<tool id="restrictTranscriptList" name="restrict transcript list">
  <description>Select the features which are located in a given locus.</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
  <command interpreter="python"> ../Java/Python/restrictTranscriptList.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 == 'sam':
			-f sam
		#elif $formatType.FormatInputFileName == 'gtf':
			-f gtf
		#end if
		
  		#if $OptionChrom.Chrom == "Yes":
			-c $OptionChrom.ChromName
  		#end if
  				
  		#if $OptionStart.start == "Yes":
			-s $OptionStart.startValue
  		#end if
  	
  		#if $OptionEnd.end == "Yes":
			-e $OptionEnd.endValue
  		#end if
  		
  	-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>
	
	<conditional name="OptionChrom">
			<param name="Chrom" type="select" label="chromosome name">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="ChromName" type="text" value="None"/>
			</when>
			<when value="No">
			</when>
	</conditional>	
  
	<conditional name="OptionStart">
			<param name="start" type="select" label="start region of the locus">
				<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 region of the locus">
				<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>    
  </inputs>

  <outputs>
    <data format="gff3" name="outputFile" label="[restrict transcript list] output file"/>
  </outputs>

  <help>
Reads a list of genomic coordinates and outputs those which on a given chromosome and / or between two given positions.
  </help>
<tests>
    <test>
      <param name="FormatInputFileName" value="gtf" />
      <param name="inputFileName" value="genes.gtf" />
	<param name="Chrom" value="Yes"/>
	<param name="ChromName" value="I"/>
	<param name="start" value="No" />
<param name="end" value="No" />
      <output name="outputFile" file="exp_restrictTranscriptList.gff3" />
    </test>
  </tests>

</tool>