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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 Galaxy - Version 0.1**

v0.1 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 

> type : "centWave"

-----

**IPO optimization process**

.. image:: https://raw.githubusercontent.com/glibiseller/IPO/master/vignettes/FlowChart.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.

-----

Github Repo IPO: https://github.com/glibiseller/IPO/blob/master/vignettes/IPO.Rmd

Publication :    http://www.biomedcentral.com/1471-2105/16/118

-----

**Dependencies**

  Install all dependencies for IPO

    > source("http://bioconductor.org/biocLite.R")

    > biocLite("CAMERA")

    > biocLite("xcms")

    > install.packages("rsm")

  Install RTools

  For windows:

    Download and install RTools from http://cran.r-project.org/bin/windows/Rtools/

  For Unix:

    Install the R-development-packages (r-devel or r-base-dev)

  Install packages needed for installation from github

    > install.packages("devtools")

  Install IPO

    > library("devtools")
    
    > install_github("glibiseller/IPO") 

  </help>
</tool>