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

<pise>

  <head>
    <title>HMMER</title>
    <version>2.2g</version>
    <description>hmmfetch - retrieve an HMM from an HMM database</description>
    <authors>S. Eddy</authors>
    <category>hmm</category>
  </head>

  <command>hmmfetch</command>

  <parameters>

    <parameter type="Paragraph">
      <paragraph>
	<name>description</name>
	<prompt>Description of hmmfetch</prompt>
	<comment>
	  <value>hmmfetch is a small utility that retrieves an HMM from a HMMER model database in a new format, and prints that model to standard output. The retrieved HMM file is written in HMMER 2 ASCII format.</value>
	</comment>
	<parameters>

	  <parameter ishidden="1" type="String">
	    <name>toto</name>
	    <attributes>
	      <format>
		<language>perl</language>
		<code>""</code>
	      </format>
	      <group>1000</group>
	    </attributes>
	  </parameter>

	</parameters>
      </paragraph>

    </parameter>

    <parameter iscommand="1" ishidden="1" type="String">
      <name>hmmfetch</name>
      <attributes>
	<format>
	  <language>perl</language>
	  <code>"hmmfetch"</code>
	</format>
	<group>0</group>
      </attributes>
    </parameter>

    <parameter ismandatory="1" type="String">
      <name>name</name>
      <attributes>
	<prompt>name of the HMM</prompt>
	<format>
	  <language>perl</language>
	  <code>" $value"</code>
	</format>
	<group>2</group>
      </attributes>
    </parameter>

    <parameter ismandatory="1" type="Excl">
      <name>HMMDB</name>
      <attributes>
	<prompt>HMM database</prompt>
	<format>
	  <language>perl</language>
	  <code>" $value"</code>
	</format>
	<vdef><value>Pfam</value></vdef>
	<group>1</group>
	<vlist>
	  <value>Pfam</value>
	  <label>Pfam</label>
	  <value>PfamFrag</value>
	  <label>PfamFrag</label>
	</vlist>
      </attributes>
    </parameter>

    <parameter type="Results">
      <name>hmmfile</name>
      <attributes>
	<filenames>"hmmfetch.out"</filenames>
	<pipe>
	  <pipetype>hmmer_HMM</pipetype>
	  <language>perl</language>
	  <code>1</code>
	</pipe>
      </attributes>
    </parameter>

  </parameters>
</pise>
