<tool id="restrictFromSize" name="restrict from size">
	<description>Select the elements of a list of sequences or transcripts with a given size.</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
	<command interpreter="python">
		../Java/Python/restrictFromSize.py -i $formatType.inputFileName
		#if $formatType.FormatInputFileName == 'fasta':
			-f fasta
		#elif $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 == 'sam':
			-f sam
		#elif $formatType.FormatInputFileName == 'gtf':
			-f gtf
		#end if

		#if $OptionMax.maximum == "Yes":
			-M $OptionMax.max
		#end if		
		#if $OptionMin.minimum == "Yes":
			-m $OptionMin.min
		#end if	
				
		-o $outputFileGff 
	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName" type="select" label="Input File Format">
				<option value="fasta">fasta</option>
				<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="fasta">
				<param name="inputFileName" format="fasta" type="data" label="Input File"/>
			</when>
			<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>
		
		<conditional name="OptionMax">
			<param name="maximum" type="select" label="maximum number of np">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		
		<conditional name="OptionMin">
			<param name="minimum" type="select" label="minimum number of np">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
			</when>
			<when value="No">
			</when>
		</conditional>	
		
	</inputs>

	<outputs>
		<data name="outputFileGff" format="gff3" label="[restrict from size] output file"/>
	</outputs> 
	
	<help>
Reads a list of sequences or genomic coordinates and outputs those which are longer and / or shorter than a given size ---which you provide.
	</help>

</tool>