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1 <tool id="seqshuffle2" name="shuffle sequence">
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2 <description>preserving dinucleotide frequency</description>
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3 <command interpreter="python">fasta-dinucleotide-shuffle.py -f $input -t $tag -c $n -s $seed > $output </command>
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4 <inputs>
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5 <param name="input" format="fasta" type="data" label="Original sequence file"/>
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6 <param name="tag" type="text" size="40" value="-shuffled" label="tag added to shuffled sequence name"/>
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7 <param name="n" type="integer" value="1" label="number of shuffled copies for each sequence"/>
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8 <param name="seed" type="integer" value="1" label="random seed" help="the same seed gives the same random sequences"/>
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9 </inputs>
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10 <outputs>
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11 <data format="fasta" name="output" />
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12 </outputs>
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13 <help>
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14
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15 **What it does**
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16
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17 This tool shuffles the sequences in the input file but preserves the dinucleotide frequency of each sequence.
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18
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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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20
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21 Code adapted from http://bioinformatics.bc.edu/clotelab/RNAdinucleotideShuffle/dinucleotideShuffle.html
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22
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23 </help>
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24 </tool>
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