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Merge pull request #90 from Marie59/obisindicators
Add retrieving occurences data from obis
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,57 @@ | ||
| #Rscript | ||
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| ########################################### | ||
| ## Retrieve Obis occurences data ## | ||
| ########################################### | ||
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| ##### Packages : robis | ||
| # https://iobis.github.io/robis/articles/getting-started.html | ||
| # Get args | ||
| args <- commandArgs(trailingOnly = TRUE) | ||
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| if (length(args) < 1) { | ||
| stop("This tool needs at least 1 argument : longitude, latitude, species or taxonID") | ||
| }else { | ||
| sname <- args[1] | ||
| taxid <- args[2] | ||
| lat_min <- args[3] | ||
| lat_max <- args[4] | ||
| long_min <- args[5] | ||
| long_max <- args[6] | ||
| } | ||
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| if (lat_min == "0.0" & lat_max == "0.0" & long_min == "0.0" & long_max == "0.0") { | ||
| lat_min <- "" | ||
| lat_max <- "" | ||
| long_min <- "" | ||
| long_max <- "" | ||
| } | ||
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| ##### Import data | ||
| # Get biological occurrences | ||
| if (lat_min != "" & sname != "" & taxid != "") { | ||
| my_occs <- robis::occurrence(scientificname = sname, taxonid = taxid, geometry = paste("POLYGON ((", long_min, lat_min, ", ", long_min, lat_max, ", ", long_max, lat_min, ", ", long_max, lat_max, ", ", long_min, lat_min, "))")) | ||
| }else if (lat_min != "" & sname != "" & taxid == "") { | ||
| my_occs <- robis::occurrence(scientificname = sname, geometry = paste("POLYGON ((", long_min, lat_min, ", ", long_min, lat_max, ", ", long_max, lat_min, ", ", long_max, lat_max, ", ", long_min, lat_min, "))")) | ||
| }else if (lat_min != "" & sname == "" & taxid != "") { | ||
| my_occs <- robis::occurrence(taxonid = taxid, geometry = paste("POLYGON ((", long_min, lat_min, ", ", long_min, lat_max, ", ", long_max, lat_min, ", ", long_max, lat_max, ", ", long_min, lat_min, "))")) | ||
| }else if (lat_min != "" & sname == "" & taxid == "") { | ||
| my_occs <- robis::occurrence(geometry = paste("POLYGON ((", long_min, lat_min, ", ", long_min, lat_max, ", ", long_max, lat_min, ", ", long_max, lat_max, ", ", long_min, lat_min, "))")) | ||
| }else if (lat_min == "" & sname != "" & taxid != "") { | ||
| my_occs <- robis::occurrence(scientificname = sname, taxonid = taxid) | ||
| }else if (lat_min == "" & sname == "" & taxid != "") { | ||
| my_occs <- robis::occurrence(taxonid = taxid) | ||
| }else if (lat_min == "" & sname != "" & taxid == "") { | ||
| my_occs <- robis::occurrence(scientificname = sname) | ||
| } | ||
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| # Dispay results | ||
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| # If empty | ||
| if(length(my_occs) == 0) { | ||
| cat("\nNo occurrences found.\nLittle tip : Check your input typo, some databases are case sensitive : Genus species.\n") | ||
| } | ||
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| write.table(file = "output.tab", my_occs, sep = "\t", dec = ".", na = "", row.names = FALSE, col.names = TRUE, quote = FALSE) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,98 @@ | ||
| <tool id="obis_data" name="OBIS occurences" version="@VERSION@" profile="20.01"> | ||
| <description>retrieve data</description> | ||
| <macros> | ||
| <import>macro.xml</import> | ||
| </macros> | ||
| <expand macro="topic"/> | ||
| <expand macro="requirements"> | ||
| <requirement type="package" version="2.11.3">r-robis</requirement> | ||
| </expand> | ||
| <required_files> | ||
| <include type="literal" path="robis.r"/> | ||
| </required_files> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| Rscript | ||
| '$__tool_directory__/robis.r' | ||
| '$species' | ||
| '$taxon' | ||
| '$lat_min' | ||
| '$lat_max' | ||
| '$long_min' | ||
| '$long_max' | ||
| '$output' | ||
| ]]> | ||
| </command> | ||
| <inputs> | ||
| <param name="species" type="text" label="Scientific name of the species" help="Genus species format, eg : Scomber scombrus"> | ||
| <validator type="regex">^[A-Za-z ]*$</validator> | ||
| </param> | ||
| <param name="taxon" type="text" label="Taxon ID"> | ||
| <validator type="regex">^[0-9]*$</validator> | ||
| </param> | ||
| <param name="lat_min" type="float" min="-90" max="90" value="0" label="Input latitude min (+north/-south):" optional="true"/> | ||
| <param name="lat_max" type="float" min="-90" max="90" value="0" label="Input latitude max (+north/-south):" optional="true"/> | ||
| <param name="long_min" type="float" min="-90" max="90" value="0" label="Input longitude min (+east/-west):" optional="true"/> | ||
| <param name="long_max" type="float" min="-90" max="90" value="0" label="Input longitude max (+east/-west):" optional="true"/> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs="1"> | ||
| <param name="species" value="Scomber scombrus"/> | ||
| <output name="output"> | ||
| <assert_contents> | ||
| <has_text text="Scombridae"/> | ||
| <has_n_columns n="163"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <test expect_num_outputs="1"> | ||
| <param name="lat_min" value="6"/> | ||
| <param name="lat_max" value="12"/> | ||
| <param name="long_min" value="40"/> | ||
| <param name="long_max" value="43"/> | ||
| <output name="output"> | ||
| <assert_contents> | ||
| <has_text text="basisOfRecord"/> | ||
| <has_n_columns n="144"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| =========================== | ||
| Get species occurences data | ||
| =========================== | ||
| **What it does** | ||
| Search and retrieve species occurences across OBIS database. | ||
| | | ||
| **How to use it** | ||
| Enter a species scientific name, be careful that the tool is case sensitive. Eg : Scomber scombrus. | ||
| Or enter the latitude longitude of the area you want to retrieve data from. | ||
| | | ||
| **Output** | ||
| The tool returns a table with the species observations available in OBIS database. | ||
| Output file will have at least the following attributes : BasisOfRecords, longitude, latitude, species, individualcount. | ||
| | | ||
| **How it works** | ||
| This tool use the robis R package. | ||
| Includes functionality for retrieving species occurrence data, and combining those data. | ||
| ]]></help> | ||
| <expand macro="obis_doiref"/> | ||
| </tool> |