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comparison SMART/DiffExpAnal/gsnap_parallel_unSQL.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 <tool id="gsnap_parallel_unSQL" name="GSNAP (for DEA in parallel)" version="1.0.0">
2 <description>Genomic Short-read Nucleotide Alignment Program in parallel for Differential Expression Analysis (DEA)</description>
3 <command interpreter="python">gsnap_parallel_unSQL.py
4 -i $genome_file
5 -q $fastq_file_list
6 -o $output_file_list
7 -d $genome_prefix
8 -k $kmer_size
9 #if $OptionPairedEnd.pairedEnd == 'Yes':
10 -p $pairedEnd_input
11 #end if
12
13 </command>
14 <inputs>
15 <param name="genome_file" type="data" format="fasta" label="Genome fasta file" />
16 <param name="fastq_file_list" type="data" format="txt" label="Fastq file list" />
17 <param name="genome_prefix" type="text" format="txt" label="Prefix used to name genome index " />
18 <param name="kmer_size" type="integer" value="12" label="Kmer size"/>
19
20 <conditional name="OptionPairedEnd">
21 <param name="pairedEnd" type="select" label="For paired-end analysis.">
22 <option value="Yes">Yes</option>
23 <option value="No" selected="true">No</option>
24 </param>
25 <when value="Yes">
26 <param name="pairedEnd_input" type="data" format="txt" label="input paired-end files list"/>
27 </when>
28 <when value="No">
29 </when>
30 </conditional>
31
32 </inputs>
33
34 <outputs>
35 <data name="output_file_list" format="txt"/>
36 </outputs>
37 <help>
38 **What it does**
39
40 To complete
41
42 **Citation**
43
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"
45 </help>
46 </tool>