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<tool id="dnapars" name="Phylip DNAPARS" version="0.1.0">
    <description>carries out unrooted parsimony on DNA sequences</description>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
	cp $infasta infile;
	echo $inoptions | sed 's/; /\n/g; s/;/\n/g'| /usr/lib/phylip/bin/dnapars infile;
	cp outfile $outfile;
	cp outtree $outtree
    ]]></command>
    <inputs>
        <param type="data" name="infasta" format="txt" label="Aligned fasta sequences" />
	<param type="text" value= "Y;" name="inoptions" format="txt" label="Keyboard responses separated by semicolon and space (see example below)" />
    </inputs>
    <outputs>
        <data name="outfile" format="txt" label="${tool.name} on ${on_string}: Outfile" />
	<data name="outtree" format="txt" label="${tool.name} on ${on_string}: Tree" />
    </outputs>

    <help><![CDATA[
**What it does**        

This program carries out unrooted parsimony (analogous to Wagner trees) (Eck and Dayhoff, 1966; Kluge and Farris, 1969) on DNA sequences. The method of Fitch (1971) is used to count the number of changes of base needed on a given tree.
Reference: http://evolution.genetics.washington.edu/phylip/doc/dnapars.html

**Prototyping keyboard response files**

Making the proper files of keyboard responses for use with command files is most easily done if you prototype the process by simply running the program and keeping a careful record of the keyboard responses that you need to give to get the program to run properly. Then create a file in an editor and type those keyboard responses into it. Thus if the program requires that you answer a question about what to do with the output file with a keyboard response of R, then wants you to type a menu selection of U (to have it use a User tree), then wants you to answer Y to end the menu, and another R to tell it to replace the output file, you would have the file of keyboard responses be::

  R; U; Y; R;

Testing the keyboard responses with an interactive run will be essential to having batch runs succeed.

    ]]></help>

</tool>