# HG changeset patch
# User cs76
# Date 1449486313 18000
# Node ID 5cd5308cc3981eae2aa17d4cc60a322f6b6438f8

Uploaded - version 0.1

diff -r 000000000000 -r 5cd5308cc398 ipo.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipo.xml	Mon Dec 07 06:05:13 2015 -0500
@@ -0,0 +1,51 @@
+<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>
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