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

<pise>

  <head>
    <title>SAM</title>
    <description>sampleseqs - generate typical sequences from a model</description>
    <authors>R. Hughey, A. Krogh</authors>
  </head>


<command>sampleseqs</command>

<parameters>

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

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

</attributes>
</parameter>

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

	<prompt>Run name</prompt>
	<format>
		<language>perl</language>
		<code>" $value"</code>
	</format>
	<vdef><value>test</value></vdef>
	<group>1</group>

</attributes>
</parameter>

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

	<prompt>Model (-i)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -i $value" : ""</code>
	</format>
	<group>2</group>
	<pipe>
		<pipetype>sam_model</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>

<parameter ismandatory="1" issimple="1" type="Integer">
<name>nseq</name>
<attributes>

	<prompt>How many sequences (-nseq)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -nseq $value" : "" </code>
	</format>
	<group>2</group>

</attributes>
</parameter>

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

	<filenames>*.seq</filenames>
	<pipe>
		<pipetype>seqsfile</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>


</parameters>
</pise>
