<?xml version="1.0" encoding="ISO-8859-1" ?>
<!DOCTYPE pise SYSTEM "PARSER/pise.dtd" [
<!ENTITY phylip_header SYSTEM "XMLDIR/phylip_header.xml">
]>

<pise>

<head>
   <title>DRUID</title>
   <description>Localization of recombination breakpoints in an
   alignment of sequences</description>
   <authors>M. Zelwer, MF. Sagot</authors>
    <category>phylogeny</category>
</head>

<command>druid</command>

<parameters>

   <parameter iscommand="1" ishidden="1" type="String">
   <name>druid</name>
   <attributes>

        <format>
                <language>perl</language>
                <code> "druid" </code>
        </format>
        <group>0</group>

   </attributes>
</parameter>

<parameter ismandatory="1" issimple="1" type="Sequence">
   <name>sequences</name>
   <attributes>

        <prompt>DNA Sequence File (at least 4 sequences)</prompt>
        <format>
                <language>perl</language>
                <code>" $value"</code>
        </format>
        <group>4</group>
	<seqfmt>
             <value>12</value>
        </seqfmt>
	<pipe>
	      <pipetype>readseq_ok_alig</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>
	<comment>
		<value>The data should be an alignment of DNA sequences containing at least four sequences</value>
	</comment>

   </attributes>
</parameter>

<parameter type="Integer">
    <name>window_size</name>
    <attributes>
    	<prompt>window_size (-w)</prompt>
    	<format>
    	<language>perl</language>
    	<code> (defined $value &amp;&amp; $value ne $vdef)? " -w $value" : ""</code>
    	</format>
   	 <vdef><value>5</value></vdef>
    	<group>2</group>
	<comment>
	  <value>This parameter sets the size of each half of the double window.    </value>
	</comment>
    </attributes>
</parameter>

<parameter type="Integer">
    <name>iterations</name>
    <attributes>
    <prompt>number of iterations (-n)</prompt>
    <format>
    <language>perl</language>
    <code> (defined $value &amp;&amp; $value ne $vdef)? " -n $value" : ""</code>
    </format>
    <vdef><value>1000</value></vdef>
	<ctrls>
	  <ctrl>
	    <message>If you want to run the program with this parameter set a value greater than 2000, please contact the authors.</message>
	    <language>perl</language>
	    <code>$value &gt; 2000</code>
	  </ctrl>
	</ctrls>
    <group>3</group>
    <comment>
    <value>This option specifies how many separate datasets should be simulated for each  Farris' ILD test.</value>
    </comment>
    </attributes>
</parameter>

</parameters>
</pise>
