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

<pise>

<head>
<title>QATEST</title>
<description>ACD file for QA testing (EMBOSS)</description>
<category>test</category>
<doclink>http://bioweb.pasteur.fr/docs/EMBOSS/qatest.html</doclink>
</head>

<command>qatest</command>

<parameters>

&emboss_init;

<parameter type="Sequence" ismandatory="1" issimple="1" ishidden="0">
<name>asequence</name>
<attributes>
	<prompt>asequence [single sequence] (-asequence)</prompt>
	<format>
		<language>perl</language>
		<code>" -asequence=$value -sformat=fasta"</code>
	</format>
	<group>1</group>
	<seqtype><value></value></seqtype>
	<seqfmt>
		<value>8</value>
	</seqfmt>
</attributes>
</parameter>

<parameter type="Sequence" ismandatory="1" issimple="1" ishidden="0">
<name>bsequence</name>
<attributes>
	<prompt>bsequence [single sequence] (-bsequence)</prompt>
	<format>
		<language>perl</language>
		<code>" -bsequence=$value -sformat=fasta"</code>
	</format>
	<group>2</group>
	<seqtype><value></value></seqtype>
	<seqfmt>
		<value>8</value>
	</seqfmt>
</attributes>
</parameter>

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

<parameter type="Integer" ismandatory="0" issimple="0" ishidden="0">
<name>aint</name>
<attributes>
	<prompt>first integer (-aint)</prompt>
	<format>
		<language>perl</language>
		<code>($value)? " -aint=$value" : ""</code>
	</format>
	<group>4</group>
</attributes>
</parameter>

<parameter type="Integer" ismandatory="0" issimple="0" ishidden="0">
<name>bint</name>
<attributes>
	<prompt>second integer (-bint)</prompt>
	<vdef>
		<value>57</value>
	</vdef>
	<format>
		<language>perl</language>
		<code>(defined $value &amp;&amp; $value != $vdef)? " -bint=$value" : ""</code>
	</format>
	<group>5</group>
</attributes>
</parameter>

<parameter type="String" ismandatory="0" issimple="0" ishidden="0">
<name>testalen</name>
<attributes>
	<prompt>asequence length $asequence.length (-testalen)</prompt>
	<format>
		<language>perl</language>
		<code>($value)? " -testalen=$value" : ""</code>
	</format>
	<group>6</group>
</attributes>
</parameter>

<parameter type="String" ismandatory="0" issimple="0" ishidden="0">
<name>testblen</name>
<attributes>
	<prompt>bsequence length $bsequence.length (-testblen)</prompt>
	<format>
		<language>perl</language>
		<code>($value)? " -testblen=$value" : ""</code>
	</format>
	<group>7</group>
</attributes>
</parameter>

<parameter type="String" ishidden="1">
<name>auto</name>
<attributes>
	<format>
		<language>perl</language>
		<code>" -auto -stdout"</code>
	</format>
	<group>8</group>
</attributes>
</parameter>

</parameters>
</pise>
