<tool id="vigiechiro_bilanenrichipf" name="Advanced restitution: 'Point fixe' protocol" version="@VERSION@">
    <description>from Animal Detection on Acoustic Recordings</description>
    <macros>
        <import>vigiechiro_macros.xml</import>
    </macros>   
    <expand macro="vigiechiro_requirements">
        <expand macro="vigiechiro_bilanenrichi_requirements"/>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/BilanEnrichiPF.R' 
            '$idc2' 
            '$__tool_directory__/refPF.csv' 
            '$__tool_directory__/SpeciesList.csv' 
        &&
        tail -n +2 output-summary.html > tmp && mv tmp output-summary.html &&
        tail -n +2 output-nightly.html > tmp && mv tmp output-nightly.html &&
        tail -n +2 output-hourly.html > tmp && mv tmp output-hourly.html
]]>
    </command>
    <inputs>
        <param name="idc2" type="data" format="tabular" label="Corrected and validated observation file" help="Use output file from 'Tadarida identifications integration' : a sampling session file corrected and validated. Point fixe protocol"/>
        <param name="output_choice" type="select" multiple="True" optional="FALSE" label="Select a summary display" help="Chose whether your want a nigthly, hourly or global summary">
            <option value="nightly">nigthly summary</option>
            <option value="hourly">hourly summary</option>
            <option value="global" selected="true">global summary</option>
        </param>		
    </inputs>
    <outputs>
        <data name="output_summary_tabular" format="tabular" from_work_dir="output-summary.tabular" label="${tool.name} on ${on_string} Global Summary">
            <filter>'global' in output_choice</filter>
        </data>    
        <data name="output_summary_html" format="html" from_work_dir="output-summary.html" label="${tool.name} on ${on_string} Global Summary">
            <filter>'global' in output_choice</filter>
        </data>
        <data name="output_nightly_tabular" format="tabular" from_work_dir="output-nightly.tabular" label="${tool.name} on ${on_string} Nightly">
            <filter>'nightly' in output_choice</filter>
        </data>
        <data name="output_nightly_html" format="html" from_work_dir="output-nightly.html" label="${tool.name} on ${on_string} Nightly">
            <filter>'nightly' in output_choice</filter>
        </data>
        <data name="output_hourly_tabular" format="tabular" from_work_dir="output-hourly.tabular" label="${tool.name} on ${on_string} Hourly">
           <filter>'hourly' in output_choice</filter>
       </data> 
       <data name="output_hourly_html" format="html" from_work_dir="output-hourly.html" label="${tool.name} on ${on_string} Hourly">
           <filter>'hourly' in output_choice</filter>
       </data>    
    </outputs>
    <tests>
        <test>
            <param name="idc2" value="BilanEnrichiPF_Test1.tabular"/>
            <param name="output_choice" value="global,nightly,hourly"/> 
            <output name="output_summary_tabular" file="BilanEnrichiPF_Test1_out_tab.tabular" ftype="tabular"/>
            <output name="output_hourly_tabular" file="BilanEnrichiPF_Test1_hourly.tabular" ftype="tabular"/>
            <output name="output_nightly_tabular" file="BilanEnrichiPF_Test1_nightly.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark 

==========================
Advanced restitution 
==========================

**What it does**

The tool treats observations made with the "Point fixe" protocol:  

**Arguments**

- Input is an observation/participation file corrected by the tools Tadarida data cleaner and Tadarida identifications integration.
- Outputs are Summary/Nightly/Hourly raw tabulars, and html visualisations.
    ]]></help>
    <expand macro="vigiechiro_bibref" />
</tool>