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1 <tool id="IdValid" name="Tadarida identifications integration" version="0.1">
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2 <description>Integrate identifications from animal detection on acoustic recordings</description>
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3 <requirements>
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4 <requirement type="package" version="1.10.4">r-data.table</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 Rscript
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8 '$__tool_directory__/IdValid.R' '$inputfile' '$__tool_directory__/Referentiel_seuils_C2.csv' '$output'
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9 ]]>
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10 </command>
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11 <inputs>
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12 <param name="inputfile" type="data" format="tabular" label="IdCorrect 2nd layer output"/>
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13 </inputs>
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14 <outputs>
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15 <data name="output" format="tabular" from_work_dir="output.tabular" label="${tool.name} on ${on_string}"/>
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16 </outputs>
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17
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18 <tests>
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19 <test>
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20 <param name="inputfile" value="IdCor2Layer_Test1_out.tabular"/>
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21 <output name="output" file="BilanEnrichiPF_Test1.tabular"/>
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22 </test>
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23 </tests>
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24
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25
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26 <help><![CDATA[
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27
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28 .. class:: infomark
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29
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30 =====================================
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31 Tadarida identifications integration
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32 =====================================
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33
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34 **What it does**
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35
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36 This tool allows to integrate identifications made by observers and validators and will provide an input for synthesis of participations.
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37
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38
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39 **Arguments**
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40
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41 - The input is a tabular file, output from the tool IdCorrect_2ndLayer.
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42 - The output is a single tabular file with validated Ids
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43
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44 ]]></help>
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45 <citations>
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46 <citation type="bibtex">
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47 @article{kerbiriou2015vigie,
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48 title={Vigie-Chiro: 9 ans de suivi des tendances des esp{\`e}ces communes},
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49 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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50 journal={Symbioses, nouvelle s{\'e}rie},
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51 number={34},
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52 year={2015}
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53 }
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54 </citation>
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55 <citation type="bibtex">
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56 @inproceedings{bas2013automatic,
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57 title={Automatic echolocation calls identification in Europe vs. Neotropics: more species does not mean more difficult},
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58 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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59 }
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60 </citation>
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61 <citation type="bibtex">
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62 @inproceedings{kerbiriou2010long,
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63 title={Long term trends monitoring of bats, from biodiversity indicator production to species specialization assessment},
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64 author={Kerbiriou, C and Bas, Y and Dufr{\^e}ne, L and Robert, A and Julien, JF},
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65 booktitle={24th Annual Meeting of the Society for Conservation Biology, Edmonton, Canada},
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66 year={2010}
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67 }
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68 </citation>
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69 <citation type="doi">10.5334/jors.154</citation>
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70 </citations>
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71 </tool>
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