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<?xml version="1.0" encoding="ISO-8859-1"?>
<!-- XML Authors: Corinne Maufrais and Nicolas Joly, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>cpgreport</name>
<package>
<name>EMBOSS</name>
<version>6.3.1</version>
<doc>
<title>EMBOSS</title>
<description>
<text lang="en">European Molecular Biology Open Software Suite</text>
</description>
<authors>Rice,P. Longden,I. and Bleasby, A.</authors>
<reference>EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice,P. Longden,I. and Bleasby, A. Trends in Genetics 16, (6) pp276--277</reference>
<sourcelink>http://emboss.sourceforge.net/download</sourcelink>
<homepagelink>http://emboss.sourceforge.net</homepagelink>
</doc>
</package>
<doc>
<title>cpgreport</title>
<description>
<text lang="en">Identify and report CpG-rich regions in nucleotide sequence(s)</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/cpgreport.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>sequence:nucleic:cpg_islands</category>
<command>cpgreport</command>
</head>
<parameters>
<paragraph>
<name>e_input</name>
<prompt lang="en">Input section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_sequence</name>
<prompt lang="en">sequence option</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>EMBL</dataFormat>
<dataFormat>FASTA</dataFormat>
<dataFormat>GCG</dataFormat>
<dataFormat>GENBANK</dataFormat>
<dataFormat>NBRF</dataFormat>
<dataFormat>CODATA</dataFormat>
<dataFormat>RAW</dataFormat>
<dataFormat>SWISSPROT</dataFormat>
<dataFormat>GFF</dataFormat>
<card>1,n</card>
</type>
<format>
<code proglang="python">("", " -sequence=" + str(value))[value is not None]</code>
</format>
<argpos>1</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_required</name>
<prompt lang="en">Required section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_score</name>
<prompt lang="en">Cpg score (value from 1 to 200)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>17</value>
</vdef>
<format>
<code proglang="python">("", " -score=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 1 is required</text>
</message>
<code proglang="python">value >= 1</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 200 is required</text>
</message>
<code proglang="python">value <= 200</code>
</ctrl>
<argpos>2</argpos>
<comment>
<text lang="en">This sets the score for each CG sequence found. A value of 17 is more sensitive, but 28 has also been used with some success.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<parameter>
<name>e_outfile</name>
<prompt lang="en">Name of the report file</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>cpgreport.e_outfile</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>CpgreportReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="python">e_outfile</code>
</filenames>
</parameter>
<parameter>
<name>e_outfeat</name>
<prompt lang="en">Name of the output feature file (e_outfeat)</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>cpgreport.e_outfeat</value>
</vdef>
<format>
<code proglang="python">("" , " -outfeat=" + str(value))[value is not None]</code>
</format>
<argpos>4</argpos>
<comment>
<text lang="en">File for output features</text>
</comment>
</parameter>
<parameter>
<name>e_offormat_outfeat</name>
<prompt lang="en">Choose the feature output format</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>GFF</value>
</vdef>
<vlist>
<velem>
<value>GFF</value>
<label>Gff</label>
</velem>
<velem>
<value>EMBL</value>
<label>Embl</label>
</velem>
<velem>
<value>SWISSPROT</value>
<label>Swissprot</label>
</velem>
<velem>
<value>NBRF</value>
<label>Nbrf</label>
</velem>
<velem>
<value>CODATA</value>
<label>Codata</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -offormat=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>5</argpos>
</parameter>
<parameter isout="1">
<name>e_outfeat_out</name>
<prompt lang="en">outfeat_out option</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Feature</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>
<ref param="e_offormat_outfeat">
</ref>
</dataFormat>
</type>
<filenames>
<code proglang="python">e_outfeat</code>
</filenames>
</parameter>
</parameters>
</paragraph>
<parameter ishidden="1">
<name>auto</name>
<prompt lang="en">Turn off any prompting</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">" -auto -stdout"</code>
</format>
<argpos>6</argpos>
</parameter>
</parameters>
</program>
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