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1 <tool id="rnafold" name="RNAfold" version="2.1.6.0">
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2 <description>Calculate minimum free energy secondary structures and partition function of RNAs</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@">RNAfold</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 RNAfold
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13 -T $temperature
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14 --dangles=$dangling
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15 #if $measelect.mea == "yes":
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16 --MEA=$measelect.meavalue
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17 #else
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18 $measelect.pf
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19 #end if
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20 #if $varExists('$advancedOptions.nogu'):
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21 $advancedOptions.noconversion
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22 $advancedOptions.gquad
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23 $advancedOptions.nolp
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24 $advancedOptions.nogu
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25 $advancedOptions.noclosinggu
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26 $advancedOptions.canonicalonly
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27 $advancedOptions.circular
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28 #end if
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29
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30 < $fasta_input
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31
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32 > $tabular_file
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33 ]]>
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34 </command>
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35
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36 <inputs>
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37 <param format="fasta" name="fasta_input" type="data" label="FASTA file"/>
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38 <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
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39 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
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40 <option value="0">0: ignore dangling ends</option>
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41 <option value="1">1: unpaired bases participate in one dangling end only</option>
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42 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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43 <option value="3">3: allow coaxial stacking</option>
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44 </param>
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45 <conditional name="measelect">
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46 <param name="mea" type="select" label="Calculate Maximum Expected accuracy" help="--MEA">
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47 <option value="no">No</option>
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48 <option value="yes">Yes</option>
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49 </param>
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50 <when value="yes">
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51 <param name="meavalue" size="6" type="float" value="1.0" label="Gamma Value"/>
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52 </when>
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53 <when value="no">
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54 <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
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55 </when>
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56 </conditional>
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57 <conditional name="advancedOptions">
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58 <param name="advancedSelector" type="boolean" checked="false" label=" advanced options"/>
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59 <when value="true">
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60 <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="no conversion" help="--noconv do not convert thymine to uracile (T -> U)."/>
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61 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="-g take into account G Quadruplex formation"/>
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62 <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="--noLP don't allow lonely pairs."/>
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63 <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/> <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="--noClosingGU don't allow pairing of G and U at the ends of helices."/> <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
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64 <param name="canonicalonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Canonical basepairing only" help="--canonicalBPonly"/>
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65 <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
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66 </when>
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67 </conditional>
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68 </inputs>
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69 <outputs>
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70 <data format="tabular" name="tabular_file"/>
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1
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71 <collection name="sequence_outputs" type="list" label="rna_eps outputs">
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72 <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" />
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73 </collection>
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74 <collection name="matrix_outputs" type="list" label="rna_eps outputs">
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0
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75 <filter>measelect['pf'] is True</filter>
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76 <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/>
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1
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77 </collection>
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78
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0
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79 </outputs>
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80 <tests>
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81 </tests>
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82 <help>
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83 <![CDATA[
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84 **RNAfold**
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85
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86 The program reads RNA sequences, calculates their minimum free
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87 energy (mfe) structure and the mfe structure in dot-bracket notation.
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88
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89 If the -p option was given it also computes the
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90 partition function (pf) and base pairing probability matrix.
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91
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92 The dot plot of the base pairing probability matrix shows a matrix of squares with area proportional to the pairing
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93 probability in the upper right half, and one square for each pair in the
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94 minimum free energy structure in the lower left half. For each pair i-j with
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95 probability p>10E-6 there is a line of the form
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96
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97 i j sqrt(p) ubox
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98
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99 in the PostScript file, so that the pair probabilities can be easily extracted.
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100
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101 The sequences have to be provided in FASTA format. The first word (max. 42 char) of the FASTA header will be used for output file names. PostScript files "name_ss.ps" and "name_dp.ps" are produced for the structure and dot plot, respectively.
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102 The program will read the whole FASTA input file and provide output for each found sequence.
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103
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104
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105 -----
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106
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107 **Input format**
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108
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109 RNAfold requires one input file
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110 - FASTA file
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111
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112 ------
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113
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114 **Outputs**
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115
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116 - Secondary structures in dot-bracket notation
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117
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118 - several possible postscript images bundled together in a tar file
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119 - secondary structure for each sequence in the input file
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120 - if partition function is calculated (--MEA or --partfunc is set) then also the pairing probabilty matrix is generated for each sequence
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121
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122 ]]>
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123 </help>
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124 <expand macro="citations" />
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125 </tool>
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