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

<pise>

<head>
<title>STSSEARCH</title>
<description>Searches a DNA database for matches with a set of STS primers (EMBOSS)</description>
<category>nucleic:primers</category>
<doclink>http://bioweb.pasteur.fr/docs/EMBOSS/stssearch.html</doclink>
</head>

<command>stssearch</command>

<parameters>

&emboss_init;


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

<parameters>
	<parameter type="Sequence" ismandatory="1" issimple="1" ishidden="0">
	<name>seqall</name>
	<attributes>
		<prompt>seqall -- dna [sequences] (-seqall)</prompt>
		<format>
			<language>perl</language>
			<code>" -seqall=$value -sformat=fasta"</code>
		</format>
		<group>1</group>
		<seqtype><value>dna</value></seqtype>
		<seqfmt>
			<value>8</value>
		</seqfmt>
		<pipe>
			<pipetype>seqsfile</pipetype>
				<language>perl</language>
				<code>1</code>
		</pipe>
	</attributes>
	</parameter>

	<parameter type="InFile" ismandatory="1" issimple="1" ishidden="0">
	<name>primersfile</name>
	<attributes>
		<prompt>Primer file (-primersfile)</prompt>
		<format>
			<language>perl</language>
			<code>" -primersfile=$value"</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>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>

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

<parameter type="String" ishidden="1">
<name>auto</name>
<attributes>
	<format>
		<language>perl</language>
		<code>" -auto -stdout"</code>
	</format>
	<group>4</group>
</attributes>
</parameter>

</parameters>
</pise>
