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<tool id="ipo" name="XCMS - IPO" version="0.1.0">
  <description>: A Tool for automated Optimization of XCMS Parameters</description>
  <command interpreter="Rscript">ipo.R $input $html_file $html_file.files_path</command>
  <inputs>
    <param format="cdf" name="input" type="data" label="Source file"/>
  </inputs>
  <outputs>
    <data format="html" name="html_file" label="ipo_output.html"/>
  </outputs>
  <help>
**IPO - Version 0.1**

Version 0.1 uses the following XCMS parameters as default

> peakpickingParameters$min_peakwidth : c(10,20) 

> peakpickingParameters$max_peakwidth : c(26,42)

> peakpickingParameters$ppm : 20 

> peakpickingParameters$nSlaves : 4 # as.numeric(args[3])

> type : "centWave"

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**IPO optimization process**

.. image:: ${static_path}/images/ipo.jpg
   :height: 400
   :width: 429

-----

To optimize parameters different values (levels) have to tested for these parameters. To efficiently test many different levels design of experiment (DoE) is used. Box-Behnken and central composite designs set three evenly spaced levels for each parameter. The method 'getDefaultXcmsSetStartingParams' provides default values for the lower and upper levels defining a range. Since the levels are evenly spaced the middle level or center point is calculated automatically. To edit the starting levels of a parameter set the lower and upper level as desired. If a parameter should not be optimized, set a single default value for 'xcms' processing, do not set this parameter to NULL. 

The method 'getDefaultXcmsSetStartingParams' creates a list with default values for the optimization of the peak picking methods 'centWave' or 'matchedFilter'. To choose between these two method set the parameter accordingly.

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The method 'optimizeXcmsSet' has the following parameters:

> **files**: the raw data which is the basis for optimization. This does not necessarly need to be the whole dataset, only quality controls should suffice.
      
> **params**: a list consisting of items named according to 'xcms' peak picking methods parameters. A default list is created by 'getDefaultXcmsSetStartingParams'.
      
> **nSlaves**: the number ofexperiments of an DoE processed in parallel
    
> **subdir**: a directory where the response surface models are stored. Can also be NULL if no rsm's should be saved.
  </help>
</tool>