view raster_getdata.xml @ 1:c5a10acd34e3 draft

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<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>