<tool id="CompareOverlapping" name="Compare Overlapping">
	<description>Print all the transcripts from a first file which overlap with the transcripts from a second file.</description>
	<command interpreter="python">
		../Java/Python/CompareOverlapping.py -i $formatType.inputFileName1
		#if $formatType.FormatInputFileName1 == 'bed':
			-f bed
		#elif $formatType.FormatInputFileName1 == 'gff':
			-f gff	
		#elif $formatType.FormatInputFileName1 == 'gff2':
			-f gff2
		#elif $formatType.FormatInputFileName1 == 'gff3':
			-f gff3
		#elif $formatType.FormatInputFileName1 == 'sam':
			-f sam
		#elif $formatType.FormatInputFileName1 == 'gtf':
			-f gtf
		#end if
			
		-j $formatType2.inputFileName2
		#if $formatType2.FormatInputFileName2 == 'bed':
			-g bed
		#elif $formatType2.FormatInputFileName2 == 'gff':
			-g gff	
		#elif $formatType2.FormatInputFileName2 == 'gff2':
			-g gff2
		#elif $formatType2.FormatInputFileName2 == 'gff3':
			-g gff3
		#elif $formatType2.FormatInputFileName2 == 'sam':
			-g sam
		#elif $formatType2.FormatInputFileName2 == 'gtf':
		    -g gtf
		#end if

		-o $outputFileGff 

		#if $optionNFirstFile1.NFirstForFile1 == 'Yes':
			-S $optionNFirstFile1.firstNtFile1
		#end if
		#if $optionNFirstFile2.NFirstForFile2 == 'Yes':
			-s $optionNFirstFile2.firstNtFile2
		#end if
		#if $optionNLastFile1.NLastForFile1 == 'Yes':
			-U $optionNLastFile1.lastNtFile1
		#end if
		#if $optionNLastFile2.NLastForFile2 == 'Yes':
			-u $optionNLastFile2.lastNtFile2
		#end if
	
		#if $optionExtentionCinqFile1.extentionFile1 == 'Yes':
			-E $optionExtentionCinqFile1.extention51
		#end if
		#if $optionExtentionCinqFile2.extentionFile2 == 'Yes':
			-e $optionExtentionCinqFile2.extention52
		#end if

		#if $optionExtentionTroisFile1.extentionFile1 == 'Yes':
			-N $optionExtentionTroisFile1.extention31
		#end if
		#if $optionExtentionTroisFile2.extentionFile2 == 'Yes':
			-n $optionExtentionTroisFile2.extention32
		#end if	

		#if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
			-c 
		#elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
			-a
		#end if	

		#if $OptionDistance.Dist == 'Yes':
			-d $OptionDistance.distance
		#end if

		#if $OptionMinOverlap.MO == 'Yes':
			-m $OptionMinOverlap.minOverlap
		#end if

		$InvertMatch
		$ReportIntron
		$NotOverlapping
		
	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName1" type="select" label="Input File Format 1">
				<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="inputFileName1" format="bed" type="data" label="Input File 1"/>
			</when>
			<when value="gff">
				<param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
			</when>
			<when value="gff2">
				<param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
			</when>
			<when value="gff3">
				<param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
			</when>
			<when value="sam">
				<param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
			</when>
			<when value="gtf">
				<param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
								                        </when>
		</conditional>

		<conditional name="formatType2">
			<param name="FormatInputFileName2" type="select" label="Input File Format 2">
				<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="inputFileName2" format="bed" type="data" label="Input File 2"/>
			</when>
			<when value="gff">
				<param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
			</when>
			<when value="gff2">
				<param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
			</when>
			<when value="gff3">
				<param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
			</when>
			<when value="sam">
				<param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
			</when>
			<when value="gtf">
				<param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
			</when>
		</conditional>



		<conditional name="optionNFirstFile1">
			<param name="NFirstForFile1" type="select" label="NFirst for file 1" help="only consider the n first nucleotides of the transcripts in file 1">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="firstNtFile1" type="integer" value="1" label="n first nucleotides for input file 1" />
			</when>
			<when value="No">
			</when>
		</conditional>
		<conditional name="optionNFirstFile2">
			<param name="NFirstForFile2" type="select" label="NFirst for file 2" help="only consider the n first nucleotides of the transcripts in file 2">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="firstNtFile2" type="integer" value="1" label="n first nucleotides for input file 1" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionNLastFile1">
			<param name="NLastForFile1" type="select" label="NLast for file 1">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="lastNtFile1" type="integer" value="1" label="n last nucleotides for input file 1" help="only consider the n last nucleotides of the transcripts in file 1"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		<conditional name="optionNLastFile2">
			<param name="NLastForFile2" type="select" label="NLast for file 2">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="lastNtFile2" type="integer" value="1" label="n last nucleotides for input file 2" help="only consider the n last nucleotides of the transcripts in file 2"/>
			</when>
			<when value="No">
			</when>
		</conditional>



		<conditional name="optionExtentionCinqFile1">
			<param name="extentionFile1" type="select" label="Extension towards 5 for file 1">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="extention51" type="integer" value="1" label="in file 1" />
			</when>
			<when value="No">
			</when>
		</conditional>


		<conditional name="optionExtentionCinqFile2">
			<param name="extentionFile2" type="select" label="Extension towards 5 for file 2">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="extention52" type="integer" value="1" label="in file 2"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionExtentionTroisFile1">
			<param name="extentionFile1" type="select" label="Extension towards 3 for file 1">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="extention31" type="integer" value="1" label="in file 1" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionExtentionTroisFile2">
			<param name="extentionFile2" type="select" label="Extension towards 3 for file 2">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="extention32" type="integer" value="1" label="in file 2" />
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="OptionColinearOrAntiSens">
			<param name="OptionCA" type="select" label="Colinear or anti-sens">
				<option value="Colinear">Colinear</option>
				<option value="AntiSens">AntiSens</option>
				<option value="NONE" selected="true">NONE</option>
			</param>
			<when value="Colinear">
			</when>
			<when value="AntiSens">
			</when>
			<when value="NONE">
			</when>
		</conditional>

		<conditional name="OptionDistance">
			<param name="Dist" type="select" label="Maximum Distance between two reads">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="distance" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="OptionMinOverlap">
			<param name="MO" type="select" label="Minimum number of overlapping between two reads">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="minOverlap" type="integer" value="1"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		<param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>
		<param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Report intron"/>
		<param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/>
		
	</inputs>

	<outputs>
		<data name="outputFileGff" format="gff3"/>
	</outputs> 
	
</tool>