Mercurial > repos > rnateam > viennarna_rnaheat

annotate rnaheat.xml @ 3:fa85a3a77a33 draft

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author rnateam
date Wed, 12 Jul 2017 14:22:22 -0400
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1 <tool id="viennarna_rnaheat" name="@EXECUTABLE@" version="@VERSION@.0">
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2 <description>Calculate energies of RNA in a temperature range</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">RNAheat</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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12 RNAheat < '$input' > '$output'
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13 --Tmin $tmin --Tmax $tmax -d$dangling --stepsize=$stepsize --ipoints=$ipoints
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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 #if $advancedOptions.nsp
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21 --nsp='$advancedOptions.nsp'
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22 #end if
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23 #end if
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24 ]]>
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25 </command>
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26
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27 <inputs>
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28 <param format="fasta" name="input" type="data" label="Input file"/>
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29 <param name="tmin" type="float" value="0.0" label="minimal temperature [°C]" help="--Tmin"/>
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30 <param name="tmax" type="float" value="100.0" label="maximal temperature [°C]" help="--Tmax"/>
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31 <param name="stepsize" type="float" value="1.0" label="stepsize [°C]" help="--stepsize"/>
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32 <param name="ipoints" type="integer" value="2" label="data points to fit parabola to: 2*value+1" help="--ipoints"/>
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33 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
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34 <option value="0">0: ignore dangling ends</option>
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35 <option value="1">1: unpaired bases participate in one dangling end only</option>
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36 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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37 <option value="3">3: allow coaxial stacking</option>
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38 </param>
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39 <conditional name="advancedOptions">
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40 <param name="advancedSelector" type="select" label="advanced options">
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41 <option value="basic">basic Options</option>
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42 <option value="advanced">advanced Options</option>
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43 </param>
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44 <when value="advanced">
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45 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
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46 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
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47 <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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48 <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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49 <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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50 <param argument="--nsp" type="text" value="" label="Allow other pairs in addition to the usual AU,GC,and GU pairs."
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51 help="Its argument is a comma separated list of additionally allowed pairs. If the first character is '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy." />
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52 </when>
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53 <when value="basic">
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54 </when>
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55 </conditional>
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56 </inputs>
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57 <outputs>
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58 <data format="txt" name="output"/>
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="input" value="rnaheat_input1.fa"/>
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63 <output name="out_file" file="rnaheat_result1.txt"/>
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64 </test>
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65 </tests>
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66 <help>
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67 <![CDATA[
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68 **RNAheat**
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69
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70 Calculates the specific heat of RNA sequences in the temperature range t1 to t2, from the partition function by numeric differentiation. The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter produces a smoother curve.
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71
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72
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73 -----
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74
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75 **Input format**
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76
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77 RNAheat requires one input file Fasta format.
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78
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79
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80 ------
b885d4fab5d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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81
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82 **Outputs**
b885d4fab5d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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83
b885d4fab5d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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84 The result is written as a list of pairs of temperature in C and specific heat in Kcal/(Mol*K) for each sequence in the input file.
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85
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86
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87 ]]>
b885d4fab5d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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88 </help>
b885d4fab5d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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89 <expand macro="citations" />
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90 </tool>