--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/gsnap_parallel_unSQL.xml	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,46 @@
+<tool id="gsnap_parallel_unSQL" name="GSNAP (for DEA in parallel)" version="1.0.0">
+  <description>Genomic Short-read Nucleotide Alignment Program in parallel for Differential Expression Analysis (DEA)</description>
+  <command interpreter="python">gsnap_parallel_unSQL.py 
+ -i $genome_file
+ -q $fastq_file_list  
+ -o $output_file_list
+ -d $genome_prefix 
+ -k $kmer_size
+ #if $OptionPairedEnd.pairedEnd == 'Yes':
+ 	-p $pairedEnd_input
+ #end if
+
+</command>
+  <inputs>
+    <param name="genome_file" type="data" format="fasta" label="Genome fasta file" />
+    <param name="fastq_file_list" type="data" format="txt" label="Fastq file list" />
+    <param name="genome_prefix" type="text" format="txt" label="Prefix used to name genome index " />
+    <param name="kmer_size" type="integer" value="12" label="Kmer size"/>
+    
+  <conditional name="OptionPairedEnd">
+	  <param name="pairedEnd" type="select" label="For paired-end analysis.">
+		  <option value="Yes">Yes</option>
+		  <option value="No" selected="true">No</option>
+	  </param>
+	  <when value="Yes">
+		  <param name="pairedEnd_input" type="data" format="txt" label="input paired-end files list"/>
+	  </when>
+	  <when value="No">
+	  </when>
+  </conditional>
+
+  </inputs>
+
+  <outputs>
+    <data name="output_file_list" format="txt"/>
+  </outputs>
+  <help>
+**What it does**
+
+To complete
+
+**Citation**
+
+If you use this tool, please cite "Thomas D. Wu and Serban Nacu, Fast and SNP-tolerant detection of complex variants and splicing in short reads, Bioinformatics 2010 26:873-881"
+  </help>
+</tool>