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

<pise>

<head>
<title>PATMATTEST</title>
<description>test of pattern matching (EMBOSS)</description>
<category>test</category>
<doclink>http://bioweb.pasteur.fr/docs/EMBOSS/patmattest.html</doclink>
</head>

<command>patmattest</command>

<parameters>

&emboss_init;

<parameter type="Sequence" ismandatory="1" issimple="1" ishidden="0">
<name>sequence</name>
<attributes>
	<prompt>sequence -- any [single sequence] (-sequence)</prompt>
	<format>
		<language>perl</language>
		<code>" -sequence=$value -sformat=fasta"</code>
	</format>
	<group>1</group>
	<seqtype><value>any</value></seqtype>
	<seqfmt>
		<value>8</value>
	</seqfmt>
	<pipe>
		<pipetype>seqfile</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>
</attributes>
</parameter>

<parameter type="String" ismandatory="1" issimple="1" ishidden="0">
<name>expression</name>
<attributes>
	<prompt>Regular expression to search sequence for. (-expression)</prompt>
	<format>
		<language>perl</language>
		<code>" -expression=$value"</code>
	</format>
	<group>2</group>
</attributes>
</parameter>

<parameter type="String" ishidden="1">
<name>auto</name>
<attributes>
	<format>
		<language>perl</language>
		<code>" -auto -stdout"</code>
	</format>
	<group>3</group>
</attributes>
</parameter>

</parameters>
</pise>
