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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 affymetric expression data</description>
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3 <requirements>
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4 <container type="docker">sblanck/testtool:latest</container>
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5 </requirements>
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6 <command>
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7
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8 /galaxy-tools/stderr_wrapper.py Rscript
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9 /galaxy-tools/transcriptomics/AffyQCnormalization/AffyQCnormalization.R
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10 #for $input in $inputs
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11 "${input}"
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12 "${input.name}"
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13 #end for
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14 "${normalization}"
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15 $result_export_eset
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16 $result_html
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17 $result_html.files_path
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18 /galaxy-tools/transcriptomics/AffyQCnormalization/AffyQCnormalization_tpl.html
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19 </command>
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20
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21 <inputs>
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22
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23 <param name="inputs" type="data" format="cel" multiple="true" label=".CEL files" help=".CEL files to be used"/>
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24
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25 <param name="normalization" type="select" label="Preprocessing/normalization">
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26
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27 <option value="rma">rma (backgroung correction + quantile normalization + log2)</option>
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28 <option value="quantile">quantile normalization + log2</option>
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29 <option value="background">background correction + log2</option>
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30 <option value="log2">log2 only</option>
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31
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32
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33 </param>
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34
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35 </inputs>
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36 <outputs>
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37 <data format="rdata" name="result_export_eset" label="export expressionSet"/>
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38 <data format="html" name="result_html" label="QC result"/>
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39 </outputs>
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40
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41 <help>
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42 </help>
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43
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44 </tool> |
