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

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author mnhn65mo
date Mon, 06 Aug 2018 09:13:29 -0400
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1 <tool id="BilanEnrichiPF" name="Advanced restitution: summary" 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 '$__tool_directory__/BilanEnrichiPF.R' '$IdC2' '$__tool_directory__/refPF.csv' '$__tool_directory__/SpeciesList.csv'
13
14 &&
15 tail -n +2 output-summary.html > tmp && mv tmp output-summary.html &&
16 tail -n +2 output-nightly.html > tmp && mv tmp output-nightly.html &&
17 tail -n +2 output-hourly.html > tmp && mv tmp output-hourly.html
18 ]]>
19 </command>
20 <inputs>
21 <param name="IdC2" type="data" format="tabular" label="IdValid output"/>
22 </inputs>
23 <outputs>
24 <data name="output_summary_tabular" format="tabular" from_work_dir="output-summary.tabular" label="${tool.name} on ${on_string} Summary"/>
25 <data name="output_summary_html" format="html" from_work_dir="output-summary.html" label="${tool.name} on ${on_string} Summary"/>
26
27 <data name="output_nightly_tabular" format="tabular" from_work_dir="output-nightly.tabular" label="${tool.name} on ${on_string} Nightly"/>
28 <data name="output_nightly_html" format="html" from_work_dir="output-nightly.html" label="${tool.name} on ${on_string} Nightly"/>
29
30 <data name="output_hourly_tabular" format="tabular" from_work_dir="output-hourly.tabular" label="${tool.name} on ${on_string} Hourly"/>
31 <data name="output_hourly_html" format="html" from_work_dir="output-hourly.html" label="${tool.name} on ${on_string} Hourly"/>
32 </outputs>
33
34 <tests>
35 <test>
36 <param name="IdC2" value="BilanEnrichiPF_Test1.tabular"/>
37 <output name="output_tab" file="BilanEnrichiPF_Test1_out_tab.tabular" ftype="tabular"/>
38 </test>
39 </tests>
40
41 <help><![CDATA[
42
43 .. class:: infomark
44
45 ==========================
46 Advanced restitution
47 ==========================
48
49 **What it does**
50
51 The tool treats observations made with the "Point fixe" protocol: https://www.vigienature-ecole.fr/node/954&gt
52
53 **Arguments**
54
55 - Input is an observation/participation file corrected by the tools IdCorrect_2ndLayer and IdValid.
56 - Outputs are Summary/Nightly/Hourly raw tabulars, and html visualisations.
57
58 ]]></help>
59
60 <citations>
61 <citation type="bibtex">
62 @article{kerbiriou2015vigie,
63 title={Vigie-Chiro: 9 ans de suivi des tendances des esp{\`e}ces communes},
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},
65 journal={Symbioses, nouvelle s{\'e}rie},
66 number={34},
67 year={2015}
68 }
69 </citation>
70 <citation type="bibtex">
71 @inproceedings{bas2013automatic,
72 title={Automatic echolocation calls identification in Europe vs. Neotropics: more species does not mean more difficult},
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}
74 }
75 </citation>
76 <citation type="bibtex">
77 @inproceedings{kerbiriou2010long,
78 title={Long term trends monitoring of bats, from biodiversity indicator production to species specialization assessment},
79 author={Kerbiriou, C and Bas, Y and Dufr{\^e}ne, L and Robert, A and Julien, JF},
80 booktitle={24th Annual Meeting of the Society for Conservation Biology, Edmonton, Canada},
81 year={2010}
82 }
83 </citation>
84 <citation type="doi">10.5334/jors.154</citation>
85 </citations>
86 </tool>