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

<pise>

<head>
<title>SCOPPARSE</title>
<description>Reads raw scop classifications file and writes embl-like format scop classification file. (EMBOSS)</description>
<category>utils:database creation</category>
<doclink>http://bioweb.pasteur.fr/docs/EMBOSS/scopparse.html</doclink>
</head>

<command>scopparse</command>

<parameters>

&emboss_init;

<parameter type="InFile" ismandatory="1" issimple="1" ishidden="0">
<name>infilea</name>
<attributes>
	<prompt>Name of scop classification file for input (raw format dir.cla.scop.txt_X.XX file) (-infilea)</prompt>
	<format>
		<language>perl</language>
		<code>" -infilea=$value"</code>
	</format>
	<group>1</group>
</attributes>
</parameter>

<parameter type="InFile" ismandatory="1" issimple="1" ishidden="0">
<name>infileb</name>
<attributes>
	<prompt>Name of description file for input (raw format dir.des.scop.txt_X.XX file) (-infileb)</prompt>
	<format>
		<language>perl</language>
		<code>" -infileb=$value"</code>
	</format>
	<group>2</group>
</attributes>
</parameter>

<parameter type="OutFile" ismandatory="1" issimple="1" ishidden="0">
<name>outfile</name>
<attributes>
	<prompt>Name of scop file for output (embl-like format) (-outfile)</prompt>
	<vdef>
		<value>Escop.dat</value>
	</vdef>
	<format>
		<language>perl</language>
		<code>" -outfile=$value"</code>
	</format>
	<group>3</group>
</attributes>
</parameter>

<parameter type="String" ishidden="1">
<name>auto</name>
<attributes>
	<format>
		<language>perl</language>
		<code>" -auto -stdout"</code>
	</format>
	<group>4</group>
</attributes>
</parameter>

</parameters>
</pise>
