annotate rnaplfold.xml @ 3:04c56f5b0907 draft default tip

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author rnateam
date Fri, 13 Feb 2015 04:08:49 -0500
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1 <tool id="rnaplfold" name="RNAplfold" version="2.1.6.0">
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2 <description> predicts RNA secondary structures including pseudoknots</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@">RNAplfold</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 RNAplfold < $input
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13 -T$temperature
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14 --dangles=$dangling
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15 --cutoff=$cutoff
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16 --winsize=$winsize
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17 --span=$span
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18 $onthefly
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19 $openingenergies
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20 #if $varExists('$unpairedOption.ulength')
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21 --ulength=$unpairedOption.ulength
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22 #end if
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23
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24 #if $varExists('$advancedOptions.nolp')
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25 $advancedOptions.noconv
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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 ;ls *_basepairs *_lunp *_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" size="8" type="float" value="37.0" label="temperature [°C]" help="-T"/>
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40 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
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41 <option value="2" selected="true">unpaired bases participate in all dangling ends (2)</option>
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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" size="8" 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 <conditional name="unpairedOption">
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52 <param name="unpairedSelector" type="select" label="Compute probabilty that region is unpaired (_lunp output)">
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53 <option value="no" selected="true">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="ulength" type="integer" value="31" label="Maximal lenght of unpaired region" help="--ulength"/>
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58 </when>
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59 </conditional>
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60 <conditional name="advancedOptions">
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61 <param name="advancedSelector" type="select" label="advanced options">
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62 <option value="basic">basic Options</option>
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63 <option value="advanced">advanced Options</option>
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64 </param>
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65 <when value="advanced">
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66 <param name="noconv" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion of T -> U" help="--noconv"/>
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67 <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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68 <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/>
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69 <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."/>
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70 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
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71 </when>
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72 </conditional>
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73 </inputs>
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74 <outputs>
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75 <collection name="matrix_outputs" type="list" label="rna_eps outputs">
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76 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
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77 </collection>
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78 <data format="tar" name="outputf"/>
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79 </outputs>
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80 <tests>
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81 <test>
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82 <param name="input" value="rnaplfold_input1.fa"/>
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83 <output name="out_file" file="rnaplfold_result1.txt"/>
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84 </test>
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85 </tests>
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86 <help>
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87 <![CDATA[
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88
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89 **RNAplfold**
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90
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91 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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92
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93
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94 -----
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95
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96 **Input format**
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97
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98 RNAPplfold requires one input file
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99
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100 - Fasta file
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101
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102 ------
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103
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104 **Outputs**
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105
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106 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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107 The Dot Plot Matrices are stored in a Postscript file.
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108 The other output is packed in a tar file.
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109
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110
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111 ]]>
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112 </help>
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113 <expand macro="requirements" />
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114 </tool>