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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
author ecology
date Thu, 23 May 2019 09:58:35 -0400
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-1:000000000000 0:724ad06de5a5
1 <tool id="spocc_occ" name="Get species occurrences data" version="0.9.0">
2 <description>from GBIF, ALA, iNAT and others</description>
3 <requirements>
4 <requirement type="package" version="0.9.0">r-spocc</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 Rscript '$__tool_directory__/spocc_occ.R'
8 '$sname'
9 '$from'
10 $limit;
11
12 #if $from=='gbif':
13 sed -z -i -e 's/\n \"/ /g' -e 's/\n}/ /g' output.tab
14 #end if
15 ]]></command>
16 <inputs>
17 <param name="sname" type="text" label="Scientific name of the species" help="Genus species format, eg : Canis lupus"/>
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">
19 <option value="gbif">Global Biodiversity Information Facility : GBIF</option>
20 <option value="bison">Biodiversity Information Serving Our Nation : BISON</option>
21 <option value="inat">INaturalist : INAT</option>
22 <option value="ebird">eBbird</option>
23 <option value="antweb">AntWeb</option>
24 <option value="ala">Atlas of Living Australia : ALA</option>
25 <option value="idigbio">Integrated Digitized Biocollections : iDigBio</option>
26 <option value="obis">Oceanic Biogeographic Information System : OBIS</option>
27 <option value="ecoengine">Berkeley Ecoinformatics Engine : EcoEngine</option>
28 <option value="vernet">VerNet</option>
29 </param>
30 <param name="limit" type="integer" label="Number of records to return" help="This is passed across all sources" value="500"/>
31 </inputs>
32 <outputs>
33 <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/>
34 </outputs>
35 <tests>
36 <test>
37 <param name="sname" value="Canis lupus"/>
38 <param name="from" value="gbif,bison"/>
39 <param name="limit" value="50"/>
40 <output name="output">
41 <assert_contents>
42 <has_text text="name"/>
43 <has_text text="Canis lupus"/>
44 <has_n_columns n="6"/>
45 </assert_contents>
46 </output>
47 </test>
48 </tests>
49 <help><![CDATA[
50 ===========================
51 Get species occurences data
52 ===========================
53 **What it does**
54
55 Search species occurences across a single or many data sources.
56
57 |
58
59 **How to use it**
60
61 Enter a species scientific name, be careful that the tool is case sensitive. Eg : Canis lupus.
62
63 Select one or more data source. It can be any combination of gbif, bison, inat, ebird, antweb, ala, idigbio, obis, ecoengine and/or vertnet.
64
65 |
66
67 **Output**
68
69 The tool returns a table with the species observations available in the chosen databases.
70
71 Output file will have the following attributes : name, longituden latitude, prov, data, key.
72
73 prov is the datasouce and key the occurence corresponding unique identifier.
74
75 |
76
77 **How it works**
78
79 This tool use the spocc R package (Spocc::occ) :
80
81 A programmatic interface to many species occurrence data sources, including :
82
83 - Global Biodiversity Information Facility : GBIF
84 https://www.gbif.org/
85
86 - USGSs' Biodiversity Information Serving Our Nation : BISON
87 https://bison.usgs.gov/#home
88
89 - iNaturalist : iNat
90 https://www.inaturalist.org/,
91
92 - eBird
93 https://ebird.org/home
94
95 - Berkeley Ecoinformatics Engine : EcoEngine
96 https://ecoengine.berkeley.edu/
97
98 - AntWeb
99 https://www.antweb.org/
100
101 - Integrated Digitized Biocollections : iDigBio
102 https://www.idigbio.org/
103
104 - VertNet
105 http://vertnet.org/
106
107 - Ocean Biogeographic Information System : OBIS
108 https://obis.org/
109
110 - Atlas of Living Australia : ALA
111 https://www.ala.org.au/.
112
113
114 Includes functionality for retrieving species occurrence data, and combining those data.
115
116 |
117
118 **Sources**
119
120 Original source : https://cran.r-project.org/web/packages/spocc/index.html
121
122 Reference manual : https://cran.r-project.org/web/packages/spocc/spocc.pdf
123 ]]></help>
124 </tool>