<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>
   <requirements>
        <requirement type="package" version="1.10.4">r-data.table</requirement>
        <requirement type="package" version="4.6_12">r-randomforest</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript 
         '$__tool_directory__/IdCorrect_2ndLayer.R' '$participation_file' 

         #if $learner.condi_learner == "custom"
             '$learner.user_learner'
         #else
             '$__tool_directory__/ClassifEspC2b_180222.learner'
         #end if
         '${participation_file.name}' 
         '$output'
]]>
    </command>
    <inputs>
        <param name="participation_file" type="data" format="csv" label="Participation file" help="Summary table of TadaridaC"/>
        <param name="learner" type="data" label="Choose your leaner" format="rdata"/>
        <conditional name="learner">
            <param name="condi_learner" type="select" label="Select a classifier" help="Default is ClassifEspC2b_180222">
                <option value="c18">ClassifEspC2b_180222</option>
                <option value="custom">Custom Classifier</option>
            </param>
            <when value="c18">
            </when>
            <when value="custom">        
                <param name="user_learner" type="data" label="Choose your classifier" format="rdata"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" from_work_dir="output.tabular" format="tabular"/>
    </outputs>
    <tests>
        <test> 
            <param name="participation_file" value="IdCor2Layer_Test1_obs.csv"/>
            <param name="condi_learner" value="default_learner"/>
            <output name="output" file="IdCor2Layer_Test1_out.tabular"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark 

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

**What it does**

This tool intends to correct ids from 1st layer of Tadarida software, and improves data output according to context (= the whole output of a sampling session).

**Arguments**

It should be called with 2 consecutive arguments :

- a summary table of TadaridaC output from vigiechiro.herokuapp.com web portal. 
- the 2nd layer classifier built on validated id in Vigie-Chiro database (eg : "ClassifEspC2b_180222.learner")
  ]]></help>
    <expand macro="vigiechiro_bibref" />
</tool>