--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DiffExpAnal/gsnap.xml	Tue Jan 22 10:07:03 2013 -0500
@@ -0,0 +1,49 @@
+<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>