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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IdValiden.xml	Mon Aug 06 09:13:29 2018 -0400
@@ -0,0 +1,71 @@
+<tool id="IdValid" name="Tadarida identifications integration" version="0.1">
+    <description>Integrate identifications from animal detection on acoustic recordings</description>
+    <requirements>
+        <requirement type="package" version="1.10.4">r-data.table</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript 
+         '$__tool_directory__/IdValid.R' '$inputfile'  '$__tool_directory__/Referentiel_seuils_C2.csv'  '$output'
+]]>
+    </command>
+    <inputs>
+        <param name="inputfile" type="data" format="tabular" label="IdCorrect 2nd layer output"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" from_work_dir="output.tabular" label="${tool.name} on ${on_string}"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="inputfile" value="IdCor2Layer_Test1_out.tabular"/>
+            <output name="output" file="BilanEnrichiPF_Test1.tabular"/>
+        </test>
+    </tests>
+
+
+    <help><![CDATA[
+
+.. class:: infomark 
+
+=====================================
+Tadarida identifications integration
+=====================================
+
+**What it does**
+
+This tool allows to integrate identifications made by observers and validators and will provide an input for synthesis of participations. 
+
+
+**Arguments**
+
+- The input is a tabular file, output from the tool IdCorrect_2ndLayer.
+- The output is a single tabular file with validated Ids
+
+  ]]></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>