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1 <tool id="Rdata_exctract" name="Rdata parser" version="0.1">
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2 <requirements>
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3 <requirement type="package" version="1.20.0">r-getopt</requirement>
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4 <requirement type="package" version="7.0">readline</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 mkdir outputs &&
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8 Rscript '$__tool_directory__/rdata_extractor.R' '$rdata' $selectedattributes '$summary' '$other' '$bind_dataframe'
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9 ]]>
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10 </command>
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11 <inputs>
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12 <param name="rdata" type="data" label="Rdata file to explore" format="rdata"/>
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13 <param name="rdata_attributes" type="data" label="File with .Rdata content details" format="tabular"/>
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14
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15 <param name="selectedattributes" label="Select which attribute(s) you want to extract" type="select" display="checkboxes" multiple="true">
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16 <options from_dataset="rdata_attributes">
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17 <column name="value" index="0"/>
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18 </options>
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19 </param>
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20 <param name="bind_dataframe" label="Bind variables in a single tabular when its possible" type="boolean" truevalue="bind" falsevalue="nobind" checked="true"/>
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21 </inputs>
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22 <outputs>
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23 <data name="summary" from_work_dir="summary.tabular" format="tabular" label="Summary"/>
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24 <data name="other">
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25 <discover_datasets pattern="__designation_and_ext__" visible="true" directory="outputs"/>
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26 </data>
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27 </outputs>
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28 <help><![CDATA[
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29
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30 .. class:: infomark
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31
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32 ==========================
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33 Rdata parser
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34 ==========================
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35 **What it does**
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36
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37
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38 The Rdata parser tool allows to extract informations from a binary R file in .RData format.
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39
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40
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41 It produces a summary file and extract the selected dimensions.
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42
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43 More informations concerning R Data format and save / load functions can be found here: http://www.sthda.com/english/wiki/saving-data-into-r-data-format-rds-and-rdata>.
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44
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45 More informations concerning R Data format and save / load functions can be found here: http://www.sthda.com/english/wiki/saving-data-into-r-data-format-rds-and-rdata>.
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46
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47
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48 |
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49
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50 **How to use it**
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51
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52 First use the Rdata reader tool to get the list of dimensions available in the binary file.
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53
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54 Use the reader tool output to select the dimension(s) you want to extract.
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55
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56 If the selected variables can be displayed alongside in a tabular files the option \"Bind\" will try to do so.
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57
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58 ]]></help>
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59 </tool>
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