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

<pise>

  <head>
    <title>html4blast</title>
    <version>1.6</version>
    <description>HTML blast results formatter</description>
    <authors>Nicolas Joly</authors>
  </head>
  
  <command>html4blast</command>
  
  <parameters>
    
    <!-- ** Command ** -->
    <parameter type="String" iscommand="1" ishidden="1">
      <name>html4blast</name>
      <attributes>
	<format>
	  <language>perl</language>
	  <code>html4blast</code>
	</format>
	<group>0</group>
      </attributes>
    </parameter>

    <!-- ** Input file, blast results ** -->
    <parameter type="InFile" ismandatory="1" issimple="1">
      <name>input</name>
      <attributes>
	<prompt>Blast output file</prompt>
	<format>
	  <language>perl</language>
	  <code>" $value"</code>
	</format>
	<group>4</group>
	<pipe>
	  <pipetype>blast_output</pipetype>
	  <language>perl</language>
	  <code>1</code>
	</pipe>
      </attributes>
    </parameter>

    <!-- ** Output file ** -->
    <parameter type="Results">
      <name>output</name>
      <attributes>
	<filenames>blast.html</filenames>
      </attributes>
    </parameter>

    <!-- ** Database links selection ** -->
    <parameter type="Excl">
      <name>links</name>
      <attributes>
	<prompt>Database links</prompt>
	<format>
	  <language>perl</language>
	  <code>($value ne "") ? " $value" : ""</code>
	</format>
	<group>1</group>
	<vlist>
	  <value>-n</value>
	  <label>no links</label>
	  <value></value>
	  <label>efetch links</label>
	  <value>-s</value>
	  <label>Srs links</label>
	  <value>-e</value>
	  <label>external sites links</label>
	</vlist>
      </attributes>
    </parameter>

    <!-- ** Graphical display ** -->
    <parameter type="Switch">
      <name>graph</name>
      <attributes>
	<prompt>Graphical alignment summary</prompt>
	<vdef>
	  <value>1</value>
	</vdef>
	<format>
	  <language>perl</language>
	  <code>($value) ? " -g" : ""</code>
	</format>
	<group>2</group>
      </attributes>
    </parameter>

    <!-- ** Draw one HSP per graphic line -->
    <parameter type="Switch">
      <name>hspline</name>
      <attributes>
	<prompt>Draw one HSP per graphic line</prompt>
	<vdef>
	  <value>0</value>
	</vdef>
	<format>
	  <language>perl</language>
	  <code>($value) ? " -l" : ""</code>
	</format>
	<group>2</group>
      </attributes>
    </parameter>

    <!-- ** Generate query based image names ** -->
    <parameter type="Switch">
      <name>queryimagename</name>
      <attributes>
	<prompt>Generate query based images names</prompt>
	<vdef>
	  <value>0</value>
	</vdef>
	<format>
	  <language>perl</language>
	  <code>($value) ? " -q" : ""</code>
	</format>
	<group>2</group>
      </attributes>
    </parameter>

  </parameters>

</pise>
