="data" label="Input gff File"/>
			</when>
			<when value="-f gff2">
				<param name="inputFileName" format="gff" type="data" label="Input gff2 File"/>
			</when>
			<when value="-f gff3">
				<param name="inputFileName" format="gff3" type="data" label="Input gff3 File"/>
			</when>
			<when value="-f sam">
				<param name="inputFileName" format="sam" type="data" label="Input gff2 File"/>
			</when>
			<when value="-f gtf">
				<param name="inputFileName" format="gtf" type="data" label="Input gff3 File"/>
			</when>
			<when value="-f fasta">
				<param name="inputFileName" format="fasta" type="data" label="Input fasta File"/>
			</when>
			<when value="-f fastq">
				<param name="inputFileName" format="fastq" type="data" label="Input fastq File"/>
			</when>
		</conditional>

		<conditional name="OptionQuery">
			<param name="OptionQ" type="select" label="mesure type">
				<option value="-q size">size</option>
				<option value="-q intron size">intron size</option>
				<option value="-q exon size">exon size</option>
				<option value="-q 1st exon size">1st exon size</option>
				<option value="NONE" selected="true">NONE</option>
			</param>
			<when value="-q size">
			</when>
			<when value="-q intron size">
			</when>
			<when value="-q exon size">
			</when>
			<when value="-q 1st exon size">
			</when>
			<when value="NONE">
			
			</when>
		</conditional>

		<conditional name="OptionXMax">
			<param name="xMax" type="select" label="maximum x-value to plot">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="maxValue" type="integer" value="1000"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="OptionX">
			 <param name="xLab" type="select" label="X label title">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="xLabValue" type="text" value="Size" label="Notice: The title should not have spaces. EX. Size_of_transcript"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="OptionY">
			<param name="yLab" type="select" label="Y label title">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="yLabValue" type="text" value="#_reads" label="Notice: The title should not have spaces. EX. Number_of_reads"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<param name="barPlot" type="boolean" truevalue="-B" falsevalue="" checked="false" label="use barplot representation"/>
	</inputs>
	
	<outputs>
		<data name="outputFile" format="png" label="[get sizes] output file"/>
	</outputs>

	<help>
Get the sequence/annotation size distribution. A point (*x*, *y*) means that *y* elements have a size of *x* nucleotides. 

When your mapping include exon/intron structures, you can decide to count the size of the introns, the sizes of the exons or the size of the first exons.
	</help>
</tool>