annotate rna2dfold.xml @ 6:17b6ff52efc3 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29
author rnateam
date Wed, 20 Dec 2017 08:37:33 -0500
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1 <tool id="viennarna_rna2dfold" name="@EXECUTABLE@" version="@VERSION@.0">
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2 <description>explore structure space between two reference structures</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">RNA2Dfold</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 RNA2Dfold -T $temperature -d $dangling --stochBT=$nrbt
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13 #if int($nk) > -1 and int($nl) > -1
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14 --neighborhood=$nk:$nl
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15 #end if
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16 #if $varExists('$pfselect.pfscaling')
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17 --partfunc --pfScale=$pfselect.pfscaling
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18 #end if
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19 $noBT
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20 $advancedOptions.noconversion
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21 $advancedOptions.noclosinggu
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22 $advancedOptions.notetra
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23 $advancedOptions.circ
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24 #if $varExists('$advancedOptions.maxK')
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25 --maxDist1=$advancedOptions.maxK
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26 --maxDist2=$advancedOptions.maxL
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27 #end if
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28 < '$custom_input' > '$out_file'
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29 ]]>
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30 </command>
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31 <inputs>
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32 <param format="txt,dbn" name="custom_input" type="data" label="Custom File"/>
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33 <param name="temperature" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
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34 <param name="nrbt" type="integer" value="1" label="Number of backtrack of Boltzmann samples" help="--stochBT=INT"/>
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35 <param name="nk" type="integer" value="-1" label="[k]: Distance to first reference structure of neighborhood in which to backtrack" help="--neighborhood=k:l"/>
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36 <param name="nl" type="integer" value="-1" label="[l]: Distance to second reference structure of neighborhood in which to backtrack" help="--neighborhood=k:l"/>
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37 <param name="dangling" type="select" label="How to treat dangling end energies" help="-d">
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38 <option value="2" selected="true">Unpaired bases participate in all dangling ends (2)</option>
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39 <option value="0">Ignore dangling ends (0)</option>
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40 </param>
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41 <param name="noBT" type="boolean" checked="true" truevalue="" falsevalue="--noBT"
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42 label="Backtrack structures, don't calculate energy contributions only" argument="--noBT"/>
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43 <conditional name="pfselect">
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44 <param name="pf" type="select" label="Calculate partition function" help="--partfunc">
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45 <option value="no">no</option>
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46 <option value="yes">yes</option>
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47 </param>
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48 <when value="yes">
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49 <param name="pfscaling" type="float" value="1.0" label="Scaling factor for the partition function"/>
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50 </when>
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51 <when value="no">
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52 </when>
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53 </conditional>
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54 <section name="advancedOptions" title="Advanced options">
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55 <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/>
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56 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>
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57 <param name="notetra" type="boolean" truevalue="" falsevalue="--noTetra" checked="true" label="Allow stabilization for loops, hairpins etc." help=" Include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (--noTetra)"/>
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58 <param argument="--circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Model as circular RNA structure"/>
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59 <param name="maxK" type="integer" value="10" max="44" label="Maximum distance to first reference structure" argument="--maxDist1"/>
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60 <param name="maxL" type="integer" value="10" max="43" label="Maximum distance to second reference structure" argument="--maxDist2"/>
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61 <!-- This argument causes "Segmentation fault"-->
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62 <!-- <param name="nogu" type="boolean" truevalue="" falsevalue="- -noGU" checked="true" label="Allow GU pairing" help="Allow wobbly pairs G-U."/> -->
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63 </section>
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64 </inputs>
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65 <outputs>
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66 <data format="dbn" name="out_file"/>
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67 </outputs>
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68 <tests>
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69 <test>
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70 <param name="custom_input" value="rna2dfold_input1.txt"/>
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71 <param name="nrbt" value="0"/>
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72 <output name="out_file1" file="rna2dfold_result1.txt"/>
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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 **RNA2Dfold**
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78
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79 The program partitions the secondary structure space into (basepair)distance
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80 classes according to two fixed reference structures. It expects a sequence and
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81 two secondary structures in dot-bracket notation as its inputs. For each
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82 distance class, the MFE representative, Boltzmann probabilities and Gibbs free
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83 energy is computed. Additionally, a stochastic backtracking routine allows to
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84 produce samples of representative suboptimal secondary structures from each
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85 partition.
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86 The k-distance corresponds to the distance to the first reference structure, and
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87 the l-distance corresponds to the distance to the second reference structure
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88
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89 -----
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90
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91 **Input format**
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92
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93 RNA2Dfold requires one input file in the following format
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94
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95 - 1st line: RNA sequence
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96 - 2nd line: first reference structure in dot-bracket format
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97 - 3rd line: second reference structure in dot-bracket format
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98
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99 ------
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100
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101 **Outputs**
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102
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103 - text output with several secondary structures and its energies
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104
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105 ]]>
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106 </help>
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107 <expand macro="citations" />
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108 </tool>