comparison seq_shuffle_dinucleotide.xml @ 0:aad0a5d475ce

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author xuebing
date Sat, 31 Mar 2012 21:47:42 -0400
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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**
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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.
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21 Code adapted from http://bioinformatics.bc.edu/clotelab/RNAdinucleotideShuffle/dinucleotideShuffle.html
22
23 </help>
24 </tool>