view robis.xml @ 1:5bae75c49f2e draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 13ac67c0a21d742b29e6273cdff058560abad770

<tool id="obis_data" name="OBIS occurences" version="@VERSION@" profile="20.01">
    <description>retrieve data</description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro="topic"/>
    <expand macro="requirements">
        <requirement type="package" version="2.11.3">r-robis</requirement>
    </expand>
    <required_files>
        <include type="literal" path="robis.r"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
        Rscript
            '$__tool_directory__/robis.r'
            '$species'
            '$taxon'
            '$lat_min'
            '$lat_max'
            '$long_min'
            '$long_max'
            '$output'
        ]]>
    </command>
    <inputs>
        <param name="species" type="text" label="Scientific name of the species" help="Genus species format, eg : Scomber scombrus">
            <validator type="regex">^[A-Za-z ]*$</validator>
        </param>
        <param name="taxon" type="text" label="Taxon ID">
            <validator type="regex">^[0-9]*$</validator>
        </param>
        <param name="lat_min" type="float" min="-90" max="90" value="0" label="Input latitude min (+north/-south):" optional="true"/>
        <param name="lat_max" type="float" min="-90" max="90" value="0" label="Input latitude max (+north/-south):" optional="true"/>
        <param name="long_min" type="float" min="-90" max="90" value="0" label="Input longitude min (+east/-west):" optional="true"/>
        <param name="long_max" type="float" min="-90" max="90" value="0" label="Input longitude max (+east/-west):" optional="true"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="species" value="Scomber scombrus"/>
            <output name="output">
                <assert_contents>
                    <has_text text="Scombridae"/>
                    <has_n_columns n="167"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="lat_min" value="6"/>
            <param name="lat_max" value="12"/>
            <param name="long_min" value="40"/>
            <param name="long_max" value="43"/>
            <output name="output">
                <assert_contents>
                    <has_text text="basisOfRecord"/>
                    <has_n_columns n="148"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
===========================
Get species occurences data
===========================      
**What it does**

Search and retrieve species occurences across OBIS database.

|

**How to use it**

Enter a species scientific name, be careful that the tool is case sensitive. Eg : Scomber scombrus.

Or enter the latitude longitude of the area you want to retrieve data from.


|

**Output**

The tool returns a table with the species observations available in OBIS database.

Output file will have at least the following attributes : BasisOfRecords, longitude, latitude, species, individualcount.

|

**How it works**

This tool use the robis R package.


Includes functionality for retrieving species occurrence data, and combining those data.
    ]]></help>
    <expand macro="obis_doiref"/>
</tool>