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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BilanEnrichiPFen.xml	Mon Aug 06 09:13:29 2018 -0400
@@ -0,0 +1,86 @@
+<tool id="BilanEnrichiPF" name="Advanced restitution: summary" version="0.1">
+    <description>from Animal Detection on Acoustic Recordings</description>
+    <requirements>
+        <requirement type="package" version="1.4.3">r-reshape2</requirement> 
+        <requirement type="package" version="1.10.4">r-data.table</requirement>
+        <requirement type="package" version="0.2">r-dt</requirement>
+        <requirement type="package" version="0.9">r-htmlwidgets</requirement>
+        <requirement type="package" version="2.1.1">pandoc</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript 
+            '$__tool_directory__/BilanEnrichiPF.R' '$IdC2' '$__tool_directory__/refPF.csv' '$__tool_directory__/SpeciesList.csv' 
+ 
+        &&
+        tail -n +2 output-summary.html > tmp && mv tmp output-summary.html &&
+        tail -n +2 output-nightly.html > tmp && mv tmp output-nightly.html &&
+        tail -n +2 output-hourly.html > tmp && mv tmp output-hourly.html
+]]>
+    </command>
+    <inputs>
+        <param name="IdC2" type="data" format="tabular" label="IdValid output"/>
+    </inputs>
+    <outputs>
+        <data name="output_summary_tabular" format="tabular" from_work_dir="output-summary.tabular" label="${tool.name} on ${on_string} Summary"/>
+        <data name="output_summary_html" format="html" from_work_dir="output-summary.html" label="${tool.name} on ${on_string} Summary"/>
+
+        <data name="output_nightly_tabular" format="tabular" from_work_dir="output-nightly.tabular" label="${tool.name} on ${on_string} Nightly"/>
+        <data name="output_nightly_html" format="html" from_work_dir="output-nightly.html" label="${tool.name} on ${on_string} Nightly"/>
+
+        <data name="output_hourly_tabular" format="tabular" from_work_dir="output-hourly.tabular" label="${tool.name} on ${on_string} Hourly"/>
+        <data name="output_hourly_html" format="html" from_work_dir="output-hourly.html" label="${tool.name} on ${on_string} Hourly"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="IdC2" value="BilanEnrichiPF_Test1.tabular"/>
+            <output name="output_tab" file="BilanEnrichiPF_Test1_out_tab.tabular" ftype="tabular"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+.. class:: infomark 
+
+==========================
+Advanced restitution 
+==========================
+
+**What it does**
+
+The tool treats observations made with the "Point fixe" protocol:  https://www.vigienature-ecole.fr/node/954&gt
+
+**Arguments**
+
+- Input is an observation/participation file corrected by the tools IdCorrect_2ndLayer and IdValid.
+- Outputs are Summary/Nightly/Hourly raw tabulars, and html visualisations.
+
+    ]]></help>
+
+    <citations>
+        <citation type="bibtex">
+            @article{kerbiriou2015vigie,
+            title={Vigie-Chiro: 9 ans de suivi des tendances des esp{\`e}ces communes},
+            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},
+            journal={Symbioses, nouvelle s{\'e}rie},
+            number={34},
+            year={2015}
+            }
+        </citation>
+        <citation type="bibtex">
+            @inproceedings{bas2013automatic,
+            title={Automatic echolocation calls identification in Europe vs. Neotropics: more species does not mean more difficult},
+            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}
+            }
+        </citation>
+        <citation type="bibtex">
+            @inproceedings{kerbiriou2010long,
+            title={Long term trends monitoring of bats, from biodiversity indicator production to species specialization assessment},
+            author={Kerbiriou, C and Bas, Y and Dufr{\^e}ne, L and Robert, A and Julien, JF},
+            booktitle={24th Annual Meeting of the Society for Conservation Biology, Edmonton, Canada},
+            year={2010}
+            }
+        </citation>
+        <citation type="doi">10.5334/jors.154</citation>  
+    </citations>
+</tool>