view tools/mytools/fastamarkov.xml @ 1:cdcb0ce84a1b

author xuebing
date Fri, 09 Mar 2012 19:45:15 -0500
parents 9071e359b9a3
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<tool id="fastamarkov" name="background model">
  <description>of DNA sequence</description>
  <command>cat $input | fasta-get-markov -m $m $norc > $output 2> err.txt
      <param name="input" type="data" format="fasta" label="Sequence file (FASTA)"/>
      <param name="m" size="10" type="integer" value="0" label="Order of Markov model to use"/>
    <param name="norc" label="Combine forward and reverse complement frequencies" type="boolean" truevalue="" falsevalue="-norc" checked="True"/>
    <data format="txt" name="output" />

**What it does**

This tool generates a markov model from a fasta sequence file.