<tool id="mergeTranscriptLists" name="merge transcript lists">
	<description>Merge the elements of two lists of genomic coordinates.</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
	<command interpreter="python">
		../Java/Python/mergeTranscriptLists.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
			
		$all
		$normalize
				
		#if $OptionDistance.dis == 'Yes':
			-d $OptionDistance.disVal
		#end if	
		
		#if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
			-c 
		#elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
			-a
		#end if	
		
		-o $outputFileGff 
	</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>


		<param name="all" type="boolean" truevalue="-k" falsevalue="" checked="false" label="print all the transcripts, not only those overlapping"/>
		<param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize the number of reads per cluster by the number of mappings per read "/>
		
		<conditional name="OptionDistance">
			<param name="dis" type="select" label="provide the number of reads" >
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="disVal" type="integer" value="0" label="max. distance between two transcripts" />
			</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>

	</inputs>

	<outputs>
		<data name="outputFileGff" format="gff3" label="[merge transcript lists] output file"/>
	</outputs> 
	
	<help>
The script is similar to *compare overlapping*, except that when data of two different sets overlap, they are merged. You can use the same parameters as *compare overlapping* and use them to look for transcription on both strands, for example.

Optionally, you can also add to the output all the elements from the first set which do not overlap with the second set.
	</help>
</tool>