--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IdCorrect_2ndLayer_en.xml	Mon Aug 06 09:13:29 2018 -0400
@@ -0,0 +1,102 @@
+<tool id="IdCorrect_2ndLayer" name="Tadarida data cleaner" version="0.1">
+    <description>clean data from animal detection on acoustic recordings</description>
+    <requirements>
+        <requirement type="package" version="1.10.4">r-data.table</requirement>
+        <requirement type="package" version="4.6_12">r-randomforest</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript 
+         '$__tool_directory__/IdCorrect_2ndLayer.R' '$participation_file' 
+
+         #if $learner.condi_learner == "custom":
+             '$learner.user_learner'
+         #else
+             '$__tool_directory__/ClassifEspC2b_180222.learner'
+         #end if
+
+         '${participation_file.name}' 
+         
+         '$output'
+]]>
+    </command>
+    <inputs>
+        <param name="participation_file" type="data" format="csv" label="Participation file"/>
+        <param name="learner" type="data" label="Choose your leaner" format="rdata"/>
+
+        <conditional name="learner">
+            <param name="condi_learner" type="select" label="Select a classifier" help="Default is ClassifEspC2b_180222">
+                <option value="c18">ClassifEspC2b_180222</option>
+                <option value="custom">Custom Classifier</option>
+            </param>
+
+            <when value="c18">
+            </when>
+            <when value="custom">        
+                <param name="user_learner" type="data" label="Choose your classifier" format="rdata"/>
+            </when>
+        </conditional>
+
+    </inputs>
+    <outputs>
+        <data name="output" from_work_dir="output.tabular" format="tabular"/>
+    </outputs>
+    <tests>
+        <test> 
+            <param name="participation_file" value="IdCor2Layer_Test1_obs.csv"/>
+            <param name="condi_learner" value="default_learner"/>
+            <output name="output" file="IdCor2Layer_Test1_out.tabular"/>
+        </test>
+        <test>             
+            <param name="participation_file" value="IdCor2Layer_Test1_obs.csv"/>
+            <param name="condi_learner" value="custom_learner"/>
+            <param name="user_learner" value="ClassifEspC2b_171206.learner"/>
+            <output name="output" file="IdCor2Layer_Test1_out.tabular"/>
+        </test> 
+
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark 
+
+==========================
+Tadarida data cleaner
+==========================
+
+**What it does**
+
+This tool intend to correct ids from 1st layer of Tadarida software, and improve data output according to context (= the whole output of a sampling session).
+
+**Arguments**
+
+It should be called with 2 consecutive arguments :
+
+- a summary table of TadaridaC output from vigiechiro.herokuapp.com web portal. 
+- the 2nd layer classifier built on validated id in Vigie-Chiro database (eg : "ClassifEspC2b_180222.learner")
+  ]]></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>