<tool id="getReadDistribution" name="get read distribution">
	<description>Get Read Distribution v1.0.1: Plot the number of identical reads and give the most represented.</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
	<command interpreter="python">
		../Java/Python/WrappGetReadDistribution.py -i $formatType.inputFileName
		#if $formatType.FormatInputFileName == 'fasta':
			-f fasta
		#elif $formatType.FormatInputFileName == 'fastq':
			-f fastq	
		#end if
			
		#if $optionnumber.number == 'Yes':
			-n $optionnumber.bestNumber
		#end if
		#if $optionpercent.percent == 'Yes':
			-p $optionpercent.percentage
		#end if
		-o $outputFile
	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName" type="select" label="Sequence input File Format ">
				<option value="fasta">fasta</option>
				<option value="fastq">fastq</option>
			</param>
			<when value="fasta">
				<param name="inputFileName" format="fasta" type="data" label="Sequence input File"/>
			</when>
			<when value="fastq">
				<param name="inputFileName" format="fastq" type="data" label="Sequence input File"/>
			</when>
		</conditional>
		
		<conditional name="optionnumber">
			<param name="number" type="select" label="keep the best n">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="bestNumber" type="integer" value="0"  />
			</when>
			<when value="No">
			</when>
		</conditional>
		
		<conditional name="optionpercent">
			<param name="percent" type="select" label="keep the best n percentage">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="percentage" type="integer" value="0" />
			</when>
			<when value="No">
			</when>
		</conditional>

	</inputs>

	<outputs>
		<data name="outputFile" format="tar" label="[get read distribution] tar out file" help="You can not see the results directly from galaxy, but you can download this tar output file."/>
	</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>