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<tool id="IdValid" name="Tadarida identifications integration" version="0.1">
    <description>Integrate identifications from animal detection on acoustic recordings</description>
    <requirements>
        <requirement type="package" version="1.10.4">r-data.table</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript 
         '$__tool_directory__/IdValid.R' '$inputfile'  '$__tool_directory__/Referentiel_seuils_C2.csv'  '$output'
]]>
    </command>
    <inputs>
        <param name="inputfile" type="data" format="tabular" label="IdCorrect 2nd layer output"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" from_work_dir="output.tabular" label="${tool.name} on ${on_string}"/>
    </outputs>

    <tests>
        <test>
            <param name="inputfile" value="IdCor2Layer_Test1_out.tabular"/>
            <output name="output" file="BilanEnrichiPF_Test1.tabular"/>
        </test>
    </tests>


    <help><![CDATA[

.. class:: infomark 

=====================================
Tadarida identifications integration
=====================================

**What it does**

This tool allows to integrate identifications made by observers and validators and will provide an input for synthesis of participations. 


**Arguments**

- The input is a tabular file, output from the tool IdCorrect_2ndLayer.
- The output is a single tabular file with validated Ids

  ]]></help>
    <citations>
        <citation type="bibtex">
            @article{kerbiriou2015vigie,
            title={Vigie-Chiro: 9 ans de suivi des tendances des esp{\`e}ces communes},
            author={Kerbiriou, C and Julien, JF and Bas, Y and Marmet, J and Le Viol, I and Lorrilliere, R and Azam, C and Gasc, A and Lois, G},
            journal={Symbioses, nouvelle s{\'e}rie},
            number={34},
            year={2015}
            }
        </citation>
        <citation type="bibtex">
            @inproceedings{bas2013automatic,
            title={Automatic echolocation calls identification in Europe vs. Neotropics: more species does not mean more difficult},
            author={Bas, Yves and Escallon, Antoine and Ferre, Matthieu and Haquart, Alexandre and Rufray, Vincent and Disca, Thierry and Julien, Jean-Fran{\c{c}}ois}
            }
        </citation>
        <citation type="bibtex">
            @inproceedings{kerbiriou2010long,
            title={Long term trends monitoring of bats, from biodiversity indicator production to species specialization assessment},
            author={Kerbiriou, C and Bas, Y and Dufr{\^e}ne, L and Robert, A and Julien, JF},
            booktitle={24th Annual Meeting of the Society for Conservation Biology, Edmonton, Canada},
            year={2010}
            }
        </citation>
        <citation type="doi">10.5334/jors.154</citation>  
    </citations>
</tool>