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author mnhn65mo
date Mon, 06 Aug 2018 09:13:29 -0400
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1 <tool id="BilanEnrichiRP" name="Advanced restitution: raw approach" version="0.1">
2 <description>from Animal Detection on Acoustic Recordings</description>
3 <requirements>
4 <requirement type="package" version="1.4.3">r-reshape2</requirement>
5 <requirement type="package" version="1.10.4">r-data.table</requirement>
6 <requirement type="package" version="0.2">r-dt</requirement>
7 <requirement type="package" version="0.9">r-htmlwidgets</requirement>
8 <requirement type="package" version="2.1.1">pandoc</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 Rscript
12 '$__tool_directory__/BilanEnrichiRP.R' '$IdC2' '$__tool_directory__/refRPSeuil50.csv' '$__tool_directory__/SpeciesList.csv'
13 &&
14 tail -n +2 output-summaryRP.html > tmp && mv tmp output-summaryRP.html &&
15 tail -n +2 output-detailRP.html > tmp && mv tmp output-detailRP.html
16 ]]>
17 </command>
18 <inputs>
19 <param name="IdC2" type="data" format="tabular" label="IdValid output"/>
20 </inputs>
21 <outputs>
22 <data name="output_summary_tabular" format="tabular" from_work_dir="output-summaryRP.tabular" label="${tool.name} on ${on_string} Summary"/>
23 <data name="output_summary_html" format="html" from_work_dir="output-summaryRP.html" label="${tool.name} on ${on_string} Summary"/>
24 <data name="output_detail_tabular" format="tabular" from_work_dir="output-detailRP.tabular" label="${tool.name} on ${on_string} Detail"/>
25 <data name="output_detail_html" format="html" from_work_dir="output-detailRP.html" label="${tool.name} on ${on_string} Detail"/>
26 </outputs>
27
28 <tests>
29 <test>
30 <param name="IdC2" value="BilanEnrichiPF_Test1.tabular"/>
31 <output name="output_tab" file="BilanEnrichiPF_Test1_out_tab.tabular" ftype="tabular"/>
32 </test>
33 </tests>
34
35 <help><![CDATA[
36 **What it does**
37
38 The tool analyses the observations made with the "Routier" or "Pedestre" protocols.
39
40 **Arguments**
41
42 - Input is an observation/participation file corrected by the tools IdCorrect_2ndLayer and IdValid.
43 - Outputs are Summary and details raw tabulars, and html visualisations.
44
45
46 ]]></help>
47
48 <citations>
49 <citation type="bibtex">
50 @article{kerbiriou2015vigie,
51 title={Vigie-Chiro: 9 ans de suivi des tendances des esp{\`e}ces communes},
52 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},
53 journal={Symbioses, nouvelle s{\'e}rie},
54 number={34},
55 year={2015}
56 }
57 </citation>
58 <citation type="bibtex">
59 @inproceedings{bas2013automatic,
60 title={Automatic echolocation calls identification in Europe vs. Neotropics: more species does not mean more difficult},
61 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}
62 }
63 </citation>
64 <citation type="bibtex">
65 @inproceedings{kerbiriou2010long,
66 title={Long term trends monitoring of bats, from biodiversity indicator production to species specialization assessment},
67 author={Kerbiriou, C and Bas, Y and Dufr{\^e}ne, L and Robert, A and Julien, JF},
68 booktitle={24th Annual Meeting of the Society for Conservation Biology, Edmonton, Canada},
69 year={2010}
70 }
71 </citation>
72 <citation type="doi">10.5334/jors.154</citation>
73 </citations>
74 </tool>