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annotate spocc_occ.xml @ 0:724ad06de5a5 draft

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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
parents
children f9d76a46799a
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0
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>
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4 <requirement type="package" version="0.9.0">r-spocc</requirement>
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5 </requirements>
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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'
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9 '$from'
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10 $limit;
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11
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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
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15 ]]></command>
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16 <inputs>
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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>
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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>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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23 <option value="antweb">AntWeb</option>
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24 <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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25 <option value="idigbio">Integrated Digitized Biocollections : iDigBio</option>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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26 <option value="obis">Oceanic Biogeographic Information System : OBIS</option>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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27 <option value="ecoengine">Berkeley Ecoinformatics Engine : EcoEngine</option>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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28 <option value="vernet">VerNet</option>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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29 </param>
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30 <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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31 </inputs>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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32 <outputs>
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33 <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/>
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34 </outputs>
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35 <tests>
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36 <test>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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37 <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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38 <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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39 <param name="limit" value="50"/>
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40 <output name="output">
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41 <assert_contents>
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42 <has_text text="name"/>
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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43 <has_text text="Canis lupus"/>
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44 <has_n_columns n="6"/>
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45 </assert_contents>
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46 </output>
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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50 ===========================
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51 Get species occurences data
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52 ===========================
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53 **What it does**
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54
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55 Search species occurences across a single or many data sources.
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56
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57 |
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58
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59 **How to use it**
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60
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61 Enter a species scientific name, be careful that the tool is case sensitive. Eg : Canis lupus.
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62
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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.
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64
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65 |
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66
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67 **Output**
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68
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69 The tool returns a table with the species observations available in the chosen databases.
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70
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71 Output file will have the following attributes : name, longituden latitude, prov, data, key.
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72
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73 prov is the datasouce and key the occurence corresponding unique identifier.
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74
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75 |
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76
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77 **How it works**
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78
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79 This tool use the spocc R package (Spocc::occ) :
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80
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81 A programmatic interface to many species occurrence data sources, including :
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82
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83 - Global Biodiversity Information Facility : GBIF
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84 https://www.gbif.org/
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85
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86 - USGSs' Biodiversity Information Serving Our Nation : BISON
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87 https://bison.usgs.gov/#home
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88
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89 - iNaturalist : iNat
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90 https://www.inaturalist.org/,
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91
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92 - eBird
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93 https://ebird.org/home
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94
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95 - Berkeley Ecoinformatics Engine : EcoEngine
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96 https://ecoengine.berkeley.edu/
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97
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98 - AntWeb
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99 https://www.antweb.org/
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100
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101 - Integrated Digitized Biocollections : iDigBio
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102 https://www.idigbio.org/
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103
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104 - VertNet
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105 http://vertnet.org/
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106
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107 - Ocean Biogeographic Information System : OBIS
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108 https://obis.org/
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109
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110 - Atlas of Living Australia : ALA
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111 https://www.ala.org.au/.
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112
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113
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114 Includes functionality for retrieving species occurrence data, and combining those data.
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115
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116 |
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117
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118 **Sources**
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119
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120 Original source : https://cran.r-project.org/web/packages/spocc/index.html
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121
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122 Reference manual : https://cran.r-project.org/web/packages/spocc/spocc.pdf
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123 ]]></help>
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124 </tool>