Mercurial > repos > ecology > spocc_occ
changeset 0:724ad06de5a5 draft
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 |
| files | spocc_occ.R spocc_occ.xml test-data/canis-lupus_gbif_bison1.tab |
| diffstat | 3 files changed, 282 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spocc_occ.R Thu May 23 09:58:35 2019 -0400 @@ -0,0 +1,57 @@ +#!/usr/bin/Rscript + +library(spocc) + + +##Def functions : +help<-function(){ + cat("HELP\n") + cat("Spocc::occ, Search on a single species name, or many. And search across a single or many data sources.\n\n") + cat("Need 3 args :\n") + cat(" - query : (character) One to many scientific names.\n") + cat(" - from : (character) Data source to get data from, any combination of gbif, bison, inat,ebird, ecoengine and/or vertnet.\n") + cat(" - limit : (numeric) Number of records to return. This is passed across all sources.\n") + q("no") +} + +formatSpName <- function(spName) paste(strsplit(spName, split=' ')[[1]], collapse='_') ###Wallace function + +#################################### + +args = commandArgs(trailingOnly=TRUE) + +#Help display +if(args[1]=="-h" || args[1]=="--help" || length(args)<3){help()} + +#Get args +sname<-args[1] +dbase_input<-args[2] +max<-as.integer(args[3]) + +#Get all databases +bases<-strsplit(dbase_input,",") +dbase<-c() +for (base in bases){ + dbase<-c(dbase,base) +} + +#Get occurrences +results <- spocc::occ(query=sname, from=dbase, limit=max, has_coords=TRUE) + +#Dispay results +if(length(dbase)==1){ + results_data <- results[[dbase[1]]]$data[[formatSpName(sname)]] +}else{ + res <- occ2df(results) + results_data <- res +} + +results_data<-as.matrix(results_data) + +#If empty +if(length(results_data)==0){cat("\nNo occurrences found.\nLittle tip : Check your input typo, some databases are case sensitive : Genus species.\n")} + +#Write them +write.table(file="output.tab",results_data,sep="\t",row.names=FALSE) + +q('no')
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spocc_occ.xml Thu May 23 09:58:35 2019 -0400 @@ -0,0 +1,124 @@ +<tool id="spocc_occ" name="Get species occurrences data" version="0.9.0"> + <description>from GBIF, ALA, iNAT and others</description> + <requirements> + <requirement type="package" version="0.9.0">r-spocc</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$__tool_directory__/spocc_occ.R' + '$sname' + '$from' + $limit; + + #if $from=='gbif': + sed -z -i -e 's/\n \"/ /g' -e 's/\n}/ /g' output.tab + #end if + ]]></command> + <inputs> + <param name="sname" type="text" label="Scientific name of the species" help="Genus species format, eg : Canis lupus"/> + <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"> + <option value="gbif">Global Biodiversity Information Facility : GBIF</option> + <option value="bison">Biodiversity Information Serving Our Nation : BISON</option> + <option value="inat">INaturalist : INAT</option> + <option value="ebird">eBbird</option> + <option value="antweb">AntWeb</option> + <option value="ala">Atlas of Living Australia : ALA</option> + <option value="idigbio">Integrated Digitized Biocollections : iDigBio</option> + <option value="obis">Oceanic Biogeographic Information System : OBIS</option> + <option value="ecoengine">Berkeley Ecoinformatics Engine : EcoEngine</option> + <option value="vernet">VerNet</option> + </param> + <param name="limit" type="integer" label="Number of records to return" help="This is passed across all sources" value="500"/> + </inputs> + <outputs> + <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/> + </outputs> + <tests> + <test> + <param