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

<pise>

  <head>
    <title>Glimmer</title>
    <version>2.02</version>
    <description>full-run - long ORFs extraction, model building with these ORFs, and search for genes in the same genome</description>
    &glimmer_header;
  </head>


<command>full_run</command>

<parameters>

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

	<format>
		<language>perl</language>
		<code>"full-run "</code>
	</format>
	<group>0</group>

</attributes>
</parameter>

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

	<prompt>Genome sequence file</prompt>
	<format>
		<language>perl</language>
		<code>" $value "</code>
	</format>
	<group>1</group>
	<seqfmt>
		<value>8</value>
	</seqfmt>

</attributes>
</parameter>

<parameter ismandatory="1" issimple="1" type="String">
<name>out_pre</name>
<attributes>

	<prompt>prefix for output files</prompt>
	<format>
		<language>perl</language>
		<code>" $value "</code>
	</format>
	<group>2</group>

</attributes>
</parameter>

<parameter ishidden="1" type="Results">
<name>output_files</name>
<attributes>

	<filenames>*.coord *.train *.train.deltas.context *.out</filenames>

</attributes>
</parameter>


</parameters>
</pise>
