Mercurial > repos > mnhn65mo > vigiechiro
comparison IdValiden.xml @ 0:0e3db3a308c0 draft default tip
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| author | mnhn65mo |
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| date | Mon, 06 Aug 2018 09:13:29 -0400 |
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| -1:000000000000 | 0:0e3db3a308c0 |
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| 1 <tool id="IdValid" name="Tadarida identifications integration" version="0.1"> | |
| 2 <description>Integrate identifications from animal detection on acoustic recordings</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.10.4">r-data.table</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 Rscript | |
| 8 '$__tool_directory__/IdValid.R' '$inputfile' '$__tool_directory__/Referentiel_seuils_C2.csv' '$output' | |
| 9 ]]> | |
| 10 </command> | |
| 11 <inputs> | |
| 12 <param name="inputfile" type="data" format="tabular" label="IdCorrect 2nd layer output"/> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data name="output" format="tabular" from_work_dir="output.tabular" label="${tool.name} on ${on_string}"/> | |
| 16 </outputs> | |
| 17 | |
| 18 <tests> | |
| 19 <test> | |
| 20 <param name="inputfile" value="IdCor2Layer_Test1_out.tabular"/> | |
| 21 <output name="output" file="BilanEnrichiPF_Test1.tabular"/> | |
| 22 </test> | |
| 23 </tests> | |
| 24 | |
| 25 | |
| 26 <help><![CDATA[ | |
| 27 | |
| 28 .. class:: infomark | |
| 29 | |
| 30 ===================================== | |
| 31 Tadarida identifications integration | |
| 32 ===================================== | |
| 33 | |
| 34 **What it does** | |
| 35 | |
| 36 This tool allows to integrate identifications made by observers and validators and will provide an input for synthesis of participations. | |
| 37 | |
| 38 | |
| 39 **Arguments** | |
| 40 | |
| 41 - The input is a tabular file, output from the tool IdCorrect_2ndLayer. | |
| 42 - The output is a single tabular file with validated Ids | |
| 43 | |
| 44 ]]></help> | |
| 45 <citations> | |
| 46 <citation type="bibtex"> | |
| 47 @article{kerbiriou2015vigie, | |
| 48 title={Vigie-Chiro: 9 ans de suivi des tendances des esp{\`e}ces communes}, | |
| 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}, | |
| 50 journal={Symbioses, nouvelle s{\'e}rie}, | |
| 51 number={34}, | |
| 52 year={2015} | |
| 53 } | |
| 54 </citation> | |
| 55 <citation type="bibtex"> | |
| 56 @inproceedings{bas2013automatic, | |
| 57 title={Automatic echolocation calls identification in Europe vs. Neotropics: more species does not mean more difficult}, | |
| 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} | |
| 59 } | |
| 60 </citation> | |
| 61 <citation type="bibtex"> | |
| 62 @inproceedings{kerbiriou2010long, | |
| 63 title={Long term trends monitoring of bats, from biodiversity indicator production to species specialization assessment}, | |
| 64 author={Kerbiriou, C and Bas, Y and Dufr{\^e}ne, L and Robert, A and Julien, JF}, | |
| 65 booktitle={24th Annual Meeting of the Society for Conservation Biology, Edmonton, Canada}, | |
| 66 year={2010} | |
| 67 } | |
| 68 </citation> | |
| 69 <citation type="doi">10.5334/jors.154</citation> | |
| 70 </citations> | |
| 71 </tool> |