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

<pise>

  <head>
    <title>EXTRACTCDS</title>
    <version>1.0</version>
    <description>Extracts translation(s) from a Genbank or Embl entry</description>
	<authors>C. Letondal</authors>
  </head>


  <command>extractcds</command>

  <parameters>

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

	<format>
	  <language>perl</language>
	  <code>"extractcds"</code>
	</format>
	<group>0</group>

      </attributes>
    </parameter>

    <parameter ismandatory="1" issimple="1" type="InFile">
      <name>infile</name>
      <attributes>
	
	<prompt>Entry (Genbank or Embl)</prompt>
	<format>
	  <language>perl</language>
	  <code>" $value"</code>
	</format>
	<group>10</group>
	<pipe>
	  <pipetype>seqfile</pipetype>
	  <language>perl</language>
	  <code>1</code>
	</pipe>
	
      </attributes>
    </parameter>

    <parameter issimple="1" type="Excl">
      <name>entry_format</name>
      <attributes>
	
	<prompt>Entry format (-f)</prompt>
	<vlist>
	  <value>Genbank</value>
	  <label>Genbank</label>
	  <value>Embl</value>
	  <label>Embl</label>
	</vlist>
	<format>
	  <language>perl</language>
	  <code>($value) ? " -f $value" : ""</code>
	</format>
	<group>1</group>
      </attributes>
    </parameter>

    
    <parameter type="Switch">
      <name>show_location</name>
      <attributes>
	
	<prompt>Show location in description (-l)</prompt>
	<format>
	  <language>perl</language>
	  <code>($value) ? " -l" : ""</code>
	</format>
	<group>1</group>
      </attributes>
    </parameter>

    <parameter type="Switch">
      <name>show_product</name>
      <attributes>
	
	<prompt>Show product in description (-p)</prompt>
	<format>
	  <language>perl</language>
	  <code>($value) ? " -p" : ""</code>
	</format>
	<group>1</group>
      </attributes>
    </parameter>

    
    <parameter type="Switch">
      <name>show_gene</name>
      <attributes>
	
	<prompt>Show gene in description (-g)</prompt>
	<format>
	  <language>perl</language>
	  <code>($value) ? " -g" : ""</code>
	</format>
	<group>1</group>
      </attributes>
    </parameter>

    <parameter ishidden="1" isstandout="1" type="OutFile">
      <name>seqsfile</name>
      <attributes>
	
	<vdef><value>"extractcds.out"</value></vdef>
	<pipe>
	  <pipetype>seqfile</pipetype>
	  <language>perl</language>
	  <code>1</code>
	</pipe>
	
      </attributes>
    </parameter>
    
    
  </parameters>
</pise>
