Mercurial > repos > mnhn65mo > get_worldclim_data

comparison raster_getdata.xml @ 0:bdf7d9f2ddae draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author mnhn65mo
date Thu, 09 Aug 2018 05:01:04 -0400
parents
children 008cbcc1e3f6
comparison
equal deleted inserted replaced
-1:000000000000 0:bdf7d9f2ddae
1 <tool id="raster_getdata" name="Get climatic data from Worldclim" version="0.1.0">
2 <requirements>
3
4 <!--
5 <requirement type="package" >libgcc-ng</requirement>
6 <requirement type="package" >libiconv</requirement>
7 <requirement type="package" >jpeg</requirement>
8 <requirement type="package" >libstdcxx-ng</requirement>
9 <requirement type="package" >libkml</requirement>
10
11
12 -->
13 <requirement type="package" version="1.2_18">r-rgdal</requirement>
14 <requirement type="package" version="1.20.2">r-getopt</requirement>
15 <requirement type="package" version="1.1.6">r-ncdf4</requirement>
16 <requirement type="package" version="2.6_7">r-raster</requirement>
17 <requirement type="package" version="1.1.7">r-stringr</requirement>
18
19 </requirements>
20 <command detect_errors="exit_code"><![CDATA[
21 Rscript
22 '$__tool_directory__/clim_data.R'
23 'worldclim'
24 '$usr_var'
25 $usr_res
26 '$usr_of'
27
28 #if $condi_plot.plot=='yes_plot'
29 '$usr_var$condi_plot.var_to_plot'
30 '$condi_plot.usr_country'
31 #end if
32
33 ]]></command>
34 <inputs>
35 <param name="usr_var" type="select" label="Variable" help="Temperature minimum, maximum, precipitations and bioclimatic variables.">
36 <option value="tmin">tmin</option>
37 <option value="tmax">tmax</option>
38 <option value="prec">prec</option>
39 <option value="bio">bio</option>
40 </param>
41 <param name="usr_res" type="select" label="Resolution" help="In minutes of a degree.">
42 <option value="2.5">2.5</option>
43 <option value="5">5</option>
44 <option value="10">10</option>
45 </param>
46 <param name="usr_of" type="select" label="Output raster format" >
47 <option value="raster">Native raster package format .grd</option>
48 <option value="CDF">netCDF .nc</option>
49 <option value="GTiff">GeoTiff .tif</option>
50
51 <!--
52 <option value="ascii">ESRI Ascii .asc</option>
53 <option value="SAGA">SAGA GIS .sdat</option>
54 <option value="IDRISI">IDRISI .rst</option>
55 <option value="ENVI">ENVI .hdr Labelled .envi</option>
56 <option value="EHdr">ESRI .hdr Labelled .bil</option>
57 <option value="HFA">Erdas Imagine Images .img</option>
58 -->
59
60 </param>
61 <conditional name="condi_plot">
62 <param name="plot" type="select" label="Return a layers visualisation">
63 <option value="yes_plot">Yes</option>
64 <option value="no_plot">No</option>
65 </param>
66 <when value="yes_plot">
67 <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.">
68 <option value="1">[tmin|tmax|prec]:January</option>
69 <option value="2">[tmin|tmax|prec]:February</option>
70 <option value="3">[tmin|tmax|prec]:March</option>
71 <option value="4">[tmin|tmax|prec]:April</option>
72 <option value="5">[tmin|tmax|prec]:May</option>
73 <option value="6">[tmin|tmax|prec]:June</option>
74 <option value="7">[tmin|tmax|prec]:July</option>
75 <option value="8">[tmin|tmax|prec]:August</option>
76 <option value="9">[tmin|tmax|prec]:September</option>
77 <option value="10">[tmin|tmax|prec]:October</option>
78 <option value="11">[tmin|tmax|prec]:November</option>
79 <option value="12">[tmin|tmax|prec]:December</option>
80 <option value="1">bio:Annual Mean Temperature</option>
81 <option value="2">bio:Mean Diurnal Range (Mean of monthly (max temp - min temp))</option>
