<?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>Phylip</title>
    <version>3.6a2</version>
    <description>unroot: use of RETREE to unroot a tree</description>
    &phylip_header;
  </head>

  <command>unroot</command>

  <parameters>

    <parameter iscommand="1" ishidden="1" type="String">
      <name>unroot</name>
      <attributes>
	<format>
	  <language>perl</language>
	  <code> "retree &lt; params" </code>
	</format>
	<group>0</group>
      </attributes>
    </parameter>

    <parameter ismandatory="1" issimple="1" type="InFile">
      <name>treefile</name>
      <attributes>
	<prompt>Tree File</prompt>
	<format>
	  <language>perl</language>
	  <code>"ln -s $treefile intree; "</code>
	</format>
	<group>-10</group>
	<comment>
	  <value>The program hangs when provided a tree with [...] added to branch lengths.</value>
	</comment>
	<pipe>
	  <pipetype>phylip_tree</pipetype>
	  <language>perl</language>
	  <code>1</code>
	</pipe>
      </attributes>
    </parameter>
    
    <parameter type="Results">
      <name>outtree</name>
      <attributes>
	<filenames>outtree</filenames>
        <pipe>
	  <pipetype>phylip_tree</pipetype>
	  <language>perl</language>
	  <code>1</code>
        </pipe>
      </attributes>
    </parameter>

    <parameter type="Results">
      <name>params</name>
      <attributes>
	<filenames>params</filenames>
      </attributes>
    </parameter>

    <parameter ishidden="1" type="String">
      <name>commands</name>
      <attributes>
	<format>
	  <language>perl</language>
	  <code>"Y\\nW\\nU\\nQ\\n"</code>
	</format>
	<group>1000</group>
	<paramfile>params</paramfile>
      </attributes>
    </parameter>


  </parameters>

</pise>
