# HG changeset patch
# User cs76
# Date 1449486670 18000
# Node ID cfb2d8ac67978ca913572a2f5192271316177a1d
# Parent  77d886658570fc48b2d555f30f1113d45f73a75a
Deleted selected files

diff -r 77d886658570 -r cfb2d8ac6797 ipo.xml
--- a/ipo.xml	Mon Dec 07 06:09:57 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-<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"
-
------
-
-**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.
-
------
-
-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>
\ No newline at end of file