/var/lib/mobyle/programs/rnapdist.xml is in mobyle-programs 5.1.1-1.
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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 xmlns:xi="http://www.w3.org/2001/XInclude">
<head>
<name>rnapdist</name>
<xi:include href="Entities/ViennaRNA_package.xml"/>
<doc>
<title>RNApdist</title>
<description>
<text lang="en">Calculate distances between thermodynamic RNA secondary structures ensembles</text>
</description>
<authors>Stadler, Hofacker, Bonhoeffer</authors>
<reference>Bonhoeffer S, McCaskill J S, Stadler P F, Schuster P, (1993) RNA multistructure landscapes, Euro Biophys J:22,13-24</reference>
<comment>
<text lang="en">RNApdist reads RNA sequences from stdin and calculates structure distances between the thermodynamic ensembles of their secondary structures. To do this the partition function and matrix of base pairing probabilities is computed for each sequence. The probability matrix is then condensed into a vector holding for each base the proba-bilities of being unpaired, paired upstream, or paired downstream, respectively. These profiles are compared by a standard alignment algorithm.</text>
</comment>
</doc>
<category>sequence:nucleic:2D_structure</category>
<category>structure:2D_structure</category>
<command>RNApdist</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seq</name>
<prompt lang="en">RNA Sequences File</prompt>
<type>
<biotype>DNA</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>comparison_options</name>
<prompt lang="en">Comparison options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>compare</name>
<prompt lang="en">Which comparisons (-X)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>p</value>
</vdef>
<vlist>
<velem>
<value>p</value>
<label>Pairwise (1st/2nd, 3rd/4th etc) (p)</label>
</velem>
<velem>
<value>m</value>
<label>Distance matrix between all structures (m)</label>
</velem>
<velem>
<value>f</value>
<label>Each structure to the first one (f)</label>
</velem>
<velem>
<value>c</value>
<label>Continuously, that is i-th with (i+1)th structure (c)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -X$value" : ""</code>
<code proglang="python">("", " -X" + str(value) )[value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>alignment_file</name>
<prompt lang="en">Alignment file (-B)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -B $value" : ""</code>
<code proglang="python">("" , " -B " + str(value))[ value is not None ]</code>
</format>
<comment>
<text lang="en">Print an 'alignment' with gaps of the structures, to show matching substructures. </text>
<text lang="en">( ) essentially upstream (downstream) paired bases</text>
<text lang="en">{ } weakly upstream (downstream) paired bases</text>
<text lang="en">| strongly paired bases without preference</text>
<text lang="en">, weakly paired bases without preference</text>
<text lang="en">. essentially unpaired bases.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<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 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)? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">How to treat 'dangling end' energies for bases adjacent to helices in free ends and multiloops: Normally only unpaired bases can participate in at most one dangling end. With -d2 this check is ignored, this is the default for partition function folding (-p). -d ignores dangling ends altogether. Note that by default pf and mfe folding treat dangling ends differently, use -d2 (or -d) in addition to -p to ensure that both algorithms use the same energy model. The -d2 options is available for RNAfold, RNAeval, and RNAinverse only.</text>
</comment>
</parameter>
<parameter>
<name>noGU</name>
<prompt lang="en">Do not allow GU pairs (-noGU)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($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">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>
<!-- 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 != $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 href="../../Local/Services/Programs/Env/ViennaRNA_readseq.xml" xpointer="xpointer(/readseq_path/text())" />readseq -f=19 -a $seq > $seq.tmp && (cp $seq $seq.orig && mv $seq.tmp $seq) ; "</code>
<code proglang="python">"<xi:include href="../../Local/Services/Programs/Env/ViennaRNA_readseq.xml" xpointer="xpointer(/readseq_path/text())" />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 lang="en">Postscript output 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>
<parameter isout="1">
<name>alnoutfile</name>
<prompt lang="en">Result alignment file</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $alignment_file</code>
<code proglang="python">alignment_file is not None</code>
</precond>
<filenames>
<code proglang="perl">"$alignment_file"</code>
<code proglang="python">str(alignment_file)</code>
</filenames>
</parameter>
</parameters>
</program>
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