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

<pise>

  <head>
    <title>STAMP</title>
    <version>4.2</version>
    <description>pdbseq</description>
    <authors>Russell, Barton</authors>
  </head>

  <command>pdbseq</command>

<parameters>

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

	<format>
		<language>seqlab</language>
		<code>pdbseq</code>
		<language>perl</language>
		<code>"pdbseq"</code>
	</format>
	<group>0</group>

</attributes>
</parameter>

<parameter type="InFile">
<name>domainfile</name>
<attributes>

	<prompt>Domain file (-d)</prompt>
	<format>
		<language>perl</language>
		<code>" -f $value"</code>
	</format>
	<group>1</group>
	<pipe>
		<pipetype>stamp_domains_file</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>

<parameter type="Integer">
<name>min</name>
<attributes>

	<prompt>Minimum sequence length to be output (-min)</prompt>
	<format>
		<language>perl</language>
		<code>(defined $value) ? " -min $value" : ""</code>
	</format>
	<group>2</group>

</attributes>
</parameter>

<parameter type="Integer">
<name>max</name>
<attributes>

	<prompt>Maximum sequence length to be output (-max)</prompt>
	<format>
		<language>perl</language>
		<code>(defined $value) ? " -max $value" : ""</code>
	</format>
	<group>2</group>

</attributes>
</parameter>

<parameter type="Excl">
<name>seqformat</name>
<attributes>

	<prompt>Output format (-format)</prompt>
	<format>
		<language>perl</language>
		<code>($value) ? " -format $value" : ""</code>
	</format>
	<vdef><value>pir</value></vdef>
	<group>2</group>
	<vlist>
		<value>fasta</value>
		<label>fasta</label>
		<value>pir</value>
		<label>Pir/NBRF</label>
	</vlist>

</attributes>
</parameter>

<parameter type="Integer">
<name>tl</name>
<attributes>

	<prompt>Maximum title length (title limit) (-tl)</prompt>
	<format>
		<language>perl</language>
		<code>(defined $value) ? " -tl $value" : ""</code>
	</format>
	<group>2</group>

</attributes>
</parameter>

<parameter type="Switch">
<name>separate</name>
<attributes>

	<prompt>Produce separate files for each domain in the input file (-separate)</prompt>
	<format>
		<language>perl</language>
		<code>($value) ? " -separate" : ""</code>
	</format>
	<group>2</group>

</attributes>
</parameter>

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

<precond>
	<language>perl</language>
	<code>$separate</code>
</precond>
	<filenames>*.seq</filenames>

</attributes>
</parameter>

<parameter ishidden="1" isstandout="1" type="OutFile">
<name>outfile</name>
<attributes>

	<format>
		<language>perl</language>
		<code>""</code>
	</format>
	<vdef><value>"pdbseq.out"</value></vdef>
	<pipe>
		<pipetype>amps_seqsfile</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>


</parameters>
</pise>
