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

<pise>

<head><title>SAM: hmmer2sam (R. Hughey &amp; A. Krogh)</title></head>


<command>hmmer2sam</command>

<parameters>

<parameter iscommand="1" ishidden="1" issimple="1" type="String">
<name>hmmer2sam</name>
<attributes>

	<format>
		<language>seqlab</language>
		<code>hmmer2sam</code>
		<language>perl</language>
		<code>"hmmer2sam"</code>
	</format>
	<group>0</group>

</attributes>
</parameter>

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

	<prompt>HMMER model file</prompt>
	<format>
		<language>perl</language>
		<code>" $value"</code>
	</format>
	<group>1</group>
	<pipe>
		<pipetype>hmm_textfile</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>

<parameter ismandatory="1" issimple="1" type="OutFile">
<name>model_file</name>
<attributes>

	<prompt>SAM model file</prompt>
	<format>
		<language>perl</language>
		<code>" $value"</code>
	</format>
	<group>2</group>
	<pipe>
		<pipetype>sam_model</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>


</parameters>
</pise>
