comparison IdCorrect_2ndLayer_en.xml @ 0:0e3db3a308c0 draft default tip

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<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>