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annotate spocc_occ.xml @ 1:f9d76a46799a draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc commit 8f11ecf7d465ef7b326bab46d8c8402c85cfed77
author ecology
date Fri, 14 Jun 2019 09:00:58 -0400
parents 724ad06de5a5
children f64b3c1a80a6
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724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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1 <tool id="spocc_occ" name="Get species occurrences data" version="0.9.0">
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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2 <description>from GBIF, ALA, iNAT and others</description>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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3 <requirements>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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4 <requirement type="package" version="0.9.0">r-spocc</requirement>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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5 </requirements>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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6 <command detect_errors="exit_code"><![CDATA[
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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7 Rscript '$__tool_directory__/spocc_occ.R'
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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8 '$sname'
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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9 '$from'
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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10 $limit;
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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11
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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12 #if $from=='gbif':
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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13 sed -z -i -e 's/\n \"/ /g' -e 's/\n}/ /g' output.tab
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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14 #end if
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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15 ]]></command>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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16 <inputs>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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17 <param name="sname" type="text" label="Scientific name of the species" help="Genus species format, eg : Canis lupus"/>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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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">
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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19 <option value="gbif">Global Biodiversity Information Facility : GBIF</option>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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20 <option value="bison">Biodiversity Information Serving Our Nation : BISON</option>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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21 <option value="inat">INaturalist : INAT</option>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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22 <option value="ebird">eBbird</option>
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f9d76a46799a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc commit 8f11ecf7d465ef7b326bab46d8c8402c85cfed77
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23 <!--
0
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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24 <option value="antweb">AntWeb</option>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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25 <option value="ala">Atlas of Living Australia : ALA</option>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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26 <option value="idigbio">Integrated Digitized Biocollections : iDigBio</option>
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f9d76a46799a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc commit 8f11ecf7d465ef7b326bab46d8c8402c85cfed77
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27 <option value="obis">Oceanic Biogeographic Information System : OBIS</option>
f9d76a46799a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc commit 8f11ecf7d465ef7b326bab46d8c8402c85cfed77
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28 -->
0
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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29 <option value="ecoengine">Berkeley Ecoinformatics Engine : EcoEngine</option>
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f9d76a46799a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc commit 8f11ecf7d465ef7b326bab46d8c8402c85cfed77
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30 <option value="vertnet">VertNet</option>
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724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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31 </param>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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32 <param name="limit" type="integer" label="Number of records to return" help="This is passed across all sources" value="500"/>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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33 </inputs>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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34 <outputs>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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35 <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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36 </outputs>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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37 <tests>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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38 <test>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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39 <param name="sname" value="Canis lupus"/>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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40 <param name="from" value="gbif,bison"/>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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41 <param name="limit" value="50"/>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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42 <output name="output">
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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43 <assert_contents>
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44 <has_text text="name"/>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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45 <has_text text="Canis lupus"/>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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46 <has_n_columns n="6"/>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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47 </assert_contents>
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48 </output>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52 ===========================
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53 Get species occurences data
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54 ===========================
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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55 **What it does**
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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56
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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57 Search species occurences across a single or many data sources.
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58
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59 |
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60
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61 **How to use it**
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62
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63 Enter a species scientific name, be careful that the tool is case sensitive. Eg : Canis lupus.
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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64
1
f9d76a46799a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc commit 8f11ecf7d465ef7b326bab46d8c8402c85cfed77
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65 Select one or more data source. It can be any combination of gbif, bison, inat, ebird, ecoengine and/or vertnet.
0
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66
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67 |
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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68
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69 **Output**
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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70
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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71 The tool returns a table with the species observations available in the chosen databases.
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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72
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73 Output file will have the following attributes : name, longituden latitude, prov, data, key.
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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74
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75 prov is the datasouce and key the occurence corresponding unique identifier.
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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76
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77 |
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78
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79 **How it works**
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724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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81 This tool use the spocc R package (Spocc::occ) :
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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82
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83 A programmatic interface to many species occurrence data sources, including :
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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84
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85 - Global Biodiversity Information Facility : GBIF
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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86 https://www.gbif.org/
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87
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88 - USGSs' Biodiversity Information Serving Our Nation : BISON
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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89 https://bison.usgs.gov/#home
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90
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91 - iNaturalist : iNat
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92 https://www.inaturalist.org/,
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93
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94 - eBird
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95 https://ebird.org/home
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96
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97 - Berkeley Ecoinformatics Engine : EcoEngine
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98 https://ecoengine.berkeley.edu/
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99
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100 - VertNet
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101 http://vertnet.org/
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102
1
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103 .. - AntWeb
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104 .. https://www.antweb.org/
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105
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106 .. - Integrated Digitized Biocollections : iDigBio
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107 .. https://www.idigbio.org/
0
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108
1
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109 .. - Ocean Biogeographic Information System : OBIS
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110 .. https://obis.org/
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111
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112 .. - Atlas of Living Australia : ALA
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113 .. https://www.ala.org.au/.
0
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114
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115
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116 Includes functionality for retrieving species occurrence data, and combining those data.
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117
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118 |
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119
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120 **Sources**
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121
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122 Original source : https://cran.r-project.org/web/packages/spocc/index.html
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123
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124 Reference manual : https://cran.r-project.org/web/packages/spocc/spocc.pdf
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125 ]]></help>
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126 </tool>