Mercurial > repos > rnateam > viennarna_rnalfold

annotate rnalfold.xml @ 1:05d34c651b11 draft

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author rnateam
date Wed, 21 Dec 2016 17:32:13 -0500
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1 <tool id="viennarna_rnalfold" name="@EXECUTABLE@" version="@VERSION@.0">
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2 <description>calculates locally stable secondary structures of RNA</description>
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3
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4 <macros>
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5 <token name="@EXECUTABLE@">RNALfold</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command>
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12 <![CDATA[
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13 RNALfold -L $span -T $temperature -d$dangling < '$fasta_input'
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14 #if $varExists('$advancedOptions.noconversion')
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15 $advancedOptions.noconversion
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16 $advancedOptions.gquad
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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 #if $advancedOptions.activateZscore
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22 #if str($advancedOptions.zscore) <> ""
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23 --zscore=$advancedOptions.zscore
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24 #else
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25 --zscore
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26 #end if
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27 #end if
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28 #end if
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29 | sed -r 's/(^[.()]*) +(\(.*\)) +(.*)/\1\t\2\t\3/' > '$out_file'
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30 ]]>
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31 </command>
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32 <inputs>
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33 <param format="fasta" name="fasta_input" type="data" label="FASTA file"/>
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34 <param name="span" type="integer" min="0" max="5000" value="150" label="base pair span" help="Maximal distance between two paired bases. (-L)"/>
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35 <param name="temperature" 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="2" selected="true">unpaired bases participate in all dangling ends (2)</option>
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38 <option value="0">ignore dangling ends (0)</option>
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39 <option value="1">unpaired bases participate in one dangling end only (1)</option>
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40 <option value="3">allow coaxial stacking (3)</option>
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41 </param>
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42 <conditional name="advancedOptions">
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43 <param name="advancedSelector" type="select" label="advanced options">
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44 <option value="basic">basic Options</option>
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45 <option value="advanced">advanced Options</option>
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46 </param>
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47 <when value="advanced">
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48 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="Take G Quadruplex formation into account" argument="-g"/>
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49 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
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50 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
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51 <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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52 <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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53 <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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54 <param name="activateZscore" type="boolean" checked="false" label="Activate Z−score computation. An optional argument may be supplied to set the threshold" help="(--zscore)"/>
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55 <param name="zscore" type="float" value="-2" optional="true" label="Z-score" help="An optional argument may be supplied to set the threshold"/>
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56 </when>
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57 <when value="basic">
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58 </when>
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59 </conditional>
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60 </inputs>
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61 <outputs>
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62 <data format="txt" name="out_file"/>
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="fasta_input" value="rnalfold_input1.fa"/>
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67 <output name="out_file" file="rnalfold_result1.txt"/>
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68 </test>
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69 </tests>
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70 <help>
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71 <![CDATA[
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72 **RNALfold**
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73
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74 Compute locally stable RNA secondary structure with a maximal base pair span.
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75 For a sequence of length n and a base pair span of L the algorithm uses only
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76 O(n+L*L) memory and O(n*L*L) CPU time. *Thus it is practical to "scan" very
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77 large genomes for short RNA structures*.
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78 Output consists of a list of secondary structure components of size <= L, one
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79 entry per line. Each output line contains the predicted local structure its
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80 energy in kcal/mol and the starting position of the local structure.
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82 -----
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83
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84 **Input format**
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85
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86 - RNALfold requires one input file in FASTA format
a59547093b10 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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87
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88 ------
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89
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90 **Outputs**
a59547093b10 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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91
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92 - text output with dot-bracket notation and free energies of the secondary structures
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93
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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>