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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc commit 69bd23adfce0944555888db6712266687276892e
author ecology
date Thu, 08 Jun 2023 08:35:01 +0000
parents f9d76a46799a
children
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1:f9d76a46799a 2:f64b3c1a80a6
1 <tool id="spocc_occ" name="Get species occurrences data" version="0.9.0"> 1 <tool id="spocc_occ" name="Get species occurrences data" version="@VERSION@">
2 <description>from GBIF, ALA, iNAT and others</description> 2 <description>from GBIF, OBIS, ALA, iNAT and others</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.9.0">r-spocc</requirement> 4 <import>macro.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="occ_requirements">
7 </expand>
6 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
7 Rscript '$__tool_directory__/spocc_occ.R' 9 Rscript '$__tool_directory__/spocc_occ.R'
8 '$sname' 10 '$sname'
9 '$from' 11 '$from'
10 $limit; 12 $limit;
18 <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"> 20 <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">
19 <option value="gbif">Global Biodiversity Information Facility : GBIF</option> 21 <option value="gbif">Global Biodiversity Information Facility : GBIF</option>
20 <option value="bison">Biodiversity Information Serving Our Nation : BISON</option> 22 <option value="bison">Biodiversity Information Serving Our Nation : BISON</option>
21 <option value="inat">INaturalist : INAT</option> 23 <option value="inat">INaturalist : INAT</option>
22 <option value="ebird">eBbird</option> 24 <option value="ebird">eBbird</option>
23 <!--
24 <option value="antweb">AntWeb</option>
25 <option value="ala">Atlas of Living Australia : ALA</option> 25 <option value="ala">Atlas of Living Australia : ALA</option>
26 <option value="idigbio">Integrated Digitized Biocollections : iDigBio</option> 26 <option value="idigbio">Integrated Digitized Biocollections : iDigBio</option>
27 <option value="obis">Oceanic Biogeographic Information System : OBIS</option> 27 <option value="obis">Oceanic Biogeographic Information System : OBIS</option>
28 -->
29 <option value="ecoengine">Berkeley Ecoinformatics Engine : EcoEngine</option> 28 <option value="ecoengine">Berkeley Ecoinformatics Engine : EcoEngine</option>
30 <option value="vertnet">VertNet</option> 29 <option value="vertnet">VertNet</option>
31 </param> 30 </param>
32 <param name="limit" type="integer" label="Number of records to return" help="This is passed across all sources" value="500"/> 31 <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"/>
33 </inputs> 32 </inputs>
34 <outputs> 33 <outputs>
35 <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/> 34 <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/>
36 </outputs> 35 </outputs>
37 <tests> 36 <tests>
46 <has_n_columns n="6"/> 45 <has_n_columns n="6"/>
47 </assert_contents> 46 </assert_contents>
48 </output> 47 </output>
49 </test> 48 </test>
50 </tests> 49 </tests>
50 <edam_topics>
51 <edam_topic>topic_0610</edam_topic>
52 <edam_topic>topic_3050</edam_topic>
53 </edam_topics>
51 <help><![CDATA[ 54 <help><![CDATA[
52 =========================== 55 ===========================
53 Get species occurences data 56 Get species occurences data
54 =========================== 57 ===========================
55 **What it does** 58 **What it does**
98 https://ecoengine.berkeley.edu/ 101 https://ecoengine.berkeley.edu/
99 102
100 - VertNet 103 - VertNet
101 http://vertnet.org/ 104 http://vertnet.org/
102 105
103 .. - AntWeb 106 - Integrated Digitized Biocollections : iDigBio
104 .. https://www.antweb.org/ 107 https://www.idigbio.org/
105 108
106 .. - Integrated Digitized Biocollections : iDigBio 109 - Ocean Biogeographic Information System : OBIS
107 .. https://www.idigbio.org/ 110 https://obis.org/
108 111
109 .. - Ocean Biogeographic Information System : OBIS 112 - Atlas of Living Australia : ALA
110 .. https://obis.org/ 113 https://www.ala.org.au/.
111
112 .. - Atlas of Living Australia : ALA
113 .. https://www.ala.org.au/.
114 114
115 115
116 Includes functionality for retrieving species occurrence data, and combining those data. 116 Includes functionality for retrieving species occurrence data, and combining those data.
117 117
118 | 118 |
122 Original source : https://cran.r-project.org/web/packages/spocc/index.html 122 Original source : https://cran.r-project.org/web/packages/spocc/index.html
123 123
124 Reference manual : https://cran.r-project.org/web/packages/spocc/spocc.pdf 124 Reference manual : https://cran.r-project.org/web/packages/spocc/spocc.pdf
125 ]]></help> 125 ]]></help>
126 </tool> 126 </tool>
127