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

<pise>

<head>
<title>SKIPSEQ</title>
<description>Reads and writes (returns) sequences, skipping the first few (EMBOSS)</description>
<category>edit</category>
<doclink>http://bioweb.pasteur.fr/docs/EMBOSS/skipseq.html</doclink>
</head>

<command>skipseq</command>

<parameters>

&emboss_init;


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

<parameters>
	<parameter type="Switch" ismandatory="0" issimple="0" ishidden="0">
	<name>feature</name>
	<attributes>
		<prompt>Use feature information (-feature)</prompt>
		<format>
			<language>perl</language>
			<code>($value)? " -feature" : ""</code>
		</format>
		<group>1</group>
	</attributes>
	</parameter>

	<parameter type="Sequence" ismandatory="1" issimple="1" ishidden="0">
	<name>sequence</name>
	<attributes>
		<prompt>sequence -- gapany [sequences] (-sequence)</prompt>
		<format>
			<language>perl</language>
			<code>" -sequence=$value -sformat=fasta"</code>
		</format>
		<group>2</group>
		<seqtype><value>gapany</value></seqtype>
		<seqfmt>
			<value>8</value>
		</seqfmt>
		<pipe>
			<pipetype>seqsfile</pipetype>
				<language>perl</language>
				<code>1</code>
		</pipe>
	</attributes>
	</parameter>

	<parameter type="Integer" ismandatory="0" issimple="0" ishidden="0">
	<name>skip</name>
	<attributes>
		<prompt>Number of sequences to skip at start (-skip)</prompt>
		<vdef>
			<value>0</value>
		</vdef>
		<format>
			<language>perl</language>
			<code>(defined $value &amp;&amp; $value != $vdef)? " -skip=$value" : ""</code>
		</format>
		<group>3</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>outseq</name>
	<attributes>
		<prompt>outseq (-outseq)</prompt>
		<vdef><value>outseq.out</value></vdef>
		<format>
			<language>perl</language>
			<code>" -outseq=$value"</code>
		</format>
		<group>4</group>
		<pipe>
			<pipetype>seqsfile</pipetype>
				<language>perl</language>
				<code>1</code>
		</pipe>
	</attributes>
	</parameter>

	<parameter type="Excl" issimple="1">
	<name>outseq_sformat</name>
	<attributes>
		<prompt>Output format for: outseq</prompt>
		<vlist>
			<value>fasta</value>
			<label>fasta</label>
			<value>gcg</value>
			<label>gcg</label>
			<value>phylip</value>
			<label>phylip</label>
			<value>embl</value>
			<label>embl</label>
			<value>swiss</value>
			<label>swiss</label>
			<value>ncbi</value>
			<label>ncbi</label>
			<value>nbrf</value>
			<label>nbrf</label>
			<value>genbank</value>
			<label>genbank</label>
			<value>ig</value>
			<label>ig</label>
			<value>codata</value>
			<label>codata</label>
			<value>strider</value>
			<label>strider</label>
			<value>acedb</value>
			<label>acedb</label>
			<value>staden</value>
			<label>staden</label>
			<value>text</value>
			<label>text</label>
			<value>fitch</value>
			<label>fitch</label>
			<value>msf</value>
			<label>msf</label>
			<value>clustal</value>
			<label>clustal</label>
			<value>phylip</value>
			<label>phylip</label>
			<value>phylip3</value>
			<label>phylip3</label>
			<value>asn1</value>
			<label>asn1</label>
		</vlist>
		<vdef><value>fasta</value></vdef>
		<format>
			<language>perl</language>
			<code>" -osformat=$value"</code>
		</format>
		<group>5</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>
