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1 <tool id="csv2tab_R" name="CSV 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 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 Rscript '$__tool_directory__/csv2tab.R' '$input1' '$sep' '$header' '$output' ]]>
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7 </command>
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8 <inputs>
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9 <param format="csv" name="input1" type="data" label="CSV file"/>
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10 <param name="sep" type="text" label="Separator" value=",">
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11 <sanitizer sanitize="False"/>
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12 </param>
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13 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Header in file"/>
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14
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15 </inputs>
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16
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17 <outputs>
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18 <data format="tabular" name="output" from_work_dir="out.tabular" />
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19 </outputs>
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20
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21 <tests>
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22 <test>
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23 <param name="input1" value="example_csv.csv"/>
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24 <param name="sep" value=","/>
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25 <param name="header" value="FALSE"/>
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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 Convert a CSV file to a tabular.
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34
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35 Transform the chosen separator to tab. It is important to specify if the file has a header line.
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36
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37 If the field separator is a comma and there are commas inside text fields the tool will only modify the first category in tabs.
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38
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39 ------
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40
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41 **Example**
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42
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43 Input CSV :
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44
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45 "John","Smith","2 mySteet, myCity"
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46
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47 "François","LeFrançais","1 rue du Général, Paris"
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48
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49 "Other","Random","Stuff, stuff, stuff"
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50
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51
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52
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53 Output tabular :
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54
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55 "John" "Smith" "2 mySteet, myCity"
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56
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57 "François" "LeFrançais" "1 rue du Général, Paris"
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58
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59 "Other" "Random" "Stuff, stuff, stuff"
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60
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61 ------
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62
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63 **Arguments**
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64
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65 Input : csv file.
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66
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67 Separator : default is ",".
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68
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69 Header : True/False.
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70
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71
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72 </help>
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73 </tool>
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