/var/lib/mobyle/programs/rnaeval.xml is in mobyle-programs 5.1.2-2.
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<!-- 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>rnaeval</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/ViennaRNA_package.xml"/>
<doc>
<title>RNAeval</title>
<description>
<text lang="en">Calculate energy of RNA sequences on given secondary structure</text>
</description>
<authors>Hofacker, Stadler</authors>
<reference>I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994) Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f. Chemie 125: 167-188</reference>
<doclink>http://www.tbi.univie.ac.at/RNA/RNAeval.html</doclink>
<comment>
<text lang="en">RNAeval evaluates the free energy of an RNA molecule in fixed secondary structure.</text>
</comment>
</doc>
<category>sequence:nucleic:2D_structure</category>
<category>structure:2D_structure</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>rnaeval</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"RNAeval"</code>
<code proglang="python">"RNAeval"</code>
</format>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>seqstruct</name>
<prompt lang="en">Sequences/Structures File</prompt>
<type>
<datatype>
<class>RNAStructure</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">" < $value" </code>
<code proglang="python">" < " + str(value) </code>
</format>
<comment>
<text lang="en">Sequences and structures are read alternately from stdin.
The energy in Kcal/Mol is written to stdout.
The program will continue to read new sequences and structures until a line
consisting of the single character "@" or an end of file condition is encountered.
If the input sequence or structure contains the separator character "&" the program
calculates the energy of the co-folding of two RNA strands, where the "&" marks the
boundary between the two strands.</text>
</comment>
<example>
ACGAUCAGAGAUCAGAGCAUACGACAGCAG
..((((...))))...((........))..
UUUUUUUAAUAUAAA&AGACAAAAAGUCGGG
.(.(.(()).).)..&.(((.....)))...
@
</example>
<argpos>1000</argpos>
</parameter>
<paragraph>
<name>others_options</name>
<prompt lang="en">Other options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>temperature</name>
<prompt lang="en">Rescale energy parameters to a temperature of temp C. (-T)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>37.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -T $value" : ""</code>
<code proglang="python">( "" , " -T " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>tetraloops</name>
<prompt lang="en">Do not include special stabilizing energies for certain tetraloops (-4)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -4" : ""</code>
<code proglang="python">( "" , " -4" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>dangling</name>
<prompt lang="en">How to treat dangling end energies for bases adjacent to helices in free ends and multiloops (-d)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>-d1</value>
</vdef>
<vlist>
<velem>
<value>-d1</value>
<label>Only unpaired bases can participate in at most one dangling end (-d1)</label>
</velem>
<velem>
<value>-d</value>
<label>Ignores dangling ends altogether (-d)</label>
</velem>
<velem>
<value>-d2</value>
<label>The check is ignored, this is the default for partition function folding (-d2)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">How to treat 'dangling end' energies for bases adjacent to helices in free
ends and multiloops: Normally only unpaired bases can participate in at most one dangling end.
</text>
<text lang="en">
-d Do not give stabilizing energies to unpaired bases adjacent to helices in
multiloops and free ends ("dangling ends"). Same as -d0, opposite of -d1
(the default).
</text>
<text lang="en">
-d2 Treat dangling ends as in the partition function algorithm, i.e. bases adjacent
to helices in multiloops and free ends give a stabilizing energy contribution,
regardless whether they're paired or unpaired.
</text>
<text lang="en">
-d3 Allow coaxial stacking of adjacent helices in multi-loops.
</text>
</comment>
</parameter>
<parameter>
<name>logML</name>
<prompt lang="en">Let multiloop energies depend logarithmically on the size (-logML)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -logML" : ""</code>
<code proglang="python">( "" , " -logML" )[ value ]</code>
</format>
<comment>
<text lang="en">Let multiloop energies depend logarithmically on the size,
instead of the usual linear energy function.</text>
</comment>
</parameter>
<parameter>
<name>circular</name>
<prompt lang="en">-circ Assume a cricular (rather than linear) RNA molecule.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -circ" : ""</code>
<code proglang="python">( "" , " -circ" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>parameter</name>
<prompt lang="en">Energy parameter file (-P)</prompt>
<type>
<datatype>
<class>EnergyParameterFile</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -P $value" : ""</code>
<code proglang="python">( "" , " -P " + str(value) )[ value is not None ]</code>
</format>
<comment>
<p xmlns="http://www.w3.org/1999/xhtml">Read energy parameters from paramfile, instead of using the default parameter set.
<a target="ParamFile" href="http://www.tbi.univie.ac.at/~ivo/RNA/RNAlib/Param-Files.html">( documentation for details on the file format.)</a>
</p>
</comment>
</parameter>
<!-- core dumped
<parameter>
<name>energy</name>
<prompt lang="en">Energy parameters for the artificial ABCD... alphabet (-e)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>Null</value>
</vdef>
<vlist>
<velem undef="1">
<value>Null</value>
<label>No energy for the artificial ABCD</label>
</velem>
<velem>
<value>1</value>
<label>Use energy parameters for GC pairs (1)</label>
</velem>
<velem>
<value>2</value>
<label>Use energy parameters for AU pairs (2)</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value)? " -e $value" : ""</code>
<code proglang="python">( "" , " -e " + str(value) )[ value is not None ]</code>
</format>
</parameter>
-->
<paragraph>
<name>output_options</name>
<prompt lang="en">Output options</prompt>
<parameters>
<parameter>
<name>verbose</name>
<prompt lang="en"> Print out energy contribution of each loop in the structure.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -v ": ""</code>
<code proglang="python">( "" , " -v ")[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
</parameters>
</program>
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