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

<pise>

<head>
<title>CUTSEQ</title>
<description>Removes a specified section from a sequence. (EMBOSS)</description>
<category>edit</category>
<doclink>http://bioweb.pasteur.fr/docs/EMBOSS/cutseq.html</doclink>
</head>

<command>cutseq</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 -- gapany [single sequence] (-sequence)</prompt>
		<format>
			<language>perl</language>
			<code>" -sequence=$value -sformat=fasta"</code>
		</format>
		<group>1</group>
		<seqtype><value>gapany</value></seqtype>
		<seqfmt>
			<value>8</value>
		</seqfmt>
		<pipe>
			<pipetype>seqfile</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="Integer" ismandatory="1" issimple="1" ishidden="0">
	<name>from</name>
	<attributes>
		<prompt>Start of region to delete (-from)</prompt>
		<vdef>
			<language>acd</language>
			<code>$sequence.begin</code>
		</vdef>
		<format>
			<language>perl</language>
			<code>" -from=$value"</code>
		</format>
		<group>2</group>
		<comment>
			<value>This is the start position (inclusive) of the section of the sequence that you wish to remove.</value>
		</comment>
		<scalemin>
			<language>acd</language>
			<code>$sequence.begin</code>
		</scalemin>
		<scalemax>
			<language>acd</language>
			<code>$sequence.end</code>
		</scalemax>
	</attributes>
	</parameter>

	<parameter type="Integer" ismandatory="1" issimple="1" ishidden="0">
	<name>to</name>
	<attributes>
		<prompt>End of region to delete (-to)</prompt>
		<vdef>
			<language>acd</language>
			<code>$sequence.end</code>
		</vdef>
		<format>
			<language>perl</language>
			<code>" -to=$value"</code>
		</format>
		<group>3</group>
		<comment>
			<value>This is the end position (inclusive) of the section of the sequence that you wish to remove.</value>
		</comment>
		<scalemin>
			<language>acd</language>
			<code>$from</code>
		</scalemin>
		<scalemax>
			<language>acd</language>
			<code>$sequence.end</code>
		</scalemax>
	</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>seqfile</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>
