view BilanEnrichiPFen.xml @ 0:0e3db3a308c0 draft default tip

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<tool id="BilanEnrichiPF" name="Advanced restitution: summary" version="0.1">
    <description>from Animal Detection on Acoustic Recordings</description>
    <requirements>
        <requirement type="package" version="1.4.3">r-reshape2</requirement> 
        <requirement type="package" version="1.10.4">r-data.table</requirement>
        <requirement type="package" version="0.2">r-dt</requirement>
        <requirement type="package" version="0.9">r-htmlwidgets</requirement>
        <requirement type="package" version="2.1.1">pandoc</requirement>
    </requirements>
    <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="IdValid output"/>
    </inputs>
    <outputs>
        <data name="output_summary_tabular" format="tabular" from_work_dir="output-summary.tabular" label="${tool.name} on ${on_string} Summary"/>
        <data name="output_summary_html" format="html" from_work_dir="output-summary.html" label="${tool.name} on ${on_string} Summary"/>

        <data name="output_nightly_tabular" format="tabular" from_work_dir="output-nightly.tabular" label="${tool.name} on ${on_string} Nightly"/>
        <data name="output_nightly_html" format="html" from_work_dir="output-nightly.html" label="${tool.name} on ${on_string} Nightly"/>

        <data name="output_hourly_tabular" format="tabular" from_work_dir="output-hourly.tabular" label="${tool.name} on ${on_string} Hourly"/>
        <data name="output_hourly_html" format="html" from_work_dir="output-hourly.html" label="${tool.name} on ${on_string} Hourly"/>
    </outputs>

    <tests>
        <test>
            <param name="IdC2" value="BilanEnrichiPF_Test1.tabular"/>
            <output name="output_tab" file="BilanEnrichiPF_Test1_out_tab.tabular" ftype="tabular"/>
        </test>
    </tests>

    <help><![CDATA[

.. class:: infomark 

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

**What it does**

The tool treats observations made with the "Point fixe" protocol:  https://www.vigienature-ecole.fr/node/954&gt

**Arguments**

- Input is an observation/participation file corrected by the tools IdCorrect_2ndLayer and IdValid.
- Outputs are Summary/Nightly/Hourly raw tabulars, and html visualisations.

    ]]></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>