Mercurial > repos > bgruening > viennarna_rnaaliduplex

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
author bgruening
date Wed, 05 Oct 2016 11:49:04 -0400
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1 <tool id="viennarna_rnaaliduplex" name="@EXECUTABLE@" version="@VERSION@.0">
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2 <description>find binding sites of two RNA alignments</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">RNAaliduplex</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 RNAaliduplex -T $temperature -d $dangling $flagsort --deltaEnergy=$deltaEnergy '$input1' '$input2'
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13 $advancedOptions.noconversion
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14 $advancedOptions.nolp
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15 $advancedOptions.nogu
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16 $advancedOptions.noclosinggu
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17 $advancedOptions.notetra
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18 #if $advancedOptions.nsp
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19 --nsp='$advancedOptions.nsp'
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20 #end if
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21 > '$out_file'
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22 ]]>
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23 </command>
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24 <inputs>
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25 <param format="txt" name="input1" type="data" label="Clustal alignment file"/>
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26 <param format="txt" name="input2" type="data" label="Clustal alignment file"/>
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27 <param name="temperature" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
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28 <param argument="--deltaEnergy" type="float" value="0.0" label="Compute suboptimal structures with energy in a certain range of the optimum [kcal/mol]"
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29 help="Default is calculation of mfe structure only."/>
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30 <param name="dangling" type="select" label="How to treat dangling end energiesHow to treat dangling end energies for bases adjacent to helices in free ends and multi-loops" argument="-d">
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31 <option value="0">0: ignore dangling ends</option>
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32 <option value="1">1: unpaired bases participate in one dangling end only</option>
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33 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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34 <option value="3">3: allow coaxial stacking</option>
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35 </param>
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36 <param name="flagsort" type="boolean" checked="false" label="Output will be sorted by free energy" truevalue="--sorted" falsevalue="" help="--sorted"/>
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37 <section name="advancedOptions" title="Advanced options">
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38 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
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39 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
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40 <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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41 <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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42 <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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43 <param name="nsp" type="text" value="" label="Allow other pairs in addition to the usual AU,GC,and GU pairs."
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44 help="Its argument is a comma separated list of additionally allowed pairs. If the first character is '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy."
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45 argument="--nsp"/>
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46 </section>
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47 </inputs>
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48 <outputs>
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49 <data format="dbn" name="out_file"/>
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="input1" value="rnaaliduplex_input1.clustal"/>
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54 <param name="input2" value="rnaaliduplex_input1.clustal"/>
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55 <output name="out_file1" file="rnaaliduplex_result1.txt"/>
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56 </test>
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57 </tests>
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58 <help>
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59 <![CDATA[
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60 **RNAaliduplex**
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61
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62 The program reads two alignments of RNA sequences in CLUSTAL format and
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63 predicts optimal and suboptimal binding sites, hybridization energies and the
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64 corresponding structures. The calculation takes only inter-molecular base pairs
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65 into account, for the general case use RNAcofold. The use of alignments allows
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66 to focus on binding sites that are evolutionary conserved. Note, that the two
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67 input alignments need to have an equal number of sequences and the same order,
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68 i.e. the 1st sequence in file1 will be hybridized to the 1st in file2 etc.
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69
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70 The computed binding sites, energies, and structures are written to stdout, one
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71 structure per line. Each line consist of: The structure in dot bracket format
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72 with a & separating the two strands. The range of the structure in the two
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73 sequences in the format "from,to : from,to"; the energy of duplex structure
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74 in kcal/mol.
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75 The format is especially useful for computing the hybrid structure between a
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76 small probe sequence and a long target sequence.
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77
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78
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79
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80 -----
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82 **Input format**
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84 RNAaliduplex takes two alignment files generated with Clustal (\*.aln).
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87 -----
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89 **Outputs**
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91 text output with several secondary structures and its energies
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93 ]]>
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94 </help>
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95 <expand macro="citations" />
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96 </tool>