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

<pise>

  <head>
    <title>PHYLOQUART</title>
    <version>1.3</version>
    <description>qstar - reliable phylogeny reconstruction from a set of quartets</description>
    <authors>Berry</authors>
    <category>phylogeny</category>
  </head>

  <command>qstar</command>

<parameters>

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

	<format>
		<language>seqlab</language>
		<code>qstar</code>
		<language>perl</language>
		<code>"qstar"</code>
	</format>
	<group>0</group>

</attributes>
</parameter>

<parameter ismandatory="1" issimple="1" type="InFile">
<name>quartfile</name>
<attributes>

	<prompt>quartfile containing the list of quartets</prompt>
	<format>
		<language>perl</language>
		<code>"ln -s $quartfile quartfile; "</code>
	</format>
	<group>-10</group>
	<comment>
		<value>This file is computed by quartet inference programs (parciquart and distquart) which infer a set of quartets from biological data, mainly nucleotide sequences for the species or inter-species distances.</value>
	</comment>
	<pipe>
		<pipetype>quartfile</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>

<parameter ishidden="1" type="OutFile">
<name>quartfile_res</name>
<attributes>

	<vdef><value>"quartfile.res"</value></vdef>

</attributes>
</parameter>

<parameter ishidden="1" type="OutFile">
<name>quartfile_left</name>
<attributes>

	<vdef><value>"quartfile.left"</value></vdef>

</attributes>
</parameter>

<parameter ishidden="1" type="OutFile">
<name>bipfile</name>
<attributes>

	<vdef><value>"bipfile"</value></vdef>
	<pipe>
		<pipetype>bipfile</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>
	<withpipe>
		<pipetype>bipfile</pipetype>
			<parametername>quartfile_left</parametername>
			<parametername>quartfile_res</parametername>
	</withpipe>

</attributes>
</parameter>

<parameter ishidden="1" type="Switch">
<name>tree_pop</name>
<attributes>

	<format>
		<language>perl</language>
		<code>" ;tree-pop"</code>
	</format>
	<group>2</group>

</attributes>
</parameter>

<parameter type="Results">
<name>treefile</name>
<attributes>

	<filenames>treefile</filenames>
	<pipe>
		<pipetype>phylip_tree</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>


</parameters>
</pise>
