view butterfly_analysis/butterfly_crossplot.xml @ 8:73d80db53ecc draft default tip

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<tool id="butterfly_crossplot" name="Butterfly data analysis and graph display" version="0.1.0">
    <requirements>
        <requirement type="package" version="2.2.1">r-ggplot2</requirement>
	<requirement type="package" version="1.5_9">r-cairo</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/butterfly_crossplot.R' 
          '$__tool_directory__/stat_bag.r' 
          '$butterfly_db'
          '$__tool_directory__/code_couleurs.csv' 
          $function
    ]]></command>
    <inputs>
        <param name="function" type="select" multiple="True" optional="false" label="Select your analyse" help="Chose at least one element you want to compare. It can be geographical regions, local networks or production methods.">
            <option value="ggCompareLevel">Compare production methods</option>
            <option value="ggfiltre1niveau">Compare regions</option>
            <option value="gglocal">Compare local networks</option>
        </param>
        <param name="butterfly_db" type="data" format="csv,tabular" label="Butterfly datafile" help="Describe file content."/>
    </inputs>
    <outputs>
        <data format="png" name="ggCompareLevel" label="Compare production methods" from_work_dir="resultats/Papillons_CONDUITEPARCELLE_comparaison.png">
            <filter>'ggCompareLevel' in function</filter>
        </data>
        <collection type="list" name="output_ggfiltre" label="Compare regions">
            <discover_datasets pattern="region(?P&lt;designation&gt;.+)\.png" visible="false" format="png" directory="resultats"/>
                <filter>'ggfiltre1niveau' in function</filter>
        </collection>
        <collection type="list" name="output_gglocal" label="Compare local networks">
            <discover_datasets pattern="network(?P&lt;designation&gt;.+)\.png" visible="false" format="png" directory="resultats"/>
                <filter>'gglocal' in function</filter>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="butterfly_db" value="shortBDD_PAPILLONS_2016.txt"/>
            <param name="function" value="ggCompareLevel"/>
            <output name="ggCompareLevel" value="output_ggcomparelevel.png" ftype="png"/>
        </test>
        <test>
            <param name="butterfly_db" value="shortBDD_PAPILLONS_2016.txt"/>
            <param name="function" value="ggfiltre1niveau"/>
            <output_collection name="output_ggfiltre" type="list">
                <element name="Papillons_BOURGOGNE" value="bourgogne.png" ftype="png"/>
            </output_collection>
        </test>
    </tests>    
    <help><![CDATA[

=====================================
Butterfly analysis and data display
=====================================

**What it does**
  
This tool allows to compare butterfly diversity and abundance across regions, observation networks, and production methods.

It uses measures from the Observatoire Agricole de la Biodiversity.
    
Plots show abundance (x) versus diversity (y). 

Line lenght gives information about dispertion, longer lines means bigger heterogeneity accross fields.

|

**How to use it**

Chose a database file, and one or more data display.

|

**Outputs**

*Compare production methods* option will show differences accross agricultural production methods accross all data.

*Compare regions* option will create a collection of graph. One plot for each region in created, they show data informations in that region compared with global data.

*Compare local networks* does the same as the 'regions' option but for every observation networks.

    ]]></help>
</tool>