<tool id="csv2tab_R" name="CSV to Tabular" version="0.1">
    <requirements>
        <requirement type="package" version="3.2.1">R</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/csv2tab.R' '$input1' '$sep' '$header' '$output' ]]>
    </command>
    <inputs>
        <param format="csv" name="input1" type="data" label="CSV file"/>
        <param name="sep" type="text" label="Separator" value=",">
            <sanitizer sanitize="False"/>
        </param>
        <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Header in file"/>

    </inputs>

    <outputs>
        <data format="tabular" name="output" from_work_dir="out.tabular" />
    </outputs>
    
    <tests>
        <test>
            <param name="input1" value="example_csv.csv"/>
            <param name="sep" value=","/>
            <param name="header" value="FALSE"/>
            <output name="output" file="out.tabular"/>
        </test>
    </tests>

    <help>
**What it does**

Convert a CSV file to a tabular.

Transform the chosen separator to tab. It is important to specify if the file has a header line.

If the field separator is a comma and there are commas inside text fields the tool will only modify the first category in tabs.

------

**Example**

Input CSV :

	"John","Smith","2 mySteet, myCity"

	"François","LeFrançais","1 rue du Général, Paris"

	"Other","Random","Stuff, stuff, stuff"



Output tabular :

	"John"	"Smith"	"2 mySteet, myCity"

	"François"	"LeFrançais"	"1 rue du Général, Paris"

	"Other"	"Random"	"Stuff, stuff, stuff"

------

**Arguments**

Input : csv file.

Separator : default is ",".

Header : True/False.


    </help>
</tool>