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annotate spocc_occ.xml @ 2:f64b3c1a80a6 draft default tip

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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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rev   line source
2
f64b3c1a80a6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc commit 69bd23adfce0944555888db6712266687276892e
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1 <tool id="spocc_occ" name="Get species occurrences data" version="@VERSION@">
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2 <description>from GBIF, OBIS, ALA, iNAT and others</description>
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3 <macros>
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4 <import>macro.xml</import>
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5 </macros>
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6 <expand macro="occ_requirements">
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7 </expand>
0
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript '$__tool_directory__/spocc_occ.R'
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10 '$sname'
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11 '$from'
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12 $limit;
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13
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14 #if $from=='gbif':
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15 sed -z -i -e 's/\n \"/ /g' -e 's/\n}/ /g' output.tab
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16 #end if
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17 ]]></command>
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18 <inputs>
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19 <param name="sname" type="text" label="Scientific name of the species" help="Genus species format, eg : Canis lupus"/>
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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">
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21 <option value="gbif">Global Biodiversity Information Facility : GBIF</option>
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22 <option value="bison">Biodiversity Information Serving Our Nation : BISON</option>
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23 <option value="inat">INaturalist : INAT</option>
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24 <option value="ebird">eBbird</option>
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25 <option value="ala">Atlas of Living Australia : ALA</option>
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26 <option value="idigbio">Integrated Digitized Biocollections : iDigBio</option>
1
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27 <option value="obis">Oceanic Biogeographic Information System : OBIS</option>
0
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28 <option value="ecoengine">Berkeley Ecoinformatics Engine : EcoEngine</option>
1
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29 <option value="vertnet">VertNet</option>
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30 </param>
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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"/>
0
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32 </inputs>
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33 <outputs>
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34 <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="sname" value="Canis lupus"/>
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39 <param name="from" value="gbif,bison"/>
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40 <param name="limit" value="50"/>
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41 <output name="output">
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42 <assert_contents>
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43 <has_text text="name"/>
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44 <has_text text="Canis lupus"/>
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45 <has_n_columns n="6"/>
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46 </assert_contents>
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47 </output>
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48 </test>
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49 </tests>
2
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50 <edam_topics>
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51 <edam_topic>topic_0610</edam_topic>
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52 <edam_topic>topic_3050</edam_topic>
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53 </edam_topics>
0
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54 <help><![CDATA[
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55 ===========================
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56 Get species occurences data
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57 ===========================
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58 **What it does**
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59
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60 Search species occurences across a single or many data sources.
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61
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62 |
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63
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64 **How to use it**
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65
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66 Enter a species scientific name, be careful that the tool is case sensitive. Eg : Canis lupus.
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67
1
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68 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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69
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70 |
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71
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72 **Output**
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73
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74 The tool returns a table with the species observations available in the chosen databases.
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75
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76 Output file will have the following attributes : name, longituden latitude, prov, data, key.
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77
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78 prov is the datasouce and key the occurence corresponding unique identifier.
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80 |
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81
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82 **How it works**
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83
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84 This tool use the spocc R package (Spocc::occ) :
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85
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86 A programmatic interface to many species occurrence data sources, including :
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87
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88 - Global Biodiversity Information Facility : GBIF
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89 https://www.gbif.org/
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90
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91 - USGSs' Biodiversity Information Serving Our Nation : BISON
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92 https://bison.usgs.gov/#home
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93
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94 - iNaturalist : iNat
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95 https://www.inaturalist.org/,
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96
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97 - eBird
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98 https://ebird.org/home
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99
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100 - Berkeley Ecoinformatics Engine : EcoEngine
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101 https://ecoengine.berkeley.edu/
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102
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103 - VertNet
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104 http://vertnet.org/
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105
2
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106 - Integrated Digitized Biocollections : iDigBio
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107 https://www.idigbio.org/
0
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108
2
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109 - Ocean Biogeographic Information System : OBIS
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110 https://obis.org/
1
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111
2
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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>
2
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127