Mercurial > repos > xuebing > sharplabtool
comparison mytools/fastashuffle2.xml @ 7:f0dc65e7f6c0
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:59:07 -0500 |
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| 6:094f377db4e5 | 7:f0dc65e7f6c0 |
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| 1 <tool id="seqshuffle2" name="shuffle sequence"> | |
| 2 <description>preserving dinucleotide frequency</description> | |
| 3 <command interpreter="python">fasta-dinucleotide-shuffle.py -f $input -t $tag -c $n -s $seed > $output </command> | |
| 4 <inputs> | |
| 5 <param name="input" format="fasta" type="data" label="Original sequence file"/> | |
| 6 <param name="tag" type="text" size="40" value="-shuffled" label="tag added to shuffled sequence name"/> | |
| 7 <param name="n" type="integer" value="1" label="number of shuffled copies for each sequence"/> | |
| 8 <param name="seed" type="integer" value="1" label="random seed" help="the same seed gives the same random sequences"/> | |
| 9 </inputs> | |
| 10 <outputs> | |
| 11 <data format="fasta" name="output" /> | |
| 12 </outputs> | |
| 13 <help> | |
| 14 | |
| 15 **What it does** | |
| 16 | |
| 17 This tool shuffles the sequences in the input file but preserves the dinucleotide frequency of each sequence. | |
| 18 | |
| 19 The code implements the Altschul-Erikson dinucleotide shuffle algorithm, described in "Significance of nucleotide sequence alignments: A method for random sequence permutation that preserves dinucleotide and codon usage", S.F. Altschul and B.W. Erikson, Mol. Biol. Evol., 2(6):526--538, 1985. | |
| 20 | |
| 21 Code adapted from http://bioinformatics.bc.edu/clotelab/RNAdinucleotideShuffle/dinucleotideShuffle.html | |
| 22 | |
| 23 </help> | |
| 24 </tool> |