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1 <tool id="rnaduplex" name="RNAduplex" version="2.1.6.0">
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2 <description>Compute the structure upon hybridization of two RNA strands</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@">RNAduplex</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 RNAduplex < $input > $tabularFile
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13 -T$temperature -d$dangling --deltaEnergy=$denergy
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14 #if $varExists('$advancedOptions.noconversion')
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15 $advancedOptions.noconversion
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16 $advancedOptions.nolp
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17 $advancedOptions.nogu
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18 $advancedOptions.noclosinggu
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19 $advancedOptions.notetra
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20 #end if
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21 ]]>
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22 </command>
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23
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24 <inputs>
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25 <param format="fasta" name="input" type="data" label="Fasta file"/>
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26 <param name="temperature" size="6" type="float" value="37.0" label="temperature [°C]" help="-T"/>
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27 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
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28 <option value="0">0: ignore dangling ends</option>
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29 <option value="1">1: unpaired bases participate in one dangling end only</option>
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30 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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31 <option value="3">3: allow coaxial stacking</option>
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32 </param>
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33 <param name="denergy" size="6" type="float" value="0.0" label="delta energy range [kcal/mol] for suboptimal structures" help="-deltaEnergy"/>
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34 <param name="sorted" type="boolean" truevalue="--sorted" falsevalue="" checked="false" label="Sort by energy" help="--sorted"/>
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35
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36 <conditional name="advancedOptions">
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37 <param name="advancedSelector" type="select" label="advanced options">
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38 <option value="basic">basic Options</option>
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39 <option value="advanced">advanced Options</option>
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40 </param>
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41 <when value="advanced">
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42 <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No converstion from T->U" help="--noconv"/>
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43 <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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44 <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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45 <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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46 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
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47 </when>
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48 </conditional>
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49 </inputs>
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50 <outputs>
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51 <data format="txt" name="tabularFile"/>
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52 </outputs>
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53 <tests>
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2
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54 <test>
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55 <param name="input" value="rnaduplex_input1.fa"/>
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56 <output name="out_file" file="rnaduplex_result1.txt"/>
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57 </test>
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0
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58 </tests>
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59 <help>
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60 <![CDATA[
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61 **RNAduplex**
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62 RNA duplex reads two RNA sequences and computes optimal and suboptimal secondary structures for their hybridization. The calculation is simplified by allowing only inter−molecular base pairs, for the general case use RNAcofold. The computed optimal and suboptimal structure are written to stdout, one structure per line. Suboptimal structures are computed with energy in a certain range of the optimum (kcal/mol). Default is calculation of mfe structure only.
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63
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64 -----
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65
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66 **Input format**
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67
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68 RNAduplex requires one input file in Fasta format. The secondary strucures will be calculated pairwise: 1st sequence with 2nd sequence, 3rd sequence with 4th sequence, etc.
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69
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70 ------
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71
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72 **Outputs**
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73
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74 Each line consist of: The structure in dot bracket format with a "&" separating the two strands. The range of the structure in the two sequences in the format "from,to : from,to"; the energy of duplex structure in kcal/mol. The format is especially useful for computing the hybrid structure between a small probe sequence and a long target sequence.
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75
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76
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77 ]]>
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78 </help>
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79 <expand macro="requirements" />
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80 </tool>
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