Mercurial > repos > mnhn65mo > butterfly_analysis
diff raster_getdata.xml @ 1:c5a10acd34e3 draft
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| author | mnhn65mo |
|---|---|
| date | Mon, 13 Aug 2018 04:47:57 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/raster_getdata.xml Mon Aug 13 04:47:57 2018 -0400 @@ -0,0 +1,208 @@ +<tool id="raster_getdata" name="Get climatic data from Worldclim" version="0.1.0"> + <requirements> + +<!-- + <requirement type="package" >libgcc-ng</requirement> + <requirement type="package" >libiconv</requirement> + <requirement type="package" >jpeg</requirement> + <requirement type="package" >libstdcxx-ng</requirement> + <requirement type="package" >libkml</requirement> + <requirement type="package" version="1.2_18">r-rgdal</requirement> +--> + + <requirement type="package" version="1.20.2">r-getopt</requirement> + <requirement type="package" version="1.1.6">r-ncdf4</requirement> + <requirement type="package" version="2.6_7">r-raster</requirement> + <requirement type="package" version="1.3.1">r-stringr</requirement> + + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript + '$__tool_directory__/clim_data.R' + 'worldclim' + '$usr_var' + $usr_res + '$usr_of' + + #if $condi_plot.plot=='yes_plot' + '$usr_var$condi_plot.var_to_plot' + '$condi_plot.usr_country' + #end if + + ]]></command> + <inputs> + <param name="usr_var" type="select" label="Variable" help="Temperature minimum, maximum, precipitations and bioclimatic variables."> + <option value="tmin">tmin</option> + <option value="tmax">tmax</option> + <option value="prec">prec</option> + <option value="bio">bio</option> + </param> + <param name="usr_res" type="select" label="Resolution" help="In minutes of a degree."> + <option value="2.5">2.5</option> + <option value="5">5</option> + <option value="10">10</option> + </param> + <param name="usr_of" type="select" label="Output raster format" > + <option value="raster">Native raster package format .grd</option> + <option value="CDF">netCDF .nc</option> +<!-- + <option value="GTiff">GeoTiff .tif</option> + <option value="ascii">ESRI Ascii .asc</option> + <option value="SAGA">SAGA GIS .sdat</option> + <option value="IDRISI">IDRISI .rst</option> + <option value="ENVI">ENVI .hdr Labelled .envi</option> + <option value="EHdr">ESRI .hdr Labelled .bil</option> + <option value="HFA">Erdas Imagine Images .img</option> +--> + + </param> + <conditional name="condi_plot"> + <param name="plot" type="select" label="Return a layers visualisation"> + <option value="yes_plot">Yes</option> + <option value="no_plot">No</option> + </param> + <when value="yes_plot"> + <param name="var_to_plot" type="select" label="Select what you want to visualize" help="Be careful to select a layer that is present in the dowloaded raster. eg : bioclimatic variable (bio) and layer bio:Isothermality."> + <option value="1">[tmin|tmax|prec]:January</option> + <option value="2">[tmin|tmax|prec]:February</option> + <option value="3">[tmin|tmax|prec]:March</option> + <option value="4">[tmin|tmax|prec]:April</option> + <option value="5">[tmin|tmax|prec]:May</option> + <option value="6">[tmin|tmax|prec]:June</option> + <option value="7">[tmin|tmax|prec]:July</option> + <option value="8">[tmin|tmax|prec]:August</option> + <option value="9">[tmin|tmax|prec]:September</option> + <option value="10">[tmin|tmax|prec]:October</option> + <option value="11">[tmin|tmax|prec]:November</option> + <option value="12">[tmin|tmax|prec]:December</option> + <option value="1">bio:Annual Mean Temperature</option> + <option value="2">bio:Mean Diurnal Range (Mean of monthly (max temp - min temp))</option> + <option value="3">bio:Isothermality (BIO2/BIO7) (* 100)</option> + <option value="4">bio:Temperature Seasonality (standard deviation *100)</option> + <option value="5">bio:Max Temperature of Warmest Month</option> + <option value="6">bio:Min