<tool id="getDifference" name="get difference">
	<description>Gets all the regions of the genome, except the one given in an annotation file. Alternatively, it may also give all the elements from the first set which does not ovelap with the second set (at the nucleotide level).</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
	<command interpreter="python">
		../Java/Python/getDifference.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

		$split
		
		#if $OptionSequence.option == "Yes":
			-s $OptionSequence.sequence
		#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 "/>
			</when>
			<when value="gff">
				<param name="inputFileName1" format="gff" type="data" label="Input File "/>
			</when>
			<when value="gff2">
				<param name="inputFileName1" format="gff2" type="data" label="Input File "/>
			</when>
			<when value="gff3">
				<param name="inputFileName1" format="gff3" type="data" label="Input File "/>
			</when>
			<when value="sam">
				<param name="inputFileName1" format="sam" type="data" label="Input File "/>
			</when>
			<when value="gtf">
				<param name="inputFileName1" format="gtf" type="data" label="Input File "/>
			</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="reference file"/>
			</when>
			<when value="gff">
				<param name="inputFileName2" format="gff" type="data" label="reference file"/>
			</when>
			<when value="gff2">
				<param name="inputFileName2" format="gff2" type="data" label="reference file"/>
			</when>
			<when value="gff3">
				<param name="inputFileName2" format="gff3" type="data" label="reference file"/>
			</when>
			<when value="sam">
				<param name="inputFileName2" format="sam" type="data" label="reference file"/>
			</when>
			<when value="gtf">
				<param name="inputFileName2" format="gtf" type="data" label="reference file"/>
			</when>
		</conditional>

		<param name="split" type="boolean" truevalue="-p" falsevalue="" checked="false" label="When comparing to a set of genomic coordinates, do not join into exons."/>
		
		<conditional name="OptionSequence">
			<param name="option" type="select" label="Compare with a reference fasta file.">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="sequence" type="data" label="Fasta File" format="fasta"/>
			</when>
			<when value="No">
			</when>
		</conditional>

	</inputs>


	<outputs>
		<data name="outputFileGff" format="gff3" label="[get difference] output file."/>
	</outputs> 

	<help>
This tools has two different (but similar) uses. When given two sets of transcripts, it trims the elements of the set so that they do not overlap with the second set.

When only one set of transcripts is given, together with a reference genome, it produces a list of transcripts which complements the first set.
	</help>
</tool>