Mercurial > repos > ecology > obis_data
diff robis.xml @ 0:1fcd81d65467 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
author | ecology |
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date | Thu, 18 Jan 2024 09:33:52 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/robis.xml Thu Jan 18 09:33:52 2024 +0000 @@ -0,0 +1,98 @@ +<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="163"/> + </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="144"/> + </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>