|
0
|
1 <tool id="seq_shuffle_dinucleotide" 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>
|
