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1 <tool id="rnaheat" name="RNAheat" version="2.1.6.0">
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2 <description>Calculate energies of RNA in a temperature range</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@">RNAheat</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 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 #end if
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21 ]]>
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22 </command>
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23
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24 <inputs>
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25 <param format="fasta" name="input" type="data" label="Input file"/>
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26 <param name="tmin" size="6" type="float" value="0.0" label="minimal temperature [°C]" help="--Tmin"/>
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27 <param name="tmax" size="6" type="float" value="100.0" label="maximal temperature [°C]" help="--Tmax"/>
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28 <param name="stepsize" size="6" type="float" value="1.0" label="stepsize [°C]" help="--stepsize"/>
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29 <param name="ipoints" size="3" type="integer" value="2" label="data points to fit parabola to: 2*value+1" help="--ipoints"/>
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30 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
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31 <option value="0">0: ignore dangling ends</option>
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32 <option value="1">1: unpaired bases participate in one dangling end only</option>
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33 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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34 <option value="3">3: allow coaxial stacking</option>
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35 </param>
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36
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37 <conditional name="advancedOptions">
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38 <param name="advancedSelector" type="select" label="advanced options">
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39 <option value="basic">basic Options</option>
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40 <option value="advanced">advanced Options</option>
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41 </param>
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42 <when value="advanced">
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43 <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="no conversion" help="--noconv do not convert thymine to uracile (T -> U)."/>
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44 <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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45 <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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46 <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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47 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
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48 </when>
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49 </conditional>
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50 </inputs>
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51 <outputs>
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52 <data format="txt" name="output"/>
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53 </outputs>
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54 <tests>
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55 </tests>
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56 <help>
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57 <![CDATA[
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58 **RNAheat**
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59
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60 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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61
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62
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63 -----
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64
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65 **Input format**
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66
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67 RNAheat requires one input file Fasta format.
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68
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69
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70 ------
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71
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72 **Outputs**
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73
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74 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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75
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76
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77 ]]>
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78 </help>
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79 <expand macro="requirements" />
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80 </tool>
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