<tool id="gsnap" name="gsnap">

	<description>GSNAP version 2012-12-20. 
	             GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and
                 GSNAP: Genomic Short-read Nucleotide Alignment Program 
    </description>
    
	<requirements>
        <requirement type="package">gmap</requirement>
    </requirements>

	
	<command interpreter="python"> wrappGSNAP.py 
		-d $genomeName -D $genomeName.files_path -k $kmer -i $inputFasta -q $inputFastq -A $outputFormat 
	
		#if $optionPairedEnd.paire == 'Yes':
				-p $optionPairedEnd.pairedEndFile
		#end if
		
		> $outputSam
	
	</command>

	<inputs>
		<param name="inputFasta" type="data" format="fasta" label="Reference genome file, fasta format."/>	
		<param name="genomeName" type="text" value="Arabidopsis_Thaliana" label="Please give the reference genome a name! (Ex. Arabidopsis_Thaliana)"/>	
		<param name="kmer" type="integer" value="12" label="Choose kmer value (<=16), a big kmer value can take more RAM(4Go)." />
		<param name="inputFastq" type="data" format="fastq" label="Input fastq file."/>
		<param name="outputFormat" type="text" format="sam" label="Choose an output format [sam, goby (need to re-compile with appropriate options)]."/>
		
		<conditional name="optionPairedEnd">
			<param name="paire" type="select" label="pairedEnd fastq file">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="pairedEndFile" type="data" format="fastq"/>
			</when>
			<when value="No">
			</when>
		</conditional>
	
	</inputs>

	<outputs>
		<data format="sam" name="outputSam" label="gsnap Output"/>
	</outputs>

</tool>