Mercurial > repos > xuebing > seq_markov

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author xuebing
date Sat, 31 Mar 2012 21:45:13 -0400
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files seq_markov.xml
diffstat 1 files changed, 21 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seq_markov.xml	Sat Mar 31 21:45:13 2012 -0400
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+<tool id="seq_markov" name="markov_model">
+  <description>from DNA sequence</description>
+  <command>cat $input | fasta-get-markov -m $m $norc > $output 2> err.txt
+    
+    </command>
+  <inputs>
+      <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"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" />
+  </outputs>
+  <help>
+
+**What it does**
+
+This tool generates a markov model from a fasta sequence file. 
+
+  </help>
+</tool>