/var/lib/mobyle/programs/rnaplfold.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>rnaplfold</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/ViennaRNA_package.xml"/>
<doc>
<title>RNAplfold</title>
<description>
<text lang="en">Compute average pair probabilities for local base pairs in long sequences</text>
</description>
<authors>Stephan H Bernhart, Ivo L Hofacker, Peter F Stadler.</authors>
<reference>S. H. Bernhart, I.L. Hofacker, and P.F. Stadler (2006) "Local Base Pairing Probabilities in Large RNAs" Bioinformatics 22: 614-615</reference>
<reference>A.F. Bompfunewerer, R. Backofen, S.H. Bernhart, J. Hertel, I.L. Hofacker, P.F. Stadler, S. Will (2007) "Variations on {RNA} Folding and Alignment: Lessons from Benasque" J. Math. Biol.</reference>
<comment>
<text lang="en">RNAplfold computes local pair probabilities for base pairs with a maximal span of L. The probabilities are averaged over all windows of size L that contain the base pair. </text>
<text lang="en">Output consists of a dot plot in postscript file, where the averaged pair probabilities can easily be parsed and visually inspected.</text>
</comment>
</doc>
<category>sequence:nucleic:2D_structure</category>
<category>structure:2D_structure</category>
<command>RNAplfold</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seq</name>
<prompt lang="en">RNA Sequence File</prompt>
<type>
<biotype>RNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" < $value" </code>
<code proglang="python">" < " + str(value) </code>
</format>
<argpos>1000</argpos>
</parameter>
<paragraph>
<name>control</name>
<prompt lang="en">Control options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>winsize</name>
<prompt lang="en">Size of windows for average pair probabilities. (-W)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>70</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -W $value" : ""</code>
<code proglang="python">( "" , " -W " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>span</name>
<prompt lang="en">Allow only pairs (i,j) with j-i<=span. (-L)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value and $value <= $winsize)? " -L $value" : ""</code>
<code proglang="python">( "" , " -L " + str(value) )[ value is not None and value <= winsize ]</code>
</format>
</parameter>
<parameter>
<name>cutoff</name>
<prompt lang="en">Report only base pairs with an average probability > cutoff. (-c)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.01</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>
</parameter>
<parameter>
<name>width</name>
<prompt lang="en">Length to compute the mean probability of unpaired base. (-u)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -u $value" : ""</code>
<code proglang="python">( "" , " -u " + str(value) )[ value is not None]</code>
</format>
</parameter>
<parameter>
<name>temperature</name>
<prompt lang="en">Rescale energy parameters to a temperature of temperature Celcius (-T)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>37</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)? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">How to treat 'dangling end' energies for bases adjacent to helices in free ends and multiloops: Normally only unpaired bases can participate in at most one dangling end. With -d2 this check is ignored, this is the default for partition function folding (-p). -d ignores dangling ends altogether. Note that by default pf and mfe folding treat dangling ends differently, use -d2 (or -d) in addition to -p to ensure that both algorithms use the same energy model. The -d2 options is available for RNAfold, RNAeval, and RNAinverse only.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>input</name>
<prompt lang="en">Input parameters</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>noGU</name>
<prompt lang="en">Do not allow GU pairs (-noGU)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -noGU" : ""</code>
<code proglang="python">( "" , " -noGU" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>noCloseGU</name>
<prompt lang="en">Do not allow GU pairs at the end of helices (-noCloseGU)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -noCloseGU" : ""</code>
<code proglang="python">( "" , " -noCloseGU" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>nsp</name>
<prompt lang="en">Non standard pairs (comma seperated list) (-nsp)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -nsp $value" : "" </code>
<code proglang="python">( "" , " -nsp " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Allow other pairs in addition to the usual AU,GC,and GU pairs. pairs is a comma seperated list of additionally allowed pairs. If a the first character is a '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy.</text>
</comment>
</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>
<text lang="en">Read energy parameters from paramfile, instead of using the default parameter set. A sample parameterfile should accompany your distribution. See the RNAlib documentation for details on the file format.</text>
</comment>
</parameter>
<parameter>
<name>logout</name>
<prompt lang="en">Output is switched from probabilities to their logarithm</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value)? " -O " : ""</code>
<code proglang="python">( "" , " -O " )[ value ]</code>
</format>
<comment>
<text lang="en">Toggles -u option, output is switched from probabilities
to their logarithm, which are NOT exactly the mean energies needed to the respective stretch of bases!
</text>
</comment>
</parameter>
<!-- core dumped on raclette
<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">(defined $value and $value ne $vdef)? " -e $value" : ""</code>
<code proglang="python">( "" , " -e " + str(value) )[ value is not None and value!=vdef]</code>
</format>
</parameter>
-->
</parameters>
</paragraph>
<parameter ishidden="1">
<name>readseq</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="../../Local/Services/Programs/Env/ViennaRNA_readseq.xml" xpointer="xpointer(/readseq_path/text())"><xi:fallback/></xi:include>readseq -f=19 -a $seq > $seq.tmp && (cp $seq $seq.orig && mv $seq.tmp $seq) ; "</code>
<code proglang="python">"<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="../../Local/Services/Programs/Env/ViennaRNA_readseq.xml" xpointer="xpointer(/readseq_path/text())"><xi:fallback/></xi:include>readseq -f=19 -a "+ str(seq) + " > "+ str(seq) +".tmp && (cp "+ str(seq) +" "+ str(seq) +".orig && mv "+ str(seq) +".tmp "+ str(seq) +") ; "</code>
</format>
<argpos>-10</argpos>
</parameter>
<parameter isout="1">
<name>psfiles</name>
<prompt>Postscript file</prompt>
<type>
<datatype>
<class>PostScript</class>
<superclass>Binary</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.ps"</code>
<code proglang="python">"*.ps"</code>
</filenames>
</parameter>
</parameters>
</program>
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