<tool id="modifyGenomicCoordinates" name="modify genomic coordinates">
  <description>Extend or shrink a list of genomic coordinates.</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
  <command interpreter="python"> ../Java/Python/modifyGenomicCoordinates.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 $OptionStart.start == "Yes":
			-s $OptionStart.startValue
  		#end if
  	
  		#if $OptionEnd.end == "Yes":
			-e $OptionEnd.endValue
  		#end if
  		
  		#if $OptionFivePrim.five == "Yes":
			-5 $OptionFivePrim.fivePValue
  		#end if
  	
  		#if $OptionTroisP.TroisP == "Yes":
			-3 $OptionTroisP.ThreePValue
  		#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="OptionStart">
			<param name="start" type="select" label="shrink to the start of the feature">
				<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="shrink to the end of the feature">
				<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="OptionFivePrim">
			<param name="five" type="select" label="extend to the 5' direction">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="fivePValue" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>  
		
		<conditional name="OptionTroisP">
			<param name="TroisP" type="select" label="extend to the 3' direction">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="ThreePValue" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		
		 
  </inputs>

  <outputs>
    <data format="gff3" name="outputFile" label="[modify genomic coordinates] output file"/>
  </outputs>

  <help>
This tool reads a list of transcripts and modifies each feature by:

- shrinking it to the *n* first nucleotides or the *n* last nucleotides, or

- extending it to *n* nucleotides towards the 5' direction (upstream) or the 3' direction (downstream).

Note that the 5' or 3' direction depends on the orientation of the feature (the 5' end of a transcript located on the minus strand is on the right hand of this transcript!).

The tool needs a transcript file, its format, and outputs a new transcript file.
  </help>
</tool>