Mercurial > repos > rnateam > viennarna_kinfold

annotate kinfold.xml @ 0:4d663689cd7f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
author rnateam
date Tue, 06 Dec 2016 12:35:17 -0500
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4d663689cd7f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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1 <tool id="viennarna_kinfold" name="@EXECUTABLE@" version="1.3.0.0">
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2 <description>Simulates the stochastic folding kinetics of RNA sequences into secondary structures.</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">Kinfold</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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12 Kinfold < '$input'
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13 -T$Temp
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14 --dangle=$dangle
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15 $logML
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16 $move_set_options.noShift
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17 $move_set_options.noLP
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18 --num=$simulation_options.num
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19 --time=$simulation_options.time
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20 --grow=$simulation_options.grow
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21 --glen=$simulation_options.glen
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22 $simulation_options.fpt
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23 $simulation_options.met
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24 $output_options.lmin
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25 --cut=$output_options.cut
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26 > '$output'
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27 && cat *.log > '$log'
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28 ]]>
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29 </command>
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30
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31 <inputs>
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32 <param format="*" name="input" type="data" label="Fasta file"/>
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33 <param argument="--Temp" type="float" value="37.0" label="temperature [°C]"/>
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34 <param argument="--dangle" type="select" label="how to treat dangling end energies">
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35 <option value="0">0: none</option>
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36 <option value="2" selected="true">2: double</option>
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37 <option value="1">1: normal</option>
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38 </param>
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39 <param argument="--logML" type="boolean" truevalue="--logML" falsevalue="" checked="false" label="Logarithmic energy functions for multi-loops"/>
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40
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41 <section name="move_set_options" title="Move set options">
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42 <param argument="--noShift" type="boolean" truevalue="" falsevalue="--noShift" checked="true" label="Turn on shift moves."/>
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43 <param argument="--noLP" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow structures containing isolated base-pairs"/>
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44 </section>
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45
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46 <section name="simulation_options" title="Simulation options" >
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47 <param argument="--num" type="integer" value="1" label="Number of trajectories to compute" help="" optional="true"/>
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48 <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"/>
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49 <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"/>
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50 <param argument="--glen" type="integer" value="15" label="Start a folding during transcription simulation with an inital chain length of len." help="" optional="true" />
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51 <param argument="--fpt" type="boolean" truevalue="--fpt" falsevalue="" checked="true" label="compute first passage time" help="stop when a stop-structure is reached"/>
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52 <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)."/>
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53 </section>
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54
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55 <section name="output_options" title="Output Options">
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56 <param argument="--lmin" type="boolean" truevalue="--lmin" falsevalue="" checked="false" label="Don’t print complete trajectory, but only local minimas encountered" help=""/>
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57 <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"/>
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58 </section>
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59
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60 </inputs>
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61 <outputs>
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62 <data format="txt" name="output"/>
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63 <data format="log" name="log"/>
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="input" value="kinfold_input.txt"/>
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68 <output name="output">
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69 <assert_contents>
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70 <has_text text="..............." />
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71 </assert_contents>
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72 </output>
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73 </test>
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74 </tests>
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75 <help>
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76 <![CDATA[
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77
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78 **Kinfold**
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79
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80 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.
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81
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82 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.
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83
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84 -----
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85
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86 **Input format**
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87
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88 Input consists of an RNA sequence, optionally followed by the initial structure and one or more stop structures in dot−bracket notation.
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89
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90 ------
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91
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92 **Outputs**
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93
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94 - Trajecotires:
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95
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96 The trajectory lists stucture, energy, and time for each simulation step. The X1 signifies that the trajectory terminated in the first stop structure
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97
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98 - A log file containing summary information for each trajectory:
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99
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100 The logfile would contain information needed to reproduce the simulation results such as options and random seeds used.
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101 ]]>
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102 </help>
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103 <expand macro="citations" />
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104 </tool>