name="sname" value="Canis lupus"/> + <param name="from" value="gbif,bison"/> + <param name="limit" value="50"/> + <output name="output"> + <assert_contents> + <has_text text="name"/> + <has_text text="Canis lupus"/> + <has_n_columns n="6"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +=========================== +Get species occurences data +=========================== +**What it does** + +Search species occurences across a single or many data sources. + +| + +**How to use it** + +Enter a species scientific name, be careful that the tool is case sensitive. Eg : Canis lupus. + +Select one or more data source. It can be any combination of gbif, bison, inat, ebird, antweb, ala, idigbio, obis, ecoengine and/or vertnet. + +| + +**Output** + +The tool returns a table with the species observations available in the chosen databases. + +Output file will have the following attributes : name, longituden latitude, prov, data, key. + +prov is the datasouce and key the occurence corresponding unique identifier. + +| + +**How it works** + +This tool use the spocc R package (Spocc::occ) : + +A programmatic interface to many species occurrence data sources, including : + + - Global Biodiversity Information Facility : GBIF + https://www.gbif.org/ + + - USGSs' Biodiversity Information Serving Our Nation : BISON + https://bison.usgs.gov/#home + + - iNaturalist : iNat + https://www.inaturalist.org/, + + - eBird + https://ebird.org/home + + - Berkeley Ecoinformatics Engine : EcoEngine + https://ecoengine.berkeley.edu/ + + - AntWeb + https://www.antweb.org/ + + - Integrated Digitized Biocollections : iDigBio + https://www.idigbio.org/ + + - VertNet + http://vertnet.org/ + + - Ocean Biogeographic Information System : OBIS + https://obis.org/ + + - Atlas of Living Australia : ALA + https://www.ala.org.au/. + + +Includes functionality for retrieving species occurrence data, and combining those data. + +| + +**Sources** + +Original source : https://cran.r-project.org/web/packages/spocc/index.html + +Reference manual : https://cran.r-project.org/web/packages/spocc/spocc.pdf + ]]></help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/canis-lupus_gbif_bison1.tab Thu May 23 09:58:35 2019 -0400 @@ -0,0 +1,101 @@ +"name" "longitude" "latitude" "prov" "date" "key" +"Canis lupus Linnaeus, 1758" " 12.163912" " 60.28862" "gbif" "2019-01-18" "1988307594" +"Canis familiaris Linnaeus, 1758" " 100.405060" " 14.78179" "gbif" "2019-01-21" "2005338796" +"Canis lupus Linnaeus, 1758" " 11.048093" " 59.48167" "gbif" "2019-01-23" "2012823436" +"Canis lupus Linnaeus, 1758" " 28.973364" " 69.23767" "gbif" "2019-01-16" "2028051051" +"Canis lupus dingo Meyer, 1793" " 145.545322" "-16.27793" "gbif" "2019-01-19" "1990575442" +"Canis familiaris Linnaeus, 1758" " -78.833777" " 36.05233" "gbif" "2019-01-24" "1990576477" +"Canis lupus Linnaeus, 1758" " 11.159160" " 59.72548" "gbif" "2019-01-27" "1990656034" +"Canis familiaris Linnaeus, 1758" " 74.792893" " 13.35156" "gbif" "2019-01-07" "1986608286" +"Canis lupus Linnaeus, 1758" " 11.000690" " 59.53739" "gbif" "2019-01-19" "1988307939" +"Canis familiaris Linnaeus, 1758" "-117.216541" " 33.98280" "gbif" "2019-01-20" "2005276886" +"Canis familiaris Linnaeus, 1758" " -97.673194" " 28.42286" "gbif" "2019-01-23" "1990570437" +"Canis lupus Linnaeus, 1758" " 11.047684" " 59.48154" "gbif" "2019-01-23" "2006001212" +"Canis lupus lycaon Schreber, 1775" " -78.401972" " 