<tool id="maxent" name="splice site score">
  <description>using max entropy model</description>
  <command interpreter="perl">$script $input > $out_file1 </command>
  <inputs>
    <param name="input" format="txt" type="data" label="Sequence file" help="fasta or raw sequence (one sequence per line)"/>
    <param name="script" type="select" label="Select model">
        <option value="splicesitescore/score5.pl" selected="true">5' splice site</option>
        <option value="splicesitescore/score3.pl">3' splice site</option>
    </param>
                <param name="genome" type="select" label="Select chromsome size file" >
                <options from_file="chrsize.loc">
                    <column name="name" index="0"/>
                    <column name="value" index="1"/>
                </options>
            </param>
            
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" />
  </outputs>
  <help>

**What it does**

This tool computes splice site scores using a max entropy model. See more details here: 

http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html

-----

**Example input for 5' splice site sequence**

3 exonic and 6 intronic nucleotides flanking the junction::

    CTGGTGAGT
    AAGGTACAG

or fasta format::

    >seq1
    CTGGTGAGT
    >seq2
    AAGGTACAG

Output::

    CTGGTGAGT	10.10
    AAGGTACAG	8.04

or fasta format::

    >seq1   CTGGTGAGT	10.10
    >seq2   AAGGTACAG	8.04


-----

**Example input for 3' splice site sequence**

3 exonic and 20 intronic nucleotides flanking the junction::

    CCTGCATCCTCTGTTCCCAGGTG
    TTTCTTCCCTCCGGGAACAGTGG

Output::

    CCTGCATCCTCTGTTCCCAGGTG	10.47
    TTTCTTCCCTCCGGGAACAGTGG	6.22

  </help>
</tool>