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1 <tool id="QCnormalization" name="QCnormalization" version="0.1.0">
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2 <description>Quality control and normalization of affymetrix expression data</description>
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8
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3 <stdio>
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4 <exit_code range="1:" />
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5
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6 <regex match="Warning"
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7 source="both"
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8 level="warning"
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9 />
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10 </stdio>
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11 <requirements>
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2
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12 <!--container type="docker">sblanck/smat</container-->
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13 <requirement type="package" version="0.1.0">r-smagexp</requirement>
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14 </requirements>
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8
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15 <command>
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16 <![CDATA[
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17 Rscript
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18 ${__tool_directory__}/AffyQCnormalization.R
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19 --input "#for $input in $inputs# $input;$input.name, #end for#"
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20 --normalization ${normalization}
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21 --rdataoutput $result_export_eset
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22 --htmloutput $result_html
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23 --htmloutputpath $result_html.files_path
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24 --htmltemplate ${__tool_directory__}/AffyQCnormalization_tpl.html
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2
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25 ]]>
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26 </command>
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27
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28 <inputs>
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29
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30 <param name="inputs" type="data" format="cel" multiple="true" label=".CEL files" help=".CEL files to be used"/>
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31
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32 <param name="normalization" type="select" label="Preprocessing/normalization">
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33
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34 <option value="rma">rma (backgroung correction + quantile normalization + log2)</option>
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35 <option value="quantile">quantile normalization + log2</option>
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36 <option value="background">background correction + log2</option>
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37 <option value="log2">log2 only</option>
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38
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39
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40 </param>
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41
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42 </inputs>
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43 <outputs>
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44 <data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>
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45 <data format="html" name="result_html" label="QC result"/>
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46 </outputs>
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47
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48 <help>
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49 <![CDATA[
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50 **What it does**
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51
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52 The QCnormalization tool offers to ensure the quality of the data and to normalize them. Several normalization methods are available :
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53
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54 * rma normalization
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55 * quantile normalization + log2
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56 * background correction + log2
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57 * log2 only
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58
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59 **Results**
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60
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61 - Several quality figures : microarray images, boxplots and MA plots
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62 - Rdata object containing the normalized data for further analysis
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63
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64 ]]>
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65 </help>
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66
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67 </tool>
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