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1 <tool id="spocc_occ_no_taxrefv2" name="Get species occurrences data" version="0.2">
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2 <description>from GBIF, ALA, iNAT and others</description>
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3 <requirements>
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4 <!--
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5 <requirement type="package" version="1.2.3">r-stringi</requirement>
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6 <requirement type="package" version="7.0">readline</requirement>
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9
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7 <requirement type="package" version="3.2.1">r-base</requirement>
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8 <requirement type="package" version="0.3_28">rgeos</requirement>
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7
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9 <requirement type="package" version="3.6.2">geos</requirement>
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12
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10 <requirement type="package" version="3.2.1">r-base</requirement>
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10
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11 -->
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12
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12
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13 <requirement type="package" version="0.8.0">r-spocc</requirement>
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0
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14 </requirements>
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15 <command detect_errors="exit_code"><![CDATA[
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16 Rscript '$__tool_directory__/spocc_occ.R' '$sname' '$from' $limit;
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17
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18 #if $from=='gbif':
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19 sed -z -i -e 's/\n \"/ /g' -e 's/\n}/ /g' output.tab
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20 #end if
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21 ]]></command>
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22
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23 <inputs>
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24 <param name="sname" type="text" label="Scientific name" value="Genus species"/>
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25 <param name="from" type="text" label="Data source to get data from, any combination of gbif, bison, inat, ebird, antweb, ala, idigbio, obis, ecoengine and/or vertnet" value="gbif,bison,inat"/>
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26 <param name="limit" type="integer" label="Number of records to return. This is passed across all sources" value="500"/>
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27 </inputs>
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28 <outputs>
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29 <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/>
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30 </outputs>
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31
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32 <!-- Warning old test -->
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33 <tests>
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34 <test>
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35 <param name="sname" value="Canis lupus"/>
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36 <param name="from" value="gbif,bison"/>
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37 <param name="limit" value="50"/>
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38 <param name="taxref_choice" value="do_link_taxref"/>
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39 <output name="output" file="canis-lupus_gbif_bison.tab" ftype="tabular"/>
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40 <output name="output_taxref" file="res_taxref_grep.tab" ftype="tabular"/>
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41 </test>
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42 </tests>
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43
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44 <help><![CDATA[
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45 ==========
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46 Spocc::occ
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47 ==========
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48 **What id does**
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49
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50 Search on a single species name, or many. And search across a single or many data sources.
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51
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52 |
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53
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54 **How it works**
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55
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56 This tool use the spocc R package :
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57
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58 A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'USGSs' Biodiversity Information Serving Our Nation ('BISON'), 'iNaturalist', Berkeley 'Ecoinformatics' Engine, 'AntWeb', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.
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59
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60 |
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61
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62 Original source here : https://cran.r-project.org/web/packages/spocc/index.html
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63
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64 ]]></help>
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65 </tool>
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