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annotate AffyQCnormalization.xml @ 26:0de248d72d9e draft

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author sblanck
date Thu, 22 Mar 2018 05:40:57 -0400
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1 <tool id="QCnormalization" name="QCnormalization" version="1.0.0">
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3 <description>Quality control and normalization of affymetrix expression data</description>
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5 <requirements>
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6 <requirement type="package">bioconductor-biobase</requirement>
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7 <requirement type="package">bioconductor-geoquery</requirement>
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8 <requirement type="package">bioconductor-geometadb</requirement>
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9 <requirement type="package">bioconductor-limma</requirement>
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10 <requirement type="package">bioconductor-biobase</requirement>
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11 <requirement type="package">bioconductor-affy</requirement>
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12 <requirement type="package">bioconductor-affyPLM</requirement>
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13 <requirement type="package">r-jsonlite</requirement>
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14 <requirement type="package">r-dplyr</requirement>
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15 <requirement type="package">r-optparse</requirement>
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16 </requirements>
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17
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18 <stdio>
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19 <exit_code range="1:" />
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20 <regex match="Warning" source="both" level="warning"/>
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21 </stdio>
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22
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23 <command>
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24 <![CDATA[
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25 Rscript
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26 ${__tool_directory__}/AffyQCnormalization.R
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27 --input "#for $input in $inputs# $input;$input.name, #end for#"
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28 --normalization ${normalization}
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29 --rdataoutput $result_export_eset
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30 --htmloutput $result_html
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31 --htmloutputpath $result_html.files_path
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32 --htmltemplate ${__tool_directory__}/AffyQCnormalization_tpl.html
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33 ]]>
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34 </command>
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36 <inputs>
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37 <param name="inputs" type="data" format="cel" multiple="true" label=".CEL files" help=".CEL files to be used"/>
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38 <param name="normalization" type="select" label="Preprocessing/normalization">
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39 <option value="rma">rma (backgroung correction + quantile normalization + log2)</option>
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40 <option value="quantile">quantile normalization + log2</option>
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41 <option value="background">background correction + log2</option>
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42 <option value="log2">log2 only</option>
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43 </param>
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44 </inputs>
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46 <outputs>
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47 <data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>
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48 <data format="html" name="result_html" label="QC result"/>
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49 </outputs>
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50
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51 <help>
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52 <![CDATA[
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53 **What it does**
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54
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55 The QCnormalization tool offers to ensure the quality of the data and to normalize them. Several normalization methods are available :
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56
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57 * rma normalization
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58 * quantile normalization + log2
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59 * background correction + log2
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60 * log2 only
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62 **Results**
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64 - Several quality figures : microarray images, boxplots and MA plots
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65 - Rdata object containing the normalized data for further analysis
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67 ]]>
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68 </help>
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70 </tool>