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1 <tool id="rna2dfold" name="RNA2Dfold" version="2.1.6.0">
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2 <description>explore structure space between two reference structures</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <expand macro="stdio" />
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6 <macros>
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7 <token name="@EXECUTABLE@">RNA2Dfold</token>
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8 <import>macros.xml</import>
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9 </macros>
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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 #if $varExists('$advancedOptions.noconversion')
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20 #if $advancedOptions.noconversion
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21 --noconv
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22 #end if
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23 #if $advancedOptions.nogu
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24 --noGU
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25 #end if
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26 #if $advancedOptions.noclosinggu
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27 --noClosingGU
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28 #end if
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29 #if $advancedOptions.notetra
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30 --noTetra
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31 #end if
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32 --maxDist1=$maxK
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33 --maxDist2=$maxL
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34 #end if
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35 < $custom_input > $out_file
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36 ]]>
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37 </command>
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38 <inputs>
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39 <param format="txt" name="custom_input" type="data" label="Custom File"/>
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40 <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
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41 <param name="nrbt" type="integer" value="1" label="number of backtrack of Boltzmann samples" help="--stochBT=INT"/>
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42 <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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43 <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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44 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
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45 <option value="2" selected="true">unpaired bases participate in all dangling ends (2)</option>
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46 <option value="0">ignore dangling ends (0)</option>
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47 <option value="1">unpaired bases participate in one dangling end only (1)</option>
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48 <option value="3">allow coaxial stacking (3)</option>
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49 </param>
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50 <param name="circular" type="boolean" checked="false" label="assume circular RNA structure" help="--circ"/>
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51 <conditional name="pfselect">
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52 <param name="pf" type="select" label="calculate partition function" help="--partfunc">
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53 <option value="no">no</option>
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54 <option value="yes">yes</option>
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55 </param>
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56 <when value="yes">
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57 <param name="pfscaling" size="6" type="float" value="1.0" label="scaling factor for the partition function"/>
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58 </when>
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59 </conditional>
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60
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61 <conditional name="advancedOptions">
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62 <param name="advancedSelector" type="select" label="advanced options">
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63 <option value="basic">basic Options</option>
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64 <option value="advanced">advanced Options</option>
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65 </param>
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66 <when value="advanced">
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67 <param name="maxK" type="integer" value="50" label="Maximum distance to first reference structure" help="--maxDist1=INT"/>
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68 <param name="maxL" type="integer" value="50" label="Maximum distance to second reference structure" help="--maxDist2=INT"/>
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69 <param name="noconversion" type="boolean" checked="false" label="no conversion" help="--noconv do not convert thymine to uracile (T -> U)."/>
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70 <param name="gquad" type="boolean" checked="false" label="G Quadruplex formation" help="-g take into account G Quadruplex formation"/>
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71 <param name="nogu" type="boolean" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/>
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72 <param name="noclosinggu" type="boolean" checked="false" label="No GU pairing at the ends" help="--noClosingGU don't allow pairing of G and U at the ends of helices."/>
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73 <param name="notetra" type="boolean" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
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74 </when>
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75 </conditional>
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76 </inputs>
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77 <outputs>
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78 <data format="txt" name="out_file"/>
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79 </outputs>
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80 <tests>
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2
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81 <test>
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82 <param name="custom_input" value="rna2dfold_input1.txt"/>
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83 <param name="nrbt" value="0"/>
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84 <output name="out_file1" file="rna2dfold_result1.txt"/>
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85 </test>
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0
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86 </tests>
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87 <help>
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88 <![CDATA[
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89 **RNA2Dfold**
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90
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91 The program partitions the secondary structure space into (basepair)distance
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92 classes according to two fixed reference structures. It expects a sequence and
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93 two secondary structures in dot-bracket notation as its inputs. For each
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94 distance class, the MFE representative, Boltzmann probabilities and Gibbs free
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95 energy is computed. Additionally, a stochastic backtracking routine allows to
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96 produce samples of representative suboptimal secondary structures from each
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97 partition.
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98 The k-distance corresponds to the distance to the first reference structure, and
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99 the l-distance corresponds to the distance to the second reference structure
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100
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101 -----
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102
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103 **Input format**
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104
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105 RNA2Dfold requires one input file in the following format
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106
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107 - 1st line: RNA sequence
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108 - 2nd line: first reference structure in dot-bracket format
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109 - 3rd line: second reference structure in dot-bracket format
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110
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111 ------
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112
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113 **Outputs**
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114
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115 - text output with several secondary structures and its energies
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116
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117 ]]>
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118 </help>
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119 <expand macro="requirements" />
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120 </tool>
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