--- a/fastashuffle2.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-<tool id="seqshuffle2" 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>