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1 <tool id="create_poly_model" name="RIQC-Create Regression Model" version="1.0.2">
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2 <description>Generate coefficients to enable the regression from one GC-column
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3 to another GC-column</description>
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4 <command interpreter="Rscript">Rscripts/ridb-regression.R
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5 $ridb
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6 $out_model
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7 $out_log
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8 $min_residuals
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9 $range_mod
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10 $pvalue
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11 $rsquared
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12 $method
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13 $plot
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14 #if $plot
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15 $model_graphics
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16 #end if
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17 </command>
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18 <inputs>
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19 <param format="tabular" name="ridb" type="select" label="Retention Index (RI) and GC columns Library file"
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20 help="Select the RI library file of which all GC columns and their RI values
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21 will be used to create a model"
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22 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/RI_DB_libraries")'/>
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23
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24 <param name="method" type="select" label="Select regression method"
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25 help="Method to use for calculating the model" >
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26 <option value="poly" selected="True">Polynomial (3rd degree)</option>
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27 <option value="linear">Linear</option>
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28 </param>
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29 <param name="min_residuals" type="integer" value="10" optional="False"
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30 label="Minimum number of residuals" help="The minimum number of residuals
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31 (datapoints) that both columns should have in common when calculating
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32 the model" />
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33 <param name="range_mod" type="integer" value="0" optional="False"
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34 label="Range modifier" help="Moves the range of the usable RI space by the
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35 given percentage. Set to 0 to use the full range of available data." />
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36 <param name="pvalue" type="float" value="0.05" optional="False" min="0" max="1"
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37 label="Pvalue to filter on" help="Set the upper limit for the pvalue (calculated)
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38 by performing an ANOVA analysis on the created model). All models with higher
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39 pvalues are discarded." />
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40 <param name="rsquared" type="float" value="0.95" optional="False" min="0" max="1"
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41 label="R-squared to filter on" help="Set the lower limit for the R-squared,
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42 all models with lower values are discarded." />
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43 <param name="plot" type="boolean" label="Create a separate plot for each model"
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44 help="This will create a ZIP file in the history containing PDF plots" />
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45 </inputs>
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46 <code file="match_library.py" />
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47 <outputs>
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48 <data format="zip" label="Model Graphics of ${on_string}" name="model_graphics" >
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49 <filter>(plot)</filter>
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50 </data>
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51 <data format="tabular" label="Regression logfile of ${on_string}" name="out_log" />
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52 <data format="tabular" label="Regression model of ${on_string}" name="out_model" />
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53 </outputs>
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54 <help>
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55 Calculates regression models for a permutation of all GC columns contained in the selected
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56 RI database file. The method used for creating the model is either based on a 3rd degree
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57 polynomial or a standard linear model.
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58
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59 The *Minimum number of residuals* option will only allow regression if the columns it is based
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60 on has at least that number of datapoints on the same compound.
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61
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62 Filtering is possible by setting an upper limit for the *p-value* and / or a lower limit for
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63 the *R squared* value. The produced logfile will state how many models have been discarded due
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64 to this filtering. The output model file also includes the p-value and R squared value for
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65 each created model.
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66
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67 Graphical output of the models is available by selecting the plot option which shows the
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68 data points used for the model as well as the fit itself and the range of data that will
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69 be usable.
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70
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71 .. class:: infomark
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72
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73 **Notes**
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74
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75 The output file produced by this tool is required as input for the CasLookup tool when
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76 selecting to apply regression when finding hits in the RIDB.
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77 </help>
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78 </tool>
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