Mercurial > repos > pieterlukasse > prims_metabolomics
view create_model.xml @ 50:93102202ab79
Added more options and better documentation.
Added MsClust support for parsing XCMS alignment results.
Improved output reports for XCMS wrappers.
New tools.
author | pieter.lukasse@wur.nl |
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date | Wed, 10 Dec 2014 22:04:33 +0100 |
parents | 9d5f4f5f764b |
children |
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<tool id="create_poly_model" name="RIQC-Create Regression Model" version="1.0.2"> <description>Generate coefficients to enable the regression from one GC-column to another GC-column</description> <command interpreter="Rscript">Rscripts/ridb-regression.R $ridb $out_model $out_log $min_residuals $range_mod $pvalue $rsquared $method $plot #if $plot $model_graphics #end if </command> <inputs> <param format="tabular" name="ridb" type="select" label="Retention Index (RI) and GC columns Library file" help="Select the RI library file of which all GC columns and their RI values will be used to create a model" dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/RI_DB_libraries")'/> <param name="method" type="select" label="Select regression method" help="Method to use for calculating the model" > <option value="poly" selected="True">Polynomial (3rd degree)</option> <option value="linear">Linear</option> </param> <param name="min_residuals" type="integer" value="10" optional="False" label="Minimum number of residuals" help="The minimum number of residuals (datapoints) that both columns should have in common when calculating the model" /> <param name="range_mod" type="integer" value="0" optional="False" label="Range modifier" help="Moves the range of the usable RI space by the given percentage. Set to 0 to use the full range of available data." /> <param name="pvalue" type="float" value="0.05" optional="False" min="0" max="1" label="Pvalue to filter on" help="Set the upper limit for the pvalue (calculated) by performing an ANOVA analysis on the created model). All models with higher pvalues are discarded." /> <param name="rsquared" type="float" value="0.95" optional="False" min="0" max="1" label="R-squared to filter on" help="Set the lower limit for the R-squared, all models with lower values are discarded." /> <param name="plot" type="boolean" label="Create a separate plot for each model" help="This will create a ZIP file in the history containing PDF plots" /> </inputs> <code file="match_library.py" /> <outputs> <data format="zip" label="Model Graphics of ${on_string}" name="model_graphics" > <filter>(plot)</filter> </data> <data format="tabular" label="Regression logfile of ${on_string}" name="out_log" /> <data format="tabular" label="Regression model of ${on_string}" name="out_model" /> </outputs> <help> Calculates regression models for a permutation of all GC columns contained in the selected RI database file. The method used for creating the model is either based on a 3rd degree polynomial or a standard linear model. The *Minimum number of residuals* option will only allow regression if the columns it is based on has at least that number of datapoints on the same compound. Filtering is possible by setting an upper limit for the *p-value* and / or a lower limit for the *R squared* value. The produced logfile will state how many models have been discarded due to this filtering. The output model file also includes the p-value and R squared value for each created model. Graphical output of the models is available by selecting the plot option which shows the data points used for the model as well as the fit itself and the range of data that will be usable. .. class:: infomark **Notes** The output file produced by this tool is required as input for the CasLookup tool when selecting to apply regression when finding hits in the RIDB. </help> </tool>