45.57230" "gbif" "2019-01-02" "1986610881" +"Canis familiaris Linnaeus, 1758" "-101.629497" " 37.12117" "gbif" "2019-01-10" "1990470069" +"Canis lupus Linnaeus, 1758" " 9.030524" " 44.74131" "gbif" "2019-01-12" "1990488501" +"Canis lupus Linnaeus, 1758" " -93.110484" " 45.40214" "gbif" "2019-01-17" "1993718245" +"Canis lupus Linnaeus, 1758" " 12.003221" " 61.36278" "gbif" "2019-01-01" "2028051584" +"Canis familiaris Linnaeus, 1758" "-121.098885" " 37.08132" "gbif" "2019-01-28" "1993725010" +"Canis lupus Linnaeus, 1758" " 7.619356" " 45.69360" "gbif" "2019-01-03" "2236240391" +"Canis familiaris Linnaeus, 1758" " 8.252381" " 51.48241" "gbif" "2019-01-21" "1989765540" +"Canis lupus Linnaeus, 1758" " 7.030619" " 45.16022" "gbif" "2019-01-04" "1986578666" +"Canis lupus Linnaeus, 1758" " 11.771043" " 60.79850" "gbif" "2019-01-27" "1989766089" +"Canis lupus Linnaeus, 1758" " 11.009331" " 59.86555" "gbif" "2019-01-21" "1989766220" +"Canis lupus Linnaeus, 1758" " 11.024379" " 59.71250" "gbif" "2019-01-17" "1988308206" +"Canis lupus Linnaeus, 1758" " 11.683887" " 59.69185" "gbif" "2019-01-23" "1989766131" +"Canis lupus Linnaeus, 1758" " -93.337121" " 45.51879" "gbif" "2019-01-26" "1990625756" +"Canis lupus Linnaeus, 1758" " 10.340948" " 63.10199" "gbif" "2019-01-19" "2028054300" +"Canis familiaris Linnaeus, 1758" " -85.648400" " 32.44466" "gbif" "2019-01-22" "1993716904" +"Canis lupus Linnaeus, 1758" " 10.920536" " 59.58577" "gbif" "2019-01-10" "1988308000" +"Canis familiaris Linnaeus, 1758" " -85.646839" " 32.44423" "gbif" "2019-01-22" "2237420714" +"Canis lupus Linnaeus, 1758" " 10.994740" " 59.85693" "gbif" "2019-01-22" "1989766129" +"Canis lupus Linnaeus, 1758" "-113.686295" " 47.46992" "gbif" "2019-01-26" "1993733922" +"Canis lupus Linnaeus, 1758" " 11.329828" " 59.55214" "gbif" "2019-01-10" "1988307663" +"Canis lupus Linnaeus, 1758" " 12.037582" " 61.38100" "gbif" "2019-01-01" "2028051614" +"Canis familiaris Linnaeus, 1758" " 6.627318" " 50.70491" "gbif" "2019-01-03" "1984208185" +"Canis familiaris Linnaeus, 1758" " 120.602292" " 23.99870" "gbif" "2019-01-24" "1990574963" +"Canis familiaris Linnaeus, 1758" " 47.806338" " 30.47966" "gbif" "2019-01-07" "2005345445" +"Canis familiaris Linnaeus, 1758" " 11.450637" " 48.38851" "gbif" "2019-01-31" "1990656210" +"Canis familiaris Linnaeus, 1758" " 8.352727" " 49.68351" "gbif" "2019-01-12" "1988294116" +"Canis lupus Linnaeus, 1758" " 28.852713" " 69.22144" "gbif" "2019-01-05" "2028042974" +"Canis lupus Linnaeus, 1758" " 10.920496" " 59.58575" "gbif" "2019-01-10" "1988307998" +"Canis lupus Linnaeus, 1758" " 11.770231" " 60.79854" "gbif" "2019-01-27" "1989766090" +"Canis familiaris Linnaeus, 1758" " -17.776737" " 28.61137" "gbif" "2019-01-08" "1988294122" +"Canis lupus lycaon Schreber, 1775" " -78.465376" " 45.54244" "gbif" "2019-01-20" "1990552381" +"Canis familiaris Linnaeus, 1758" " 10.297331" " 48.93172" "gbif" "2019-01-06" "1984208101" +"Canis familiaris Linnaeus, 1758" " 8.499363" " 49.45227" "gbif" "2019-01-01" "1984208113" +"Canis familiaris Linnaeus, 1758" "-101.629348" " 37.12143" "gbif" "2019-01-10" "1986628708" +"Canis lupus baileyi Nelson & Goldman, 1929" " -85.149113" " 42.24575" "gbif" "2019-01-17" "1989894063" +"Canis lupus Linnaeus, 1758" " 11.080055" " 59.72776" "gbif" "2019-01-23" "1989766095" +"Canis familiaris Linnaeus, 1758" " 108.263023" " 16.00398" "gbif" "2019-01-22" "1990559572" +"Canis lupus" " -94.218414" " 35.97121" "bison" "1957-01-01" "919969407" +"Canis