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1 <tool id="ipo" name="XCMS - IPO" version="0.1.0">
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2 <description>: A Tool for automated Optimization of XCMS Parameters</description>
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3 <command interpreter="Rscript">ipo.R $input $html_file $html_file.files_path</command>
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4 <inputs>
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5 <param format="cdf" name="input" type="data" label="Source file"/>
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6 </inputs>
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7 <outputs>
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8 <data format="html" name="html_file" label="ipo_output.html"/>
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9 </outputs>
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10 <help>
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11 **IPO - Version 0.1**
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12
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13 Version 0.1 uses the following XCMS parameters as default
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14
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15 > peakpickingParameters$min_peakwidth : c(10,20)
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16
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17 > peakpickingParameters$max_peakwidth : c(26,42)
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18
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19 > peakpickingParameters$ppm : 20
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20
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21 > peakpickingParameters$nSlaves : 4 # as.numeric(args[3])
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22
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23 > type : "centWave"
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24
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25 -----
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26
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27 **IPO optimization process**
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28
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29 .. image:: ${static_path}/images/ipo.jpg
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30 :height: 400
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31 :width: 429
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32
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33 -----
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34
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35 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.
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36
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37 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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38
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39 -----
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40
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41 The method 'optimizeXcmsSet' has the following parameters:
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42
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43 > **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.
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44
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45 > **params**: a list consisting of items named according to 'xcms' peak picking methods parameters. A default list is created by 'getDefaultXcmsSetStartingParams'.
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46
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47 > **nSlaves**: the number ofexperiments of an DoE processed in parallel
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48
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49 > **subdir**: a directory where the response surface models are stored. Can also be NULL if no rsm's should be saved.
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50 </help>
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51 </tool> |
