<?xml version="1.0" encoding="ISO-8859-1" ?>
<!DOCTYPE pise SYSTEM "PARSER/pise.dtd" [
<!ENTITY param SYSTEM "XMLDIR/hmmpar_param.xml">
]> 
   
<pise>
  
  <head>
    <title>HMM</title>
    <version>5.2.1-90/90</version>
    <description>compares amino acid HMM models against amino acid database</description>
    <authors>Paracel</authors>
    <reference>Paracel's Hidden Markov Models use the Viterbi algorithm.
               HMM BTK 5.2.1-90/90 2003-06-12 (Fdf Client 1.500)
               Copyright 2001 Paracel, Inc</reference>
    <doclink>http://bioweb.pasteur.fr/seqanal/search/index.html</doclink>
    
  </head>
  
  <command>hmmsearchpar</command>
  
  <parameters>
    
    <parameter ismandatory="1" iscommand="1" ishidden="1" type="String">
      <name>hmmsearchpar</name>
      <attributes>
	<prompt>hmm program</prompt>
	<format>	
	  <language>perl</language>
	  <code>"btk hmm"</code>
	</format>
      </attributes>
    </parameter>
    
 
    <parameter ismandatory="1" issimple="1" type="InFile">
      <name>hmmfile</name>
      <attributes>
	<prompt>HMMER model file</prompt>
	<format>
	  <language>perl</language>
	  <code>" q=$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="Excl">
      <name>database</name>
      <attributes>
	<prompt>amino acid databases (d or ds)</prompt>
	<format>
	  <language>perl</language>
	  <code>(defined $value &amp;&amp; $value eq "embl")? " ds=$value"  : " d=$value"</code>
	</format>
	<vlist>
	  <value>nrprot</value>
	  <label>nrprot</label>
	  <value>uniprot</value>
	  <label>uniprot</label>
	</vlist>
      </attributes>
    </parameter>
    
    &param;
    
  </parameters>
  </pise>
