Mercurial > repos > rnateam > veinnarna_rnapkplex

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
author rnateam
date Wed, 05 Oct 2016 04:59:02 -0400
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a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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1 <tool id="veinnarna_rnapkplex" name="@EXECUTABLE@" version="@VERSION@.0">
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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2 <description> predicts RNA secondary structures including pseudoknots</description>
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3
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4 <macros>
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5 <token name="@EXECUTABLE@">RNAPKplex</token>
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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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[
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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13 RNAPKplex < '$input' > '$output'
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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14 -T$temperature
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15 --energyCutoff=$energycutoff
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16 #if $varExists('$advancedOptions.nolp')
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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17 --cutoff=$advancedOptions.cutoff
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18 --subopts=$advancedOptions.suboptimal
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19 $advancedOptions.verbose
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20 $advancedOptions.noconv
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21 $advancedOptions.nolp
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22 $advancedOptions.nogu
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23 $advancedOptions.noclosinggu
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24 $advancedOptions.notetra
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25 #end if
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26 ]]>
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27 </command>
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28
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29 <inputs>
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30 <param format="fasta" name="input" type="data" label="Fasta file"/>
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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31 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/>
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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32 <param name="energycutoff" type="float" value="-8.1" label="Pseudoknots cutoff. Pseudoknots with smaller energy gains are rejected." help="--energyCutoff"/>
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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33 <conditional name="advancedOptions">
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34 <param name="advancedSelector" type="select" label="advanced options">
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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35 <option value="basic">basic Options</option>
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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36 <option value="advanced">advanced Options</option>
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37 </param>
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38 <when value="advanced">
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39 <param name="suboptimal" type="float" value="0.0" label="Print suboptimal pseudoknots" help="--subopts"/>
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40 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Verbose mode, more output" help="--verbose"/>
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41 <param name="noconv" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion of T -> U" help="--noconv"/>
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42 <param name="cutoff" type="float" value="0.01" label="cutoff probability for the reporting of the base pairs in the dot plot" help="--cutoff"/>
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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 <when value="basic">
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49 </when>
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50 </conditional>
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51 </inputs>
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52 <outputs>
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53 <data format="txt" name="output"/>
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54 <collection name="matrix_outputs" type="list" label="rna_eps outputs">
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55 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.ps" ext="eps" />
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56 </collection>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="input" value="rnapkplex_input1.fa"/>
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61 <output name="out_file" file="rnapkplex_result1.txt"/>
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62 </test>
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63 </tests>
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64 <help>
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65 <![CDATA[
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66
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67 **RNAPKplex**
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68
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69 Computes RNA secondary structures by first making two sequence intervals accessible and unpaired using the algorithm of RNAplfold and then calculating the energy of the interaction of those two intervals. The algorithm uses O(n^2*w^4) CPU time and O(n*w^2) memory space. The algorithm furthermore always considers dangle=2 model.
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70
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71 It also produces a PostScript file with a plot of the pseudoknot-free secondary structure graph, in which the bases forming the pseuodknot are marked red.
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72
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73 For each structure in the Fasta input, a PostScript file is produced for the structure graph.
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74
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75 -----
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76
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77 **Input format**
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78
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79 RNAPKplex requires one input file
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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80
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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81 - fasta file
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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82
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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83 The input format is similar to fasta except that even long sequences may not be interrupted by line breaks, and the header lines are optional.
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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84
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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85 ------
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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86
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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87 **Outputs**
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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88
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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89 - secondary structure in dot-bracket format
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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90 - Images of the calculated structures
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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91
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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92 ]]>
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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93 </help>
a0dde287793e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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94 <expand macro="citations" />
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95 </tool>