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1 <tool id="rnadistance" name="RNAdistance" version="2.1.6.0">
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2 <description>Calculate distance between secondary structures of two 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@">RNAdistance</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 RNAdistance < $input > $outfile
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13 --distance=#echo ''.join(str($distance).split(','))#
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14 --compare=$compare
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15 $shapiro
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16 $backtrack
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17 #if $backtrack and str($compare)=="m"
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18 ; cat backtrack.file >> $outfile
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19 #end if
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20 ]]>
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21 </command>
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22
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23 <inputs>
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24 <param name="input" type="data" label="Primary and secondary stuctures file"/>
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25 <param name="distance" type="select" multiple="true" display="checkboxes" label="Representation to calculate the distance / alignment option">
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26 <option value="f" selected="true">full/tree</option>
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27 <option value="F">full/string</option>
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28 <option value="h">hit/tree</option>
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29 <option value="H">hit/string</option>
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30 <option value="w">weighted coarse/tree</option>
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31 <option value="W">weighted coarse/string</option>
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32 <option value="c">coarse/tree</option>
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33 <option value="C">coarse/string</option>
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34 <validator type="no_options" message="Please select at least one type."/>
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35 </param>
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36 <param name="compare" type="select" label="Comparison Option" help="-d">
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37 <option value="p" selected="True">p: pairwise (1st with 2nd, 3rd with 4th, ...)</option>
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38 <option value="m">m: matrix (each with each, output in matrix form)</option>
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39 <option value="f" >f: first (1st with 2nd, 1st with 3rd, ...)</option>
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40 <option value="c">c: continuous (1st with 2nd, 2nd with 3rd, ...)</option>
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41 </param>
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42 <param name="shapiro" type="boolean" checked="false" truevalue="--shapiro" falsevalue="" label="Use cost matrix by Bruce Shapiro" help="--shapiro"/>
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43 <param name="backtrack" type="boolean" checked="false" truevalue="--backtrack" falsevalue="" label="Print an alignment" help="--backtrack"/>
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44 </inputs>
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45 <outputs>
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46 <data format="txt" name="outfile"/>
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47 </outputs>
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48 <tests>
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2
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49 <test>
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50 <param name="input" value="rnadistance_input1.fas"/>
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51 <output name="outfile" file="rnadistance_result1.txt"/>
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52 </test>
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53 </tests>
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54 <help>
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55 <![CDATA[
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56 **RNAdistance**
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57
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58
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59 -----
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60
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61 **Input format**
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62
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63 RNAdistance requires one input file with the following structure:
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64 1st line: can be a comment line like in Fasta, begins with '>'
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65 2nd line: sequence
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66 3rd line: first secondary structure in dot-bracket notation
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67 4th line: second secondary structure in dot-bracket notation
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68 ...
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69 nth line: another sequence
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70 ...
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71
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72 Several different RNA secondary structures can be specified. The input has a Fasta-like structure but with secondary structure information.
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73
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74
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75 ------
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76
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77 **Outputs**
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78
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79 * distance of the structures
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80 * with the backtrack options it is possible to get alignment ouput
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81
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82
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83 ]]>
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84 </help>
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85 <expand macro="requirements" />
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86 </tool>
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