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

<pise>

<head>
<title>SIGPLOT</title>
<description>Generates gnuplot data files of signature performance (EMBOSS)</description>
<category>protein:3d structure</category>
<doclink>http://bioweb.pasteur.fr/docs/EMBOSS/sigplot.html</doclink>
</head>

<command>sigplot</command>

<parameters>

&emboss_init;

<parameter type="InFile" ismandatory="1" issimple="1" ishidden="0">
<name>hitsin</name>
<attributes>
	<prompt>Name of signature hits file for input (-hitsin)</prompt>
	<format>
		<language>perl</language>
		<code>" -hitsin=$value"</code>
	</format>
	<group>1</group>
</attributes>
</parameter>

<parameter type="OutFile" ismandatory="1" issimple="1" ishidden="0">
<name>datafile</name>
<attributes>
	<prompt>Name of gnuplot data file for output (-datafile)</prompt>
	<vdef>
		<value>my.dat</value>
	</vdef>
	<format>
		<language>perl</language>
		<code>" -datafile=$value"</code>
	</format>
	<group>2</group>
</attributes>
</parameter>

<parameter type="String" ismandatory="1" issimple="1" ishidden="0">
<name>true</name>
<attributes>
	<prompt>Name of data file for true hits (-true)</prompt>
	<vdef>
		<value>my_true.dat</value>
	</vdef>
	<format>
		<language>perl</language>
		<code>" -true=$value"</code>
	</format>
	<group>3</group>
</attributes>
</parameter>

<parameter type="String" ismandatory="1" issimple="1" ishidden="0">
<name>false</name>
<attributes>
	<prompt>Name of data file for false hits (-false)</prompt>
	<vdef>
		<value>my_false.dat</value>
	</vdef>
	<format>
		<language>perl</language>
		<code>" -false=$value"</code>
	</format>
	<group>4</group>
</attributes>
</parameter>

<parameter type="String" ismandatory="1" issimple="1" ishidden="0">
<name>cross</name>
<attributes>
	<prompt>Name of data file for cross hits (-cross)</prompt>
	<vdef>
		<value>my_cross.dat</value>
	</vdef>
	<format>
		<language>perl</language>
		<code>" -cross=$value"</code>
	</format>
	<group>5</group>
</attributes>
</parameter>

<parameter type="String" ismandatory="1" issimple="1" ishidden="0">
<name>unknown</name>
<attributes>
	<prompt>Name of data file for unknown hits (-unknown)</prompt>
	<vdef>
		<value>my_unknown.dat</value>
	</vdef>
	<format>
		<language>perl</language>
		<code>" -unknown=$value"</code>
	</format>
	<group>6</group>
</attributes>
</parameter>

<parameter type="String" ishidden="1">
<name>auto</name>
<attributes>
	<format>
		<language>perl</language>
		<code>" -auto -stdout"</code>
	</format>
	<group>7</group>
</attributes>
</parameter>

</parameters>
</pise>
