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<?xml version='1.0' encoding='UTF-8'?>
<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>xpound</name>
<doc>
<title>Xpound</title>
<description>
<text lang="en">Software for exon trapping</text>
</description>
<authors>Thomas and Skolnick</authors>
<reference>A probabilistic model for detecting coding regions in DNA sequences. Alun Thomas and Mark H Skolnick, IMA Journal of Mathematics Applied in Medicine and Biology, 1994, 11, 149-160.</reference>
</doc>
<category>sequence:nucleic:gene_finding</category>
<command>xpound</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seq</name>
<prompt lang="en">DNA sequence File</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>RAW</dataFormat>
<card>1,1</card>
</type>
<format>
<code proglang="perl">" <$value"</code>
<code proglang="python">" <"+str(value)</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">Everything after a % on a line in the input
file is ignored. Other than comment xpound expects only white
space, which is also ignored, or IUPAC characters:</text>
<text lang="en">A C M G R S V T W Y H K D B N</text>
<text lang="en">in upper or lower case. Characters which do
not uniquely determine a base, such as N, B, S and so on, are
all interpreted as a C.</text>
<text lang="en">Xpound will not accept the IUPAC character -,
all occurences of which should be stripped from the input file
beforehand.</text>
</comment>
</parameter>
<parameter isstdout="1">
<name>outfile</name>
<prompt lang="en">Output file</prompt>
<type>
<datatype>
<class>XpoundReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"xpound.out"</code>
<code proglang="python">"xpound.out"</code>
</filenames>
</parameter>
<paragraph>
<name>report_options</name>
<prompt lang="en">Report options</prompt>
<parameters>
<parameter>
<name>report</name>
<prompt lang="en">Reports regions of bases for which the probability of coding is high (xreport)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? " ; xreport <xpound.out " : ""</code>
<code proglang="python">( "" , " ; xreport <xpound.out " )[ value ]</code>
</format>
<argpos>20</argpos>
</parameter>
<parameter>
<name>cut_off</name>
<prompt lang="en">Cut off value for report</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$report</code>
<code proglang="python">report</code>
</precond>
<vdef>
<value>0.75</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " $value " : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>21</argpos>
</parameter>
<parameter>
<name>min_length</name>
<prompt lang="en">Minimum length value for report</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$report</code>
<code proglang="python">report</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " $value " : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>22</argpos>
</parameter>
<parameter isout="1">
<name>report_file</name>
<prompt lang="en">Report file</prompt>
<type>
<datatype>
<class>XreportReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$report</code>
<code proglang="python">report</code>
</precond>
<format>
<code proglang="perl">" >xreport.out "</code>
<code proglang="python">">xreport.out "</code>
</format>
<argpos>25</argpos>
<filenames>
<code proglang="perl">"xreport.out"</code>
<code proglang="python">"xreport.out"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>postscript_options</name>
<prompt lang="en">Postscript options</prompt>
<parameters>
<parameter>
<name>postscript</name>
<prompt lang="en">Produces a file of graphs in PostScript format (xpscript)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "; xpscript xpound.out" : ""</code>
<code proglang="python">( "" , "; xpscript xpound.out" )[ value ]</code>
</format>
<argpos>30</argpos>
</parameter>
<parameter>
<name>orientation</name>
<prompt lang="en">Orientation (-l)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$postscript</code>
<code proglang="python">postscript</code>
</precond>
<vdef>
<value>portrait</value>
</vdef>
<vlist>
<velem>
<value>portrait</value>
<label>Portrait</label>
</velem>
<velem>
<value>lanscape</value>
<label>Lanscape</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value eq "lanscape") ? " -l " : ""</code>
<code proglang="python">( "" , " -l " )[ value == "lanscape" ]</code>
</format>
<argpos>31</argpos>
</parameter>
<parameter>
<name>rows</name>
<prompt lang="en">Rows of plots per page (-r)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$postscript</code>
<code proglang="python">postscript</code>
</precond>
<vdef>
<value>5</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -r $value " : ""</code>
<code proglang="python">( "" , " -r " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>32</argpos>
</parameter>
<parameter>
<name>columns</name>
<prompt lang="en">Columns of plots per page (-c)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$postscript</code>
<code proglang="python">postscript</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -c $value " : ""</code>
<code proglang="python">( "" , " -c " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>32</argpos>
</parameter>
<parameter>
<name>high</name>
<prompt lang="en">Draw a line at this level (-hi)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$postscript</code>
<code proglang="python">postscript</code>
</precond>
<vdef>
<value>0.75</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -hi $value " : ""</code>
<code proglang="python">( "" , " -hi " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>33</argpos>
</parameter>
<parameter>
<name>low</name>
<prompt lang="en">Draw a line at this level (-lo)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$postscript</code>
<code proglang="python">postscript</code>
</precond>
<vdef>
<value>0.5</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -lo $value " : ""</code>
<code proglang="python">( "" , " -lo " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>34</argpos>
</parameter>
<parameter isout="1">
<name>psfile</name>
<prompt lang="en">PostScript file</prompt>
<type>
<datatype>
<class>PostScript</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$postscript</code>
<code proglang="python">postscript</code>
</precond>
<format>
<code proglang="perl">" >xpound.ps"</code>
<code proglang="python">" >xpound.ps"</code>
</format>
<argpos>100</argpos>
<filenames>
<code proglang="perl">"xpound.ps"</code>
<code proglang="python">"xpound.ps"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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