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

<pise>
  
  <head>
    <title>SAM</title>
    <version>3.2.1</version>
    <description>sam2hmmer</description>
    <authors>R. Hughey, A. Krogh</authors>
  </head>


  <command>sam2hmmer</command>

  <parameters>

    <parameter iscommand="1" ishidden="1" issimple="1" type="String">
      <name>sam2hmmer</name>
      <attributes>
	<format>
	  <language>seqlab</language>
	  <code>sam2hmmer</code>
	  <language>perl</language>
	  <code>"sam2hmmer"</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 type="Results">
      <name>hmmfile</name>
      <attributes>
	<filenames>*.hmmer</filenames>
	<pipe>
	  <pipetype>hmmfile</pipetype>
	  <language>perl</language>
	  <code>1</code>
	</pipe>
      </attributes>
    </parameter>

  </parameters>
</pise>
