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

<pise>

<head>
<title>SIGCLEAVE</title>
<description>Reports protein signal cleavage sites (EMBOSS)</description>
<category>protein:motifs</category>
<doclink>http://bioweb.pasteur.fr/docs/EMBOSS/sigcleave.html</doclink>
</head>

<command>sigcleave</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>sequence</name>
	<attributes>
		<prompt>sequence -- PureProtein [sequences] (-sequence)</prompt>
		<format>
			<language>perl</language>
			<code>" -sequence=$value -sformat=fasta"</code>
		</format>
		<group>1</group>
		<seqtype><value>pureprotein</value></seqtype>
		<seqfmt>
			<value>8</value>
		</seqfmt>
		<pipe>
			<pipetype>seqsfile</pipetype>
				<language>perl</language>
				<code>1</code>
		</pipe>
	</attributes>
	</parameter>

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


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

<parameters>
	<parameter type="Float" ismandatory="1" issimple="1" ishidden="0">
	<name>minweight</name>
	<attributes>
		<prompt>Minimum weight (-minweight)</prompt>
		<vdef>
			<value>3.5</value>
		</vdef>
		<format>
			<language>perl</language>
			<code>" -minweight=$value"</code>
		</format>
		<group>2</group>
		<comment>
			<value>Minimum scoring weight value for the predicted cleavage site</value>
		</comment>
		<scalemin><value>0.</value></scalemin>
		<scalemax><value>100.</value></scalemax>
	</attributes>
	</parameter>

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


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

<parameters>
	<parameter type="Switch" ismandatory="0" issimple="0" ishidden="0">
	<name>prokaryote</name>
	<attributes>
		<prompt>Use prokaryotic cleavage data (-prokaryote)</prompt>
		<format>
			<language>perl</language>
			<code>($value)? " -prokaryote" : ""</code>
		</format>
		<group>3</group>
		<comment>
			<value>Specifies the sequence is prokaryotic and changes the default scoring data file name</value>
		</comment>
	</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>4</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>
