Mercurial > repos > rnateam > viennarna_rnalalifold

annotate rnalalifold.xml @ 5:86a940341a00 draft

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author rnateam
date Thu, 28 Sep 2017 16:24:56 -0400
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1 <tool id="viennarna_rnalalifold" name="@EXECUTABLE@" version="@VERSION@.0">
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2 <description>Calculate locally stable secondary structures for a set of aligned RNAs</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">RNALalifold</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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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 #if $varExists('$advancedOptions.nolp')
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17 $advancedOptions.nolp
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18 $advancedOptions.nogu
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19 $advancedOptions.noclosinggu
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20 $advancedOptions.notetra
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21 --cfactor=$advancedOptions.cfactor
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22 --nfactor=$advancedOptions.nfactor
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23 $advancedOptions.ribosum
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24 #end if
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25 ]]>
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26 </command>
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27
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28 <inputs>
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29 <param format="txt" name="input" type="data" label="Clustal file"/>
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30 <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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31 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/>
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32 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
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33 <option value="0">0: ignore dangling ends</option>
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34 <option value="1">1: unpaired bases participate in one dangling end only</option>
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35 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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36 <option value="3">3: allow coaxial stacking</option>
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37 </param>
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38 <!-- the -p option led to segmentation faults with version 2.1.2 and 2.1.7, it was later removed from verion 2.1.10 -->
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39 <!--<param name="pf" type="boolean" checked="false" truevalue="-p" falsevalue="" label="calculate partition function" help="-p"/>-->
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40 <param name="mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="--mis"/>
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41 <conditional name="advancedOptions">
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42 <param name="advancedSelector" type="select" label="advanced options">
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43 <option value="basic">basic Options</option>
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44 <option value="advanced">advanced Options</option>
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45 </param>
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46 <when value="advanced">
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47 <!-- the -cutoff option was removed from version 2.2.10 -->
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48 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
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49 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
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50 <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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51 <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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52 <param name="cfactor" type="float" value="1.0" label="Weight of the covariance term" help="--cfactor"/>
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53 <param name="nfactor" type="float" value="1.0" label="Penalty for non-compatible sequences in the covariance term" help="--nfactor"/>
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54 <param name="ribosum" type="boolean" truevalue="--ribosum_scoring" falsevalue="" checked="false" label="Use ribosum scoring matrix" help="--ribosum_scoring"/>
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55 </when>
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56 <when value="basic">
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57 </when>
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58 </conditional>
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59 </inputs>
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60 <outputs>
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61 <data format="txt" name="output" />
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62 <!-- the program does not seem to generate a dot plot, even though that is implied in the help -->
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63 <!--<data format="tar" name="imagesFile" label="RNALalifold images"/>-->
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="input" value="rnalalifold_input1.clustal"/>
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68 <output name="output" file="rnalalifold_result1.txt"/>
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69 </test>
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70 </tests>
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71 <help>
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72 <![CDATA[
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73
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74 **RNALalifold**
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75
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76 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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77
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78
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79 -----
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81 **Input format**
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83 RNALalifold requires one input file
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84 - Clustal file
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86 ------
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88 **Outputs**
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90 - energy of the consensus structures in the clustal file
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91 - several possible postscript images bundled together in a tar file
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94 ]]>
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95 </help>
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96 <expand macro="citations" />
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97 </tool>