lupus" " -92.678590" " 36.26666" "bison" "1972-01-09" "919969412" +"Canis lupus" " -92.140495" " 35.85699" "bison" "1970-01-01" "919969420" +"Canis lupus" " -94.274990" " 35.19698" "bison" NA "919969655" +"Canis lupus" " -94.274990" " 35.19698" "bison" "1970-01-01" "919969656" +"Canis lupus" " -92.689250" " 35.26570" "bison" "1970-07-06" "919969664" +"Canis lupus" " -90.779290" " 34.77975" "bison" "1970-07-21" "919969665" +"Canis lupus" " -94.218414" " 35.97121" "bison" "1970-01-01" "919969666" +"Canis lupus" " -93.031530" " 35.45530" "bison" "1968-08-15" "919969671" +"Canis lupus" " -94.256190" " 36.33783" "bison" "1968-10-16" "919969689" +"Canis lupus" " -94.274990" " 35.19698" "bison" NA "919969690" +"Canis lupus" " -92.140495" " 35.85699" "bison" "1970-01-01" "919969694" +"Canis lupus" " -91.722780" " 33.58724" "bison" "1970-04-06" "919969702" +"Canis lupus" " -93.408300" " 34.99771" "bison" "1970-06-15" "919969708" +"Canis lupus" " -95.393036" " 29.85727" "bison" NA "919969805" +"Canis lupus" " -94.218414" " 35.97121" "bison" "1972-01-01" "919969833" +"Canis lupus" " -94.218414" " 35.97121" "bison" "1949-11-11" "919969859" +"Canis lupus" " -92.140495" " 35.85699" "bison" "1936-04-01" "919969875" +"Canis lupus" " -93.720566" " 35.21855" "bison" "1950-11-29" "919969879" +"Canis lupus" " -94.218414" " 35.97121" "bison" "1949-12-19" "919969896" +"Canis lupus" " -91.203316" " 34.67951" "bison" "1970-03-18" "919969918" +"Canis lupus" " -91.101150" " 36.04110" "bison" "1951-07-20" "919969956" +"Canis lupus" " -94.766080" " 34.11707" "bison" "1936-03-24" "919970090" +"Canis lupus" " -94.766080" " 34.11707" "bison" "1936-07-04" "919970107" +"Canis lupus" NA NA "bison" NA "919970259" +"Canis lupus" " -93.720566" " 35.21855" "bison" "1975-12-15" "919970279" +"Canis lupus" NA NA "bison" NA "919970291" +"Canis lupus" " -94.808205" " 36.39337" "bison" "1988-12-14" "919972484" +"Canis lupus" " -94.808205" " 36.39337" "bison" NA "919972528" +"Canis lupus" " -94.256190" " 36.33783" "bison" "1988-02-19" "919972597" +"Canis lupus" " -92.515976" " 35.58296" "bison" "1969-06-06" "919973097" +"Canis lupus" " -91.280140" " 47.35155" "bison" "2017-11-02" "1806350848" +"Canis lupus" " -95.261180" " 47.35066" "bison" "2018-01-19" "1806334455" +"Canis lupus" "-125.546340" " 48.94160" "bison" "2017-05-19" "1562977820" +"Canis lupus" "-110.392006" " 44.52775" "bison" "2011-07-15" "1848809578" +"Canis lupus" "-110.191980" " 44.93100" "bison" "2012-07-21" "1848805186" +"Canis lupus" " -78.560486" " 45.56983" "bison" "2000-07-19" "920908694" +"Canis lupus" " -78.560486" " 45.56983" "bison" "2000-07-20" "920921836" +"Canis lupus" " -94.137210" " 58.69291" "bison" "2010-06-07" "920989000" +"Canis lupus" "-130.648040" " 60.09208" "bison" "1967-06-01" "876159279" +"Canis lupus" " -96.000000" " 42.00000" "bison" NA "36231929" +"Canis lupus" "-103.900000" " 50.80000" "bison" NA "36231931" +"Canis lupus" " -84.830000" " 34.15000" "bison" NA "36232359" +"Canis lupus" "-145.532780" " 62.91389" "bison" "1968-12-01" "202062196" +"Canis lupus" "-114.295815" " 48.24529" "bison" "2000-09-03" "1147030583" +"Canis lupus" " -76.473480" " 42.45300" "bison" "1975-05-11" "1147032515" +"Canis lupus" "-114.295815" " 48.24529" "bison" "2000-09-03" "1147034599" +"Canis lupus" "-114.295815" " 48.24529" "bison" "2000-09-03" "1147040577" +"Canis lupus" " -76.473480" " 42.45300" "bison" "1975-05-09" "1147041973" +"Canis lupus" " -76.473480" " 42.45300" "bison" "1975-03-12" "1147042200"