annotate spocc_occ.xml @ 2:f64b3c1a80a6 draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc commit 69bd23adfce0944555888db6712266687276892e

<tool id="spocc_occ" name="Get species occurrences data" version="@VERSION@">
    <description>from GBIF, OBIS, ALA, iNAT and others</description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro="occ_requirements">
    </expand>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/spocc_occ.R' 
            '$sname' 
            '$from' 
            $limit; 

        #if $from=='gbif':
            sed -z -i -e 's/\n  \"/ /g' -e 's/\n}/ /g' output.tab
        #end if
    ]]></command>
    <inputs>
        <param name="sname" type="text" label="Scientific name of the species" help="Genus species format, eg : Canis lupus"/>
        <param name="from" type="select" multiple="true" label="Data source to get data from" help="Any combination of gbif, bison, inat, ebird, antweb, ala, idigbio, obis, ecoengine and/or vertnet" value="gbif,bison,inat">
            <option value="gbif">Global Biodiversity Information Facility : GBIF</option>
            <option value="bison">Biodiversity Information Serving Our Nation : BISON</option>
            <option value="inat">INaturalist : INAT</option>
            <option value="ebird">eBbird</option>
            <option value="ala">Atlas of Living Australia : ALA</option>
            <option value="idigbio">Integrated Digitized Biocollections : iDigBio</option>
            <option value="obis">Oceanic Biogeographic Information System : OBIS</option> 
            <option value="ecoengine">Berkeley Ecoinformatics Engine : EcoEngine</option>
            <option value="vertnet">VertNet</option>
        </param>    
        <param name="limit" type="integer" label="Number of records to return" help="This is passed across all sources. If you have an empty output you should try with a records value smaller." value="500" max="999999"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/>
    </outputs>
    <tests>
        <test> 
            <param name="sname" value="Canis lupus"/>
            <param name="from" value="gbif,bison"/>
            <param name="limit" value="50"/>
            <output name="output">
                <assert_contents>
                    <has_text text="name"/>
                    <has_text text="Canis lupus"/>
                    <has_n_columns n="6"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <edam_topics>
       <edam_topic>topic_0610</edam_topic>
       <edam_topic>topic_3050</edam_topic>
    </edam_topics>
    <help><![CDATA[
===========================
Get species occurences data
===========================      
**What it does**

Search species occurences across a single or many data sources.

|

**How to use it**

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

Select one or more data source. It can be any combination of gbif, bison, inat, ebird, ecoengine and/or vertnet.

|

**Output**

The tool returns a table with the species observations available in the chosen databases.

Output file will have the following attributes : name, longituden latitude, prov, data, key.

prov is the datasouce and key the occurence corresponding unique identifier.

|

**How it works**

This tool use the spocc R package (Spocc::occ) :

A programmatic interface to many species occurrence data sources, including :

  - Global Biodiversity Information Facility : GBIF
    https://www.gbif.org/

  - USGSs' Biodiversity Information Serving Our Nation : BISON
    https://bison.usgs.gov/#home
    
  - iNaturalist : iNat
    https://www.inaturalist.org/,

  - eBird
    https://ebird.org/home

  - Berkeley Ecoinformatics Engine : EcoEngine
    https://ecoengine.berkeley.edu/

  - VertNet
    http://vertnet.org/

  - Integrated Digitized Biocollections : iDigBio
    https://www.idigbio.org/

  - Ocean Biogeographic Information System : OBIS 
    https://obis.org/

  - Atlas of Living Australia : ALA
    https://www.ala.org.au/. 


Includes functionality for retrieving species occurrence data, and combining those data.

|

**Sources**

Original source : https://cran.r-project.org/web/packages/spocc/index.html

Reference manual : https://cran.r-project.org/web/packages/spocc/spocc.pdf
    ]]></help>
</tool>