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

<pise>

  <head>
    <title>CODNOCOD</title>
    <description>outputs feature from Genbank entries</description>
  </head>


<command>codnocod</command>

<parameters>

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

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

</attributes>
</parameter>

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

	<prompt>Genbank sequence File</prompt>
	<format>
		<language>perl</language>
		<code>" $value"</code>
	</format>
	<group>2</group>
	<seqfmt>
		<value>2</value>
	</seqfmt>
	<pipe>
		<pipetype>gb_seq</pipetype>
			<language>perl</language>
			<code>1</code>
	</pipe>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>length</name>
<attributes>

	<prompt>Length (-l)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -l" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>definition</name>
<attributes>

	<prompt>DEFINITION (-d)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -d" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>accession</name>
<attributes>

	<prompt>ACCESSION (-a)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -a" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>nid</name>
<attributes>

	<prompt>NID (-N)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -N" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>organism</name>
<attributes>

	<prompt>ORGANISM (-o)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -o" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>cds_dna</name>
<attributes>

	<prompt>Coding sequence - dna (-c)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -c" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>cds_aa</name>
<attributes>

	<prompt>Coding sequence - aa (-C)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -C" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>cinq</name>
<attributes>

	<prompt>5' sequence (-f)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -f" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>trois</name>
<attributes>

	<prompt>3' sequence (-t)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -t" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>exon_list</name>
<attributes>

	<prompt>Exon list (-e)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -e" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>exon_sequences</name>
<attributes>

	<prompt>Exon sequences (-E)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -E" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>intron_sequences</name>
<attributes>

	<prompt>Intron sequences (-I)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -I" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>all_sequences</name>
<attributes>

	<prompt>All sequences (-A)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -A" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>

</attributes>
</parameter>

<parameter issimple="1" type="Switch">
<name>srs</name>
<attributes>

	<prompt>Entries retrieved using SRS (-S)</prompt>
	<format>
		<language>perl</language>
		<code> ($value)? " -S" : "" </code>
	</format>
	<vdef><value>0</value></vdef>
	<group>1</group>
	<comment>
		<value>no ORIGIN line and sequence is numbered on the right</value>
	</comment>

</attributes>
</parameter>


</parameters>
</pise>
