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1 <tool id="rnalalifold" name="RNALalifold" version="2.1.6.0">
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2 <description>Calculate locally stable secondary structures for a set of aligned 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@">RNALalifold</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 RNALalifold $input > $output
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13 -T$temperature -d$dangling
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14 -L$span
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15 $mis
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16
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17 #if $varExists('$advancedOptions.nolp')
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18 --cutoff=$advancedOptions.cutoff
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19 $advancedOptions.nolp
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20 $advancedOptions.nogu
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21 $advancedOptions.noclosinggu
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22 $advancedOptions.notetra
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23 --cfactor=$advancedOptions.cfactor
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24 --nfactor=$advancedOptions.nfactor
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25 $advancedOptions.ribosum
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26 #end if
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27 <!--; tar -cf $imagesFile *.ps -->
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28 ]]>
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29 </command>
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30
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31 <inputs>
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32 <param format="clustal" name="input" type="data" label="Clustal file"/>
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33 <param name="span" type="integer" min="0" max="5000" value="60" label="base pair span" help="Maximal distance between two paired bases. (-L)"/>
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34
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35 <param name="temperature" size="6" type="float" value="37.0" label="temperature [°C]" help="-T"/>
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36 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
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37 <option value="0">0: ignore dangling ends</option>
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38 <option value="1">1: unpaired bases participate in one dangling end only</option>
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39 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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40 <option value="3">3: allow coaxial stacking</option>
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41 </param>
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42
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43 <!-- the -p option led to segmentation faults with version 2.1.2 and 2.1.7 -->
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44 <!--<param name="pf" type="boolean" checked="false" truevalue="-p" falsevalue="" label="calculate partition function" help="-p"/>-->
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45
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46 <param name="mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="--mis"/>
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47
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48 <conditional name="advancedOptions">
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49 <param name="advancedSelector" type="select" label="advanced options">
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50 <option value="basic">basic Options</option>
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51 <option value="advanced">advanced Options</option>
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52 </param>
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53 <when value="advanced">
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54 <param name="cutoff" type="float" value="0.01" label="cutoff probability for the reporting of the base pairs in the dot plot" help="--cutoff"/>
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55 <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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56 <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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57 <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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58 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
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59 <param name="cfactor" size="6" type="float" value="1.0" label="Weight of the covariance term" help="--cfactor"/>
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60 <param name="nfactor" size="6" type="float" value="1.0" label="Penalty for non-compatible sequences in the covariance term" help="--nfactor"/>
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61 <param name="ribosum" type="boolean" truevalue="--ribosum_scoring" falsevalue="" checked="false" label="Use ribosum scoring matrix" help="--ribosum_scoring"/>
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62 </when>
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63 </conditional>
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64 </inputs>
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65 <outputs>
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66 <data format="txt" name="output" />
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67 <!-- the program does not seem to generate a dot plot, even though that is implied in the help -->
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68 <!--<data format="tar" name="imagesFile" label="RNALalifold images"/>-->
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69 </outputs>
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70 <tests>
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71 </tests>
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72 <help>
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73 <![CDATA[
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74
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75 **RNALalifold**
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76
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77 Calculates locally stable RNA secondary structure with a maximal base pair span. For a sequence of length n and a base pair span 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 RNA
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78
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79
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80 -----
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81
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82 **Input format**
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83
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84 RNALalifold requires one input file
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85 - Clustal file
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86
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87 ------
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88
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89 **Outputs**
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90
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91 - energy of the consensus structures in the clustal file
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92 - several possible postscript images bundled together in a tar file
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93
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94
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95 ]]>
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96 </help>
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97 <expand macro="requirements" />
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98 </tool>
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