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

<pise>
  
  <head>
    <title>GeneWise</title>
    <version>5.2.1-90/90</version>
    <description>compares protein sequeces or Hidden Markov Models (HMMs)
    directly against genomic DNA data, with gene structure prediction
    implicit in subsequent matches</description>
    <authors>Paracel</authors>
    <reference>Moira Regelson, Alan Arehart, Tristan Gill, Joseph A.
    Borkowski, Guy Slater and Ewan Birney. GeneWise Port to the Paracel GeneMatcher,.
               
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>genewiseprotpar</command>
  
  <parameters>
    
    <parameter ismandatory="1" iscommand="1" ishidden="1" type="String">
      <name>genewiseprotpar</name>
      <attributes>
	<prompt>genwise programm</prompt>
	<format>	
	  <language>perl</language>
	  <code>"echo btk genewise"</code>
	</format>
      </attributes>
    </parameter>
    
   
    <parameter ismandatory="1" issimple="1" type="Sequence">
      <name>database</name>
      <attributes>
	<prompt>One protein (file in fasta format) (d)</prompt>
	<format>
	  <language>perl</language>
	  <code>" d=$value"</code>
	</format>
	<seqfmt>
	  <value>8</value>
	</seqfmt>
	<pipe>
	  <pipetype>seqfile</pipetype>
	  <language>perl</language>
	  <code>1</code>
	</pipe>
      </attributes>
    </parameter>
    


    &param;
    
   
     </parameters>
  
  </pise>
 
