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1 <tool id="BilanEnrichiPF" name="Advanced restitution: summary" version="0.1">
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2 <description>from Animal Detection on Acoustic Recordings</description>
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3 <requirements>
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4 <requirement type="package" version="1.4.3">r-reshape2</requirement>
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5 <requirement type="package" version="1.10.4">r-data.table</requirement>
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6 <requirement type="package" version="0.2">r-dt</requirement>
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7 <requirement type="package" version="0.9">r-htmlwidgets</requirement>
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8 <requirement type="package" version="2.1.1">pandoc</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 Rscript
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12 '$__tool_directory__/BilanEnrichiPF.R' '$IdC2' '$__tool_directory__/refPF.csv' '$__tool_directory__/SpeciesList.csv'
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13
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14 &&
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15 tail -n +2 output-summary.html > tmp && mv tmp output-summary.html &&
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16 tail -n +2 output-nightly.html > tmp && mv tmp output-nightly.html &&
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17 tail -n +2 output-hourly.html > tmp && mv tmp output-hourly.html
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name="IdC2" type="data" format="tabular" label="IdValid output"/>
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22 </inputs>
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23 <outputs>
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24 <data name="output_summary_tabular" format="tabular" from_work_dir="output-summary.tabular" label="${tool.name} on ${on_string} Summary"/>
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25 <data name="output_summary_html" format="html" from_work_dir="output-summary.html" label="${tool.name} on ${on_string} Summary"/>
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26
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27 <data name="output_nightly_tabular" format="tabular" from_work_dir="output-nightly.tabular" label="${tool.name} on ${on_string} Nightly"/>
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28 <data name="output_nightly_html" format="html" from_work_dir="output-nightly.html" label="${tool.name} on ${on_string} Nightly"/>
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29
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30 <data name="output_hourly_tabular" format="tabular" from_work_dir="output-hourly.tabular" label="${tool.name} on ${on_string} Hourly"/>
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31 <data name="output_hourly_html" format="html" from_work_dir="output-hourly.html" label="${tool.name} on ${on_string} Hourly"/>
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32 </outputs>
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33
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34 <tests>
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35 <test>
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36 <param name="IdC2" value="BilanEnrichiPF_Test1.tabular"/>
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37 <output name="output_tab" file="BilanEnrichiPF_Test1_out_tab.tabular" ftype="tabular"/>
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38 </test>
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39 </tests>
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40
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41 <help><![CDATA[
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42
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43 .. class:: infomark
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44
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45 ==========================
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46 Advanced restitution
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47 ==========================
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48
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49 **What it does**
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50
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51 The tool treats observations made with the "Point fixe" protocol: https://www.vigienature-ecole.fr/node/954>
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52
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53 **Arguments**
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54
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55 - Input is an observation/participation file corrected by the tools IdCorrect_2ndLayer and IdValid.
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56 - Outputs are Summary/Nightly/Hourly raw tabulars, and html visualisations.
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57
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58 ]]></help>
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59
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60 <citations>
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61 <citation type="bibtex">
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62 @article{kerbiriou2015vigie,
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63 title={Vigie-Chiro: 9 ans de suivi des tendances des esp{\`e}ces communes},
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64 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},
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65 journal={Symbioses, nouvelle s{\'e}rie},
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66 number={34},
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67 year={2015}
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68 }
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69 </citation>
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70 <citation type="bibtex">
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71 @inproceedings{bas2013automatic,
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72 title={Automatic echolocation calls identification in Europe vs. Neotropics: more species does not mean more difficult},
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73 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}
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74 }
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75 </citation>
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76 <citation type="bibtex">
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77 @inproceedings{kerbiriou2010long,
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78 title={Long term trends monitoring of bats, from biodiversity indicator production to species specialization assessment},
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79 author={Kerbiriou, C and Bas, Y and Dufr{\^e}ne, L and Robert, A and Julien, JF},
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80 booktitle={24th Annual Meeting of the Society for Conservation Biology, Edmonton, Canada},
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81 year={2010}
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82 }
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83 </citation>
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84 <citation type="doi">10.5334/jors.154</citation>
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85 </citations>
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86 </tool>
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