Mercurial > repos > xuebing > sharplab_seq_motif
comparison fastashuffle2.xml @ 15:0e221dbd17b2 default tip
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author | xuebing |
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date | Sat, 31 Mar 2012 08:53:06 -0400 |
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14:d1f0f85ee5bc | 15:0e221dbd17b2 |
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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> |