# HG changeset patch
# User xuebing
# Date 1333244862 14400
# Node ID aad0a5d475ce9a019e7338f57cc16d3e841d98d1

Uploaded

diff -r 000000000000 -r aad0a5d475ce seq_shuffle_dinucleotide.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seq_shuffle_dinucleotide.xml	Sat Mar 31 21:47:42 2012 -0400
@@ -0,0 +1,24 @@
+<tool id="seq_shuffle_dinucleotide" name="shuffle sequence">
+  <description>preserving dinucleotide frequency</description>
+  <command interpreter="python">fasta-dinucleotide-shuffle.py -f $input -t $tag -c $n -s $seed > $output </command>
+  <inputs>
+    <param name="input" format="fasta" type="data" label="Original sequence file"/>
+    <param name="tag" type="text" size="40" value="-shuffled" label="tag added to shuffled sequence name"/>
+    <param name="n" type="integer" value="1" label="number of shuffled copies for each sequence"/>
+    <param name="seed" type="integer" value="1" label="random seed" help="the same seed gives the same random sequences"/>
+  </inputs>
+  <outputs>
+    <data format="fasta" name="output" />
+  </outputs>
+  <help>
+
+**What it does**
+
+This tool shuffles the sequences in the input file but preserves the dinucleotide frequency of each sequence. 
+
+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. 
+
+Code adapted from http://bioinformatics.bc.edu/clotelab/RNAdinucleotideShuffle/dinucleotideShuffle.html
+
+  </help>
+</tool>