Mercurial > repos > yufei-luo > s_mart
comparison SMART/DiffExpAnal/gsnap_parallel_unSQL.xml @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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17:b0e8584489e6 | 18:94ab73e8a190 |
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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> |