Mercurial > repos > ecology > spocc_occ
comparison spocc_occ.xml @ 2:f64b3c1a80a6 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc commit 69bd23adfce0944555888db6712266687276892e
author | ecology |
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date | Thu, 08 Jun 2023 08:35:01 +0000 |
parents | f9d76a46799a |
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1:f9d76a46799a | 2:f64b3c1a80a6 |
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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 |