Temperature of Coldest Month</option> + <option value="7">bio:Temperature Annual Range (BIO5-BIO6)</option> + <option value="8">bio:Mean Temperature of Wettest Quarter</option> + <option value="9">bio:Mean Temperature of Driest Quarter</option> + <option value="10">bio:Mean Temperature of Warmest Quarter</option> + <option value="11">bio:Mean Temperature of Coldest Quarter</option> + <option value="12">bio:Annual Precipitation</option> + <option value="13">bio:Precipitation of Wettest Month</option> + <option value="14">bio:Precipitation of Driest Month</option> + <option value="15">bio:Precipitation Seasonality (Coefficient of Variation)</option> + <option value="16">bio:Precipitation of Wettest Quarter</option> + <option value="17">bio:Precipitation of Driest Quarter</option> + <option value="18">bio:Precipitation of Warmest Quarter</option> + <option value="19">bio:Precipitation of Coldest Quarter</option> + </param> + + <param name="usr_country" type="select" label="Select a worldmap vision or a more precise region" > + <option value="WM">Worldmap</option> + <option value="NA">North America</option> + <option value="EU">Europe</option> + <option value="AUS">Australia</option> + <option value="FRA">France</option> + <option value="DEU">Germany</option> + <option value="GBR">United Kingdom</option> + <option value="ESP">Spain</option> + <option value="ITA">Italy</option> + </param> + </when> + <when value="no_plot"> + </when> + </conditional> + </inputs> + <outputs> + <data name="output_df" from_work_dir="output_writeRaster.nc" label="WorldClim data - NetCDF format"> + <filter> usr_of=='CDF'</filter> + </data> + <data name="output_grd" from_work_dir="output_writeRaster.grd" label="WorldClim data - Native raster pkg format .grd"> + <filter> usr_of=='raster'</filter> + </data> + <data name="output_gri" from_work_dir="output_writeRaster.gri" label="WorldClim data - Native raster pkg format .gri"> + <filter> usr_of=='raster'</filter> + </data> + <data name="plot_jpeg" from_work_dir="worldclim_plot_usr_region.jpeg" format="jpg" label="WorldClim data - Visualisation"> + <filter> plot=='yes_plot'</filter> + </data> + </outputs> + <help><![CDATA[ + +.. class:: infomark + +======================================= +Get global climate data from Worldclim +======================================= + +| + +**What it does** + +This tool retrieve global climate data from Wordclim using the R raster package. + +The climatic data available are : + + * Minimum temperature (°C x10) + + * Maximum temperature (°C x10) + + * Precipitation (mm) + + * Bioclimatic variables : + + * BIO1 = Annual Mean Temperature + + * BIO2 = Mean Diurnal Range (Mean of monthly (max temp - min temp)) + + * BIO3 = Isothermality (BIO2/BIO7) (x 100) + + * BIO4 = Temperature Seasonality (standard deviation x100) + + * BIO5 = Max Temperature of Warmest Month + + * BIO6 = Min Temperature of Coldest Month + + * BIO7 = Temperature Annual Range (BIO5-BIO6) + + * BIO8 = Mean Temperature of Wettest Quarter + + * BIO9 = Mean Temperature of Driest Quarter + + * BIO10 = Mean Temperature of Warmest Quarter + + * BIO11 = Mean Temperature of Coldest Quarter + + * BIO12 = Annual Precipitation + + * BIO13 = Precipitation of Wettest Month + + * BIO14 = Precipitation of Driest Month + + * BIO15 = Precipitation Seasonality (Coefficient of Variation) + + * BIO16 = Precipitation of Wettest Quarter + + * BIO17 = Precipitation of Driest Quarter + + * BIO18 = Precipitation of Warmest Quarter + + * BIO19 = Precipitation of Coldest Quarter + +| + +**How to use it** + +Simply select the variable to return and the resolution : 2.5, 5 or 10 minutes of a degree. + +Available output format are : netcdf and grd (Native raster package format). + +| + +**Sources** + +Worldclim : http://www.worldclim.org/ + +Raster package : https://cran.r-project.org/web/packages/raster/index.html + + ]]></help> +</tool>