Mercurial > repos > rnateam > viennarna_rnadpdist

annotate rnapdist.xml @ 3:4fa593b832e8 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
author rnateam
date Wed, 12 Jul 2017 14:27:32 -0400
parents 149b7a662bcc
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149b7a662bcc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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1 <tool id="viennarna_rnadpdist" name="@EXECUTABLE@" version="@VERSION@.0">
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2 <description>Calculate distances between thermodynamic RNA secondary structure ensembles
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3 </description>
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4
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5 <macros>
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6 <token name="@EXECUTABLE@">RNApdist</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="stdio" />
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11 <expand macro="version_command" />
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12 <command>
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13 <![CDATA[
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14 RNApdist < '$input' > '$output'
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15 --compare=$compare
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16 -T$temperature -d$dangling
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17 $backtrack
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18 #if $varExists('$advancedOptions.nolp')
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19 $advancedOptions.noconversion
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20 $advancedOptions.nolp
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21 $advancedOptions.nogu
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22 $advancedOptions.noclosinggu
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23 $advancedOptions.notetra
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24 #end if
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25 #if $backtrack and str($compare)=="m"
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26 && cat backtrack.file >> '$outfile'
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27 #end if
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28
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29 ]]>
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30 </command>
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31
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32 <inputs>
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33 <param format="fasta" name="input" type="data" label="Fasta file"/>
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34 <param name="temperature" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
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35 <param name="dangling" type="select" label="How to treat dangling end energies" help="-d">
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36 <option value="0">0: ignore dangling ends</option>
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37 <option value="1">1: unpaired bases participate in one dangling end only</option>
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38 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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39 <option value="3">3: allow coaxial stacking</option>
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40 </param>
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41 <param name="compare" type="select" label="Comparison Option" help="--compare">
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42 <option value="p" selected="True">p: pairwise (1st with 2nd, 3rd with 4th, ...)</option>
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43 <option value="m">m: matrix (each with each, output in matrix form)</option>
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44 <option value="f" >f: first (1st with 2nd, 1st with 3rd, ...)</option>
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45 <option value="c">c: continuous (1st with 2nd, 2nd with 3rd, ...)</option>
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46 </param>
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47 <param name="backtrack" type="boolean" checked="false" truevalue="--backtrack" falsevalue="" label="Print an alignment" help="--backtrack"/>
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48 <conditional name="advancedOptions">
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49 <param name="advancedSelector" type="select" label="advanced options">
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50 <option value="basic">basic Options</option>
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51 <option value="advanced">advanced Options</option>
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52 </param>
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53 <when value="advanced">
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54 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
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55 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
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56 <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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57 <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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58 <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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59 </when>
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60 <when value="basic">
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61 </when>
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62 </conditional>
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63 </inputs>
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64 <outputs>
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65 <data format="txt" name="output"/>
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66 <data format="txt" name="dotplot"/>
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67 <collection name="matrix_outputs" type="list" label="rna_eps outputs">
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68 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
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69 </collection>
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70 </outputs>
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71 <tests>
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72 <test>
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73 <param name="input" value="rnapdist_input1.fa"/>
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74 <output name="out_file" file="rnapdist_result1.txt"/>
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75 </test>
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76 </tests>
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77 <help>
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78 <![CDATA[
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79
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80 **RNApdist**
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81
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82 RNApdist calculates structure distances between the thermodynamic ensembles of the secondary structures of RNA sequences.
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83
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84 -----
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85
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86 **Input format**
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87
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88 RNApdist requires one input file
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89 - Fasta file
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90
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91 ------
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93 **Outputs**
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94
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95 - output of alignment scores and alignments (if -B option is selected)
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96 - dot plot matrices in postscript format bundled together in a tar file
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97
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98 ]]>
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99 </help>
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100 <expand macro="citations" />
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101 </tool>