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update ViennaRNA #1851

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fc77835
add vienna_rna update
bgruening Aug 30, 2026
347fc60
kinwalker fixes
bgruening Aug 30, 2026
c883eeb
fix linting
bgruening Sep 4, 2026
0e36b4c
Apply suggestion from @bgruening
bgruening Sep 4, 2026
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80 changes: 34 additions & 46 deletions tools/rna_tools/vienna_rna/kinfold.xml
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Original file line number Diff line number Diff line change
@@ -1,18 +1,18 @@
<tool id="viennarna_kinfold" name="@EXECUTABLE@" version="1.3.0.0">
<description>Simulates the stochastic folding kinetics of RNA sequences into secondary structures.</description>
<tool id="viennarna_kinfold" name="Kinfold" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>Simulate stochastic folding kinetics of RNA sequences</description>
<macros>
<token name="@EXECUTABLE@">Kinfold</token>
<import>macros.xml</import>
</macros>
<expand macro="requirements" />
<expand macro="stdio" />
<expand macro="version_command" />
<command>
<![CDATA[
<expand macro="xrefs"/>
<expand macro="creator"/>
<expand macro="requirements"/>
<expand macro="version_command"/>
<command detect_errors="aggressive"><![CDATA[
Kinfold < '$input'
-T$Temp
--dangle=$dangle
$logML
$logML
$move_set_options.noShift
$move_set_options.noLP
--num=$simulation_options.num
Expand All @@ -21,84 +21,72 @@
--glen=$simulation_options.glen
$simulation_options.fpt
$simulation_options.met
$output_options.lmin
$output_options.lmin
--cut=$output_options.cut
> '$output'
&& cat *.log > '$log'
]]>
</command>

<inputs>
<param format="txt" name="input" type="data" label="Fasta file"/>
<param argument="--Temp" type="float" value="37.0" label="temperature [°C]"/>
<param argument="--dangle" type="select" label="how to treat dangling end energies">
<param format="txt" name="input" type="data" label="Input file"/>
<param argument="--Temp" type="float" value="37.0" label="Temperature [°C]"/>
<param argument="--dangle" type="select" label="How to treat dangling end energies">
<option value="0">0: none</option>
<option value="2" selected="true">2: double</option>
<option value="1">1: normal</option>
</param>
<param argument="--logML" type="boolean" truevalue="--logML" falsevalue="" checked="false" label="Logarithmic energy functions for multi-loops"/>

<section name="move_set_options" title="Move set options">
<param argument="--noShift" type="boolean" truevalue="" falsevalue="--noShift" checked="true" label="Turn on shift moves."/>
<param argument="--noShift" type="boolean" truevalue="" falsevalue="--noShift" checked="true" label="Turn on shift moves"/>
<param argument="--noLP" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow structures containing isolated base-pairs"/>
</section>

<section name="simulation_options" title="Simulation options" >
<param argument="--num" type="integer" value="1" label="Number of trajectories to compute" help="" optional="true"/>
<param argument="--time" type="float" value="500.0" label="Set maximum length of folding trajectory" help="The default (500) is very short and meant for testing purposes only." optional="true"/>
<param argument="--grow" type="float" value="0" label="Simulate folding during transcription with a chain growth event taking place every rate timesteps." help="" optional="true"/>
<param argument="--glen" type="integer" value="15" label="Start a folding during transcription simulation with an inital chain length of len." help="" optional="true" />
<param argument="--fpt" type="boolean" truevalue="--fpt" falsevalue="" checked="true" label="compute first passage time" help="stop when a stop-structure is reached"/>
<param argument="--met" type="boolean" truevalue="--met" falsevalue="" checked="false" label="Use the Metropolis rule for rate between two neighboring conformations" help="Use the Metropolis rule for rate between two neighboring conformations, i.e. k=min{1,exp(−dE/RT)}. By default Kinfold uses the symmetric Kawasaki rule k=exp(−dE/2RT)."/>
<section name="simulation_options" title="Simulation options">
<param argument="--num" type="integer" value="1" optional="true" label="Number of trajectories to compute"/>
<param argument="--time" type="float" value="500.0" optional="true" label="Set maximum length of folding trajectory" help="The default (500) is very short and meant for testing purposes only."/>
<param argument="--grow" type="float" value="0" optional="true" label="Simulate folding during transcription" help="Chain growth event taking place every rate timesteps."/>
<param argument="--glen" type="integer" value="15" optional="true" label="Initial chain length for transcription simulation"/>
<param argument="--fpt" type="boolean" truevalue="--fpt" falsevalue="" checked="true" label="Compute first passage time" help="Stop when a stop-structure is reached."/>
<param argument="--met" type="boolean" truevalue="--met" falsevalue="" checked="false" label="Use the Metropolis rule for rate between two neighboring conformations" help="Use k=min{1,exp(-dE/RT)}. By default Kinfold uses the symmetric Kawasaki rule k=exp(-dE/2RT)."/>
</section>

<section name="output_options" title="Output Options">
<param argument="--lmin" type="boolean" truevalue="--lmin" falsevalue="" checked="false" label="Don’t print complete trajectory, but only local minimas encountered" help=""/>
<param argument="--cut" type="float" value="20.0" label="Cutoff energy" help="Print only those parts of the trajectory that stays below energy." optional="true"/>
<param argument="--lmin" type="boolean" truevalue="--lmin" falsevalue="" checked="false" label="Print only local minima encountered"/>
<param argument="--cut" type="float" value="20.0" optional="true" label="Cutoff energy" help="Print only those parts of the trajectory that stay below this energy."/>
</section>

</inputs>
<outputs>
<data format="txt" name="output"/>
<data format="log" name="log"/>
<data format="txt" name="output" label="${tool.name} on ${on_string}"/>
<data format="txt" name="log" label="${tool.name} log on ${on_string}"/>
</outputs>
<tests>
<test>
<test expect_num_outputs="2">
<param name="input" value="kinfold_input.txt"/>
<output name="output">
<assert_contents>
<has_text text="..............." />
<has_text text="..............."/>
</assert_contents>
</output>
</test>
</tests>
<help>
<![CDATA[

<help format="markdown"><![CDATA[
**Kinfold**

The program Kinfold simulates the stochastic folding kinetics of RNA sequences into secondary structures. Folding trajectories are simulated using a Monte Carlo procedure using the formation, and dissociation of individual base pairs, and (optionally) the shifting of individual base pairs.
Simulates the stochastic folding kinetics of RNA sequences into secondary structures. Folding trajectories are simulated using a Monte Carlo procedure using the formation and dissociation of individual base pairs, and (optionally) the shifting of individual base pairs.

Note that all times are given in internal units that can be translated into real time only by copmparison with experiment. Very roughly one time step corresponds to about 1e−7 seconds.
Note that all times are given in internal units that can be translated into real time only by comparison with experiment. Very roughly one time step corresponds to about 1e-7 seconds.

-----

**Input format**

Input consists of an RNA sequence, optionally followed by the initial structure and one or more stop structures in dot−bracket notation.
Input consists of an RNA sequence, optionally followed by the initial structure and one or more stop structures in dot-bracket notation.

------
-----

**Outputs**

- Trajecotires:

The trajectory lists stucture, energy, and time for each simulation step. The X1 signifies that the trajectory terminated in the first stop structure

- A log file containing summary information for each trajectory:

The logfile would contain information needed to reproduce the simulation results such as options and random seeds used.
- Trajectories: lists structure, energy, and time for each simulation step
- A log file containing summary information (options and random seeds) for each trajectory
]]>
</help>
<expand macro="citations" />
<expand macro="citations"/>
</tool>
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