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1 <tool id="xlsx2tab_R" name="XLSX sheet to Tabular" version="0.1">
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2 <requirements>
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3 <requirement type="package" version="3.2.1">R</requirement>
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4 <requirement type="package" version="1.1.0">r-readxl</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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3
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7 cp '$input1' input.xlsx &&
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8 Rscript '$__tool_directory__/xlsx2tab.R' input.xlsx '$sheet' '$output' ]]>
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0
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9 </command>
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10 <inputs>
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11 <param format="xlsx" name="input1" type="data" label="XLSX file"/>
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12 <param name="sheet" type="text" label="Excel sheet name" value="biodiv_data">
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13 <sanitizer sanitize="False"/>
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14 </param>
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15
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16 </inputs>
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17
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18 <outputs>
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19 <data format="tabular" name="output" from_work_dir="out.tabular" />
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20 </outputs>
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21
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22 <tests>
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23 <test>
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24 <param name="input1" value="example_csv.csv"/>
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25 <param name="sheet" value=","/>
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26 <output name="output" file="out.tabular"/>
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27 </test>
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28 </tests>
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29
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30 <help>
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31 **What it does**
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32
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33 Extract a sheet from XLSX file to a tabular file.
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34
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35
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36 ------
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37
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38 **Example**
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39
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40 Input XLSX sheet
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41
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42
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43
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44 Output tabular :
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45
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46 "John" "Smith" "2 mySteet, myCity"
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47
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48 "François" "LeFrançais" "1 rue du Général, Paris"
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49
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50 "Other" "Random" "Stuff, stuff, stuff"
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51
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52 ------
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53
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54 **Arguments**
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55
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56 Input : xlsx file.
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57
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58
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59
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60
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61 </help>
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62 </tool>
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