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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/normalize_dataset commit 21b25425f77162c0edae4dd87b3a9e33608c5a95-dirty
author bebatut
date Fri, 15 Apr 2016 08:42:40 -0400
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72633301cc0d planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/normalize_dataset commit 21b25425f77162c0edae4dd87b3a9e33608c5a95-dirty
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1 <tool id="normalize_dataset" name="Normalize a dataset by" version="0.1.0">
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2 <description>row or column sum to obtain proportion or percentage</description>
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4 <requirements>
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5 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 <exit_code range=":-1" />
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10 </stdio>
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12 <version_command></version_command>
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14 <command><![CDATA[
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15 python $__tool_directory__/normalize_dataset.py
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16 --input_file $input_file
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17 --output_file $output_file
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18 --normalization $normalization
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19 --format $format
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20 ]]></command>
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21
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22 <inputs>
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23 <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/>
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24
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25 <param name="normalization" label="Normalization on" type="select" help="(--normalization)">
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26 <option value="column" selected="True">Column</option>
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27 <option value="row">Row</option>
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28 </param>
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29
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30 <param name="format" label="Output format" type="select" help="(--format)">
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31 <option value="proportion" selected="True">Proportion</option>
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32 <option value="percentage">Percentage</option>
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33 </param>
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34 </inputs>
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35
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36 <outputs>
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37 <data name="output_file" format="tabular"
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38 label="${tool.name} on ${on_string}: Normalized dataset" />
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39 </outputs>
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40
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41 <tests>
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42 <test>
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43 <param name="input_file" value="input_file.tabular"/>
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44 <param name="normalization" value="column"/>
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45 <param name="format" value="proportion"/>
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46 <output name="output_file" file="output_column_proportion.tabular"/>
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47 </test>
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48 <test>
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49 <param name="input_file" value="input_file.tabular"/>
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50 <param name="normalization" value="row"/>
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51 <param name="format" value="proportion"/>
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52 <output name="output_file" file="output_row_proportion.tabular"/>
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53 </test>
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54 <test>
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55 <param name="input_file" value="input_file.tabular"/>
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56 <param name="normalization" value="column"/>
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57 <param name="format" value="percentage"/>
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58 <output name="output_file" file="output_column_percentage.tabular"/>
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59 </test>
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60 </tests>
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61
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62 <help><![CDATA[
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63 **What it does**
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64
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65 This tool normalizes each row or column of a dataset by the row or column sum.
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66 The results can be in proportion or percentage.
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67
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68 The input file must be in tabular format with tab-separated columns. Only data will be used for normalization.
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69 ]]></help>
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70
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71 <citations>
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72 </citations>
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73 </tool>