<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>