<?xml version="1.0" encoding="ISO-8859-1" ?>
<!DOCTYPE pise SYSTEM "PARSER/pise.dtd">

<pise>

<head>
    <title>AMPS</title>
    <version>2.1</version>
    <description>Alignment of Multiple Protein Sequences</description>
    <authors>Barton, Sternberg</authors>
    <reference>Barton, G. J. and Sternberg, M. J. E. (1987b). J. Mol. Biol. 198, 327-337.</reference>
</head>


<command>amps</command>

<parameters>

<parameter iscommand="1" ishidden="1" type="String">
<name>amps</name>
<attributes>

	<format>
		<language>perl</language>
		<code>"ln -s $infile infile.seq; runamps infile"</code>
	</format>
	<group>0</group>

</attributes>
</parameter>

<parameter type="Results">
<name>ps_files</name>
<attributes>

	<filenames>infile_*.ps</filenames>

</attributes>
</parameter>

<parameter type="Results">
<name>blc_files</name>
<attributes>

	<filenames>infile_*.blc</filenames>
	<pipe>
		<pipetype>amps_blc_file</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>

<parameter type="Results">
<name>com_files</name>
<attributes>

	<filenames>infile_*.com</filenames>

</attributes>
</parameter>

<parameter type="Results">
<name>out_files</name>
<attributes>

	<filenames>infile_*.out</filenames>

</attributes>
</parameter>

<parameter type="Results">
<name>tree_files</name>
<attributes>

	<filenames>infile_*.tree</filenames>

</attributes>
</parameter>

<parameter type="Results">
<name>tord_files</name>
<attributes>

	<filenames>infile_*.tord</filenames>

</attributes>
</parameter>

<parameter ismandatory="1" issimple="1" type="Sequence">
<name>infile</name>
<attributes>

	<prompt>Sequences File</prompt>
	<format>
		<language>perl</language>
		<code> ""</code>
	</format>
	<group>1</group>
	<seqfmt>
		<value>3</value>
	</seqfmt>
	<pipe>
		<pipetype>amps_seqsfile</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>


</parameters>
</pise>
