Mercurial > repos > rnateam > viennarna_rnaplfold

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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 08:30:44 -0500
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22e8485bc5f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29
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1 <tool id="viennarna_rnaplfold" name="@EXECUTABLE@" version="@VERSION@.0">
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2 <description> predicts RNA secondary structures including pseudoknots</description>
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3
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4 <macros>
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5 <token name="@EXECUTABLE@">RNAplfold</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command>
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12 <![CDATA[
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13 RNAplfold < '$input'
22e8485bc5f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29
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14 -T$temperature
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15 --dangles=$dangling
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16 --cutoff=$cutoff
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17 --winsize=$winsize
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18 --span=$span
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19 $onthefly
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20 $openingenergies
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21 #if $varExists('$unpairedOption.ulength')
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22 --ulength=$unpairedOption.ulength
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23 #end if
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24 #if $varExists('$advancedOptions.nolp')
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25 $advancedOptions.noconversion
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26 $advancedOptions.nolp
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27 $advancedOptions.nogu
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28 $advancedOptions.noclosinggu
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29 $advancedOptions.notetra
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30 #end if
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31 && find -name '*_basepairs' -or -name '*_lunp' -or -name '*_openen*' > files.tmp
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32 && tar -cf '$outputf' --files-from=files.tmp
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33
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34 ]]>
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35 </command>
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36
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37 <inputs>
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38 <param format="fasta" name="input" type="data" label="Fasta file"/>
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39 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/>
22e8485bc5f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29
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40 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
22e8485bc5f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29
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41 <option value="2" selected="true">unpaired bases participate in all dangling ends (2)</option>
22e8485bc5f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29
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42 <option value="0">ignore dangling ends (0)</option>
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43 <option value="1">unpaired bases participate in one dangling end only (1)</option>
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44 <option value="3">allow coaxial stacking (3)</option>
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45 </param>
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46 <param name="winsize" type="integer" value="70" label="Average pairing probabilities over this windowsize" help="--winsize"/>
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47 <param name="span" type="integer" value="70" label="Maximum seperation between base pairs" help="--span, -L"/>
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48 <param name="cutoff" type="float" value="0.01" label="Cutoff probability for report on base pairing" help="--cutoff"/>
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49 <param name="onthefly" type="boolean" truevalue="--print_onthefly" falsevalue="" checked="false" label="Print simplified base pair probabilities (_basepairs output)" help="--print_onthefly"/>
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50 <param name="openingenergies" type="boolean" truevalue="--opening_energies" falsevalue="" checked="false" label="Output in logarithm of the probabilities (_openen output)" help="--opening_energies"/>
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51 <param argument="--plex_output" type="boolean" truevalue="--plex_output" falsevalue="" checked="false" label="" help=""/>
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52 <conditional name="unpairedOption">
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53 <param name="unpairedSelector" type="select" label="Compute probabilty that region is unpaired (_lunp output)">
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54 <option value="no" selected="true">no</option>
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55 <option value="yes">yes</option>
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56 </param>
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57 <when value="yes">
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58 <param name="ulength" type="integer" value="31" label="Maximal lenght of unpaired region" help="--ulength"/>
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59 </when>
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60 <when value="no">
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61 </when>
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62 </conditional>
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63 <conditional name="advancedOptions">
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64 <param name="advancedSelector" type="select" label="advanced options">
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65 <option value="basic">basic Options</option>
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66 <option value="advanced">advanced Options</option>
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67 </param>
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68 <when value="advanced">
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69 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
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70 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
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71 <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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72 <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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73 <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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74 </when>
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75 <when value="basic">
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76 </when>
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77 </conditional>
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78 </inputs>
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79 <outputs>
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80 <collection name="matrix_outputs" type="list" label="rna_eps outputs">
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81 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
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82 </collection>
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83 <data format="tar" name="outputf"/>
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84 </outputs>
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85 <tests>
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86 <test>
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87 <param name="input" value="rnaplfold_input1.fa"/>
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88 <output_collection name="matrix_outputs" type="list">
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89 <element name="Anolis_caro_chrUn_GL343590.trna2-A">
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90 <assert_contents>
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91 <has_text_matching expression="%%Creator: ViennaRNA-@VERSION@" />
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92 </assert_contents>
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93 </element>
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94 </output_collection>
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95 </test>
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96 </tests>
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97 <help>
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98 <![CDATA[
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99
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100 **RNAplfold**
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101
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102 Computes local pair probabilities for base pairs with a maximal span of L. The probabilities are averaged over all windows of size L that contain the base pair. For a sequence of length n and a window size of L the algorithm uses only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for short stable RNA structures.
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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 RNAPplfold requires one input file
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110
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111 - Fasta file
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112
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113 ------
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114
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115 **Outputs**
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116
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117 For each structure in the Fasta input a postscript image with dot-plot of the pairing probabilities is generated. Different output is generated with the "--ulength", "--print_onthefly" and "--opening_energies" flags.
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118 The Dot Plot Matrices are stored in a Postscript file.
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119 The other output is packed in a tar file.
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120
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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>