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

<pise>

<head>
<title>DICHET</title>
<description>Parse dictionary of heterogen groups (EMBOSS)</description>
<category>protein:3d structure</category>
<doclink>http://bioweb.pasteur.fr/docs/EMBOSS/dichet.html</doclink>
</head>

<command>dichet</command>

<parameters>

&emboss_init;


<parameter type="Paragraph">
<paragraph>
<name>input</name>
	<prompt>input Section</prompt>

<parameters>
	<parameter type="InFile" ismandatory="1" issimple="1" ishidden="0">
	<name>inf</name>
	<attributes>
		<prompt>Name of raw input file (dictionary of heterogen groups) (-inf)</prompt>
		<format>
			<language>perl</language>
			<code>" -inf=$value"</code>
		</format>
		<group>1</group>
	</attributes>
	</parameter>

	</parameters>
</paragraph>
</parameter>


<parameter type="Paragraph">
<paragraph>
<name>required</name>
	<prompt>required Section</prompt>

<parameters>
	<parameter type="Switch" ismandatory="0" issimple="0" ishidden="0">
	<name>dogrep</name>
	<attributes>
		<prompt>Search a directory of files with keywords? (-dogrep)</prompt>
		<vdef>
			<value>0</value>
		</vdef>
		<format>
			<language>perl</language>
			<code>($value)? " -dogrep" : ""</code>
		</format>
		<group>2</group>
	</attributes>
	</parameter>

	</parameters>
</paragraph>
</parameter>


<parameter type="Paragraph">
<paragraph>
<name>output</name>
	<prompt>output Section</prompt>

<parameters>
	<parameter type="OutFile" ismandatory="1" issimple="1" ishidden="0">
	<name>outf</name>
	<attributes>
		<prompt>Name of output file (-outf)</prompt>
		<vdef><value>outf.out</value></vdef>
		<format>
			<language>perl</language>
			<code>" -outf=$value"</code>
		</format>
		<group>3</group>
	</attributes>
	</parameter>

	</parameters>
</paragraph>
</parameter>


<parameter type="Paragraph">
<paragraph>
<name>advanced</name>
	<prompt>advanced Section</prompt>

<parameters>
	<parameter type="String" ismandatory="0" issimple="0" ishidden="0">
	<name>path</name>
	<attributes>
		<prompt>Directory to search with keywords (-path)</prompt>
			<precond>
				<language>perl</language>
				<code>$dogrep</code>
				<language>acd</language>
				<code>$dogrep</code>
			</precond>
		<vdef>
			<value>./</value>
		</vdef>
		<format>
			<language>perl</language>
			<code>($value &amp;&amp; $value ne $vdef)? " -path=$value" : ""</code>
		</format>
		<group>4</group>
	</attributes>
	</parameter>

	<parameter type="String" ismandatory="0" issimple="0" ishidden="0">
	<name>extn</name>
	<attributes>
		<prompt>Exension of files to search in above directory (-extn)</prompt>
			<precond>
				<language>perl</language>
				<code>$dogrep</code>
				<language>acd</language>
				<code>$dogrep</code>
			</precond>
		<vdef>
			<value>.ent</value>
		</vdef>
		<format>
			<language>perl</language>
			<code>($value &amp;&amp; $value ne $vdef)? " -extn=$value" : ""</code>
		</format>
		<group>5</group>
	</attributes>
	</parameter>

	</parameters>
</paragraph>
</parameter>

<parameter type="String" ishidden="1">
<name>auto</name>
<attributes>
	<format>
		<language>perl</language>
		<code>" -auto -stdout"</code>
	</format>
	<group>6</group>
</attributes>
</parameter>

</parameters>
</pise>
