changeset 5:16b69e94e08e draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipo.xml	Mon Dec 07 06:27:48 2015 -0500
@@ -0,0 +1,80 @@
+<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>
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