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annotate spocc_occ.R @ 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 #!/usr/bin/Rscript
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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3 library(spocc)
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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6 ##Def functions :
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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7 help<-function(){
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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8 cat("HELP\n")
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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9 cat("Spocc::occ, Search on a single species name, or many. And search across a single or many data sources.\n\n")
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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10 cat("Need 3 args :\n")
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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11 cat(" - query : (character) One to many scientific names.\n")
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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12 cat(" - from : (character) Data source to get data from, any combination of gbif, bison, inat,ebird, ecoengine and/or vertnet.\n")
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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13 cat(" - limit : (numeric) Number of records to return. This is passed across all sources.\n")
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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14 q("no")
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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15 }
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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17 formatSpName <- function(spName) paste(strsplit(spName, split=' ')[[1]], collapse='_') ###Wallace function
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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19 ####################################
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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21 args = commandArgs(trailingOnly=TRUE)
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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23 #Help display
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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24 if(args[1]=="-h" || args[1]=="--help" || length(args)<3){help()}
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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26 #Get args
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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27 sname<-args[1]
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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28 dbase_input<-args[2]
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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29 max<-as.integer(args[3])
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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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 #Get all databases
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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32 bases<-strsplit(dbase_input,",")
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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33 dbase<-c()
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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34 for (base in bases){
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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35 dbase<-c(dbase,base)
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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36 }
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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38 #Get occurrences
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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39 results <- spocc::occ(query=sname, from=dbase, limit=max, has_coords=TRUE)
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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41 #Dispay results
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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42 if(length(dbase)==1){
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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43 results_data <- results[[dbase[1]]]$data[[formatSpName(sname)]]
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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44 }else{
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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45 res <- occ2df(results)
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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46 results_data <- res
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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47 }
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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49 results_data<-as.matrix(results_data)
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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51 #If empty
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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52 if(length(results_data)==0){cat("\nNo occurrences found.\nLittle tip : Check your input typo, some databases are case sensitive : Genus species.\n")}
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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53
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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54 #Write them
724ad06de5a5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/spocc_occ commit e37f100e1c3ea68ade708868f9de3f4c0dd7e720
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55 write.table(file="output.tab",results_data,sep="\t",row.names=FALSE)
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 q('no')