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1 <tool id="gsnap_parallel_unSQL" name="GSNAP (for DEA in parallel)" version="1.0.0">
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2 <description>Genomic Short-read Nucleotide Alignment Program in parallel for Differential Expression Analysis (DEA)</description>
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3 <command interpreter="python">gsnap_parallel_unSQL.py
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4 -i $genome_file
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5 -q $fastq_file_list
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6 -o $output_file_list
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7 -d $genome_prefix
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8 -k $kmer_size
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9 #if $OptionPairedEnd.pairedEnd == 'Yes':
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10 -p $pairedEnd_input
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11 #end if
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12
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13 </command>
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14 <inputs>
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15 <param name="genome_file" type="data" format="fasta" label="Genome fasta file" />
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16 <param name="fastq_file_list" type="data" format="txt" label="Fastq file list" />
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17 <param name="genome_prefix" type="text" format="txt" label="Prefix used to name genome index " />
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18 <param name="kmer_size" type="integer" value="12" label="Kmer size"/>
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19
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20 <conditional name="OptionPairedEnd">
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21 <param name="pairedEnd" type="select" label="For paired-end analysis.">
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22 <option value="Yes">Yes</option>
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23 <option value="No" selected="true">No</option>
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24 </param>
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25 <when value="Yes">
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26 <param name="pairedEnd_input" type="data" format="txt" label="input paired-end files list"/>
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27 </when>
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28 <when value="No">
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29 </when>
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30 </conditional>
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31
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32 </inputs>
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33
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34 <outputs>
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35 <data name="output_file_list" format="txt"/>
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36 </outputs>
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37 <help>
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38 **What it does**
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39
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40 To complete
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41
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42 **Citation**
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43
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44 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"
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45 </help>
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46 </tool>
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