<tool id="vigiechiro_idcorrect_2ndlayer" name="Tadarida data cleaner" version="@VERSION@">
    <description>clean data from animal detection on acoustic recordings</description>
    <macros>
        <import>vigiechiro_macros.xml</import>
    </macros>
    <expand macro="vigiechiro_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        Rscript 
         '$__tool_directory__/Id_Tidy.R' 
         '$participation_file'
         '${participation_file.name}' 
	 '$output'
]]>
    </command>
    <inputs>
        <param name="participation_file" type="data" format="csv" label="Participation file" help="Summary table of TadaridaC"/>
    </inputs>
    <outputs>
        <data name="output" from_work_dir="Id_tidy.tabular" format="tabular"/>
    </outputs>
    <tests>
        <test> 
            <param name="participation_file" value="input_tidy_test1_obs.csv"/>
            <output name="output" file="output_tidy.tabular"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark 

==========================
Tadarida data cleaner
==========================

**What it does**

This tool intends to clean and format data from Tadarida software, and improve data output according to context (= the whole output of a sampling session). This step is mandatory before applying validations with the "Identifications validation" tool.

**Arguments**

- Input is a summary table of TadaridaC output from vigiechiro.herokuapp.com web portal.

- Output is a formated data table ready to be corrected with the validation tool.

  ]]></help>
    <expand macro="vigiechiro_bibref" />
</tool>