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<tool id="obisindicators" name="Ocean biodiversity indicators" version="@VERSION@" profile="20.01">
    <description>from OBIS</description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro="topic"/>
    <expand macro="requirements">
        <requirement type="package" version="2.0.3">r-magrittr</requirement>
        <requirement type="package" version="1.0.10">r-dplyr</requirement>
        <requirement type="package" version="1.0_7">r-sf</requirement>
        <requirement type="package" version="2.1_7.1">r-gsl</requirement>
        <requirement type="package" version="0.1.0">r-rnaturalearth</requirement>
        <requirement type="package" version="0.1.0">r-rnaturalearthdata</requirement>
        <requirement type="package" version="0.6.2">r-viridis</requirement>
        <requirement type="package" version="3.0.0">r-dggridr</requirement>
    </expand>
    <required_files>
        <include type="literal" path="analyze.r"/>
        <include type="literal" path="visualize.r"/>
        <include type="literal" path="data.r"/>
        <include type="literal" path="obisindicators.r"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
        Rscript
            '$__tool_directory__/obisindicators.r'
            '$input'
            '$colnames'
            '$separator'
            '$longitude'
            '$latitude'
            '$species'
            '$records'
            '$type'
            '$resolution'
            '$__tool_directory__/analyze.r'
            '$__tool_directory__/visualize.r'
            '$__tool_directory__/data.r'
            '$output_index'
            '$plots'
        ]]>
    </command>
    <inputs>
        <expand macro="obis_input"/>
        <param name="separator" type="select" display="radio" label="What character is the separator in your data? (Mostlikely a comma for a csv file and t for a tabular)">
            <option value="t">Tabulator (\t)</option>                 
            <option value=",">Comma (,)</option>  
        </param> 
        <param name="longitude" label="Select column containing the decimal value of the longitude " type="data_column" data_ref="input" numerical="true" use_header_names="true"/>
        <param name="latitude" label="Select column containing the decimal value of the latitude " type="data_column" data_ref="input" numerical="true" use_header_names="true"/>
        <param name="species" label="Select column containing the species " type="data_column" data_ref="input" use_header_names="true"/>
        <param name="records" label="Select column containing the number of records" type="data_column" data_ref="input" numerical="true" use_header_names="true"/>
        <param name="type" type="select" label="Type of projection for the map : select your coordinate reference system (CRS)">
            <option value="0">Robinson projection</option>
            <option value="4326">Geographic projection</option>
        </param>
        <param name="resolution" type="integer" value="9" min="1" max="30" label="Choose a resolution for the discrete global grid (a number between 1, low resolution, and 30, high resolution)" data_ref="input" help="We strongly advise to stay below 15 or else you won't see a thing. The bigger your dataset is the smaller the resolution should be."/>
    </inputs>
    <outputs>
        <data name="output_index" from_work_dir="Index.csv" format="csv" label="Index">
        </data>
        <collection type="list" name="plots">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="input" value="occ_at.tabular"/>
            <param name="colnames" value="true"/>
            <param name="separator" value="t"/>
            <param name="longitude" value="c1: decimalLongitude"/>
            <param name="latitude" value="c2: decimalLatitude"/>
            <param name="species" value="c3: species"/>
            <param name="records" value="c5: records"/>
            <param name="type" value="0"/>
            <param name="resolution" value="9"/>
            <output name="output_index" value="Index.csv"/>
            <output_collection name="plots" type="list" count="5">
                <element name="ES_50" ftype="png">
                    <assert_contents>
                        <has_text text="PNG"/>
                    </assert_contents>
                </element>
                <element name="Maxp" ftype="png">
                    <assert_contents>
                        <has_text text="PNG"/>
                    </assert_contents>
                </element>
                <element name="Records" ftype="png">
                    <assert_contents>
                        <has_text text="PNG"/>
                    </assert_contents>
                </element>
                <element name="Shannon_index" ftype="png">
                    <assert_contents>
                        <has_text text="PNG"/>
                    </assert_contents>
                </element>
               <element name="Simpson_index" ftype="png">
                    <assert_contents>
                        <has_text text="PNG"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
================================================
Calculates biodiversity indicators and maps them
================================================


**What it does**

This tool calculates the number of records, species richness, Simpson index, Shannon index, Hurlbert index (n = 50), and Hill numbers for each cell.

**Input description**

A tabular file with observation data. Must at least contain four columns longitude, latitude, taxon (any taxon level : species, family, ...) and records.


+----------+-----------+---------+------------+
| latitude | longitude |  taxon  |  records   |
+==========+===========+=========+============+
| lat      |long       | taxonID |      4     |
+----------+-----------+---------+------------+
|  ...     |    ...    |   ...   |     ...    |
+----------+-----------+---------+------------+

**Output**

- A text output that summarizes in a tabular the results of all the indicators.

- Multiple PNG files representing the indicators on a map (according to the choice of map made).
    ]]></help>
    <expand macro="obis_bibref"/>
</tool>