82 <option value="3">bio:Isothermality (BIO2/BIO7) (* 100)</option>
83 <option value="4">bio:Temperature Seasonality (standard deviation *100)</option>
84 <option value="5">bio:Max Temperature of Warmest Month</option>
85 <option value="6">bio:Min Temperature of Coldest Month</option>
86 <option value="7">bio:Temperature Annual Range (BIO5-BIO6)</option>
87 <option value="8">bio:Mean Temperature of Wettest Quarter</option>
88 <option value="9">bio:Mean Temperature of Driest Quarter</option>
89 <option value="10">bio:Mean Temperature of Warmest Quarter</option>
90 <option value="11">bio:Mean Temperature of Coldest Quarter</option>
91 <option value="12">bio:Annual Precipitation</option>
92 <option value="13">bio:Precipitation of Wettest Month</option>
93 <option value="14">bio:Precipitation of Driest Month</option>
94 <option value="15">bio:Precipitation Seasonality (Coefficient of Variation)</option>
95 <option value="16">bio:Precipitation of Wettest Quarter</option>
96 <option value="17">bio:Precipitation of Driest Quarter</option>
97 <option value="18">bio:Precipitation of Warmest Quarter</option>
98 <option value="19">bio:Precipitation of Coldest Quarter</option>
99 </param>
100
101 <param name="usr_country" type="select" label="Select a worldmap vision or a more precise region" >
102 <option value="WM">Worldmap</option>
103 <option value="NA">North America</option>
104 <option value="EU">Europe</option>
105 <option value="AUS">Australia</option>
106 <option value="FRA">France</option>
107 <option value="DEU">Germany</option>
108 <option value="GBR">United Kingdom</option>
109 <option value="ESP">Spain</option>
110 <option value="ITA">Italy</option>
111 </param>
112 </when>
113 <when value="no_plot">
114 </when>
115 </conditional>
116 </inputs>
117 <outputs>
118 <data name="output_df" from_work_dir="output_writeRaster.nc" label="WorldClim data - NetCDF format">
119 <filter> usr_of=='CDF'</filter>
120 </data>
121 <data name="output_grd" from_work_dir="output_writeRaster.grd" label="WorldClim data - Native raster pkg format .grd">
122 <filter> usr_of=='raster'</filter>
123 </data>
124 <data name="output_gri" from_work_dir="output_writeRaster.gri" label="WorldClim data - Native raster pkg format .gri">
125 <filter> usr_of=='raster'</filter>
126 </data>
127 <data name="plot_jpeg" from_work_dir="worldclim_plot_usr_region.jpeg" format="jpg" label="WorldClim data - Visualisation">
128 <filter> plot=='yes_plot'</filter>
129 </data>
130 </outputs>
131 <help><![CDATA[
132
133 .. class:: infomark
134
135 =======================================
136 Get global climate data from Worldclim
137 =======================================
138
139 |
140
141 **What it does**
142
143 This tool retrieve global climate data from Wordclim using the R raster package.
144
145 The climatic data available are :
146
147 * Minimum temperature (°C *10)
148
149 * Maximum temperature (°C *10)
150
151 * Precipitation (mm)
152
153 * Bioclimatic variables :
154
155 * BIO1 = Annual Mean Temperature
156
157 * BIO2 = Mean Diurnal Range (Mean of monthly (max temp - min temp))
158
159 * BIO3 = Isothermality (BIO2/BIO7) (x 100)
160
161 * BIO4 = Temperature Seasonality (standard deviation x100)
162
163 * BIO5 = Max Temperature of Warmest Month
164
165 * BIO6 = Min Temperature of Coldest Month
166
167 * BIO7 = Temperature Annual Range (BIO5-BIO6)
168
169 * BIO8 = Mean Temperature of Wettest Quarter
170
171 * BIO9 = Mean Temperature of Driest Quarter
172
173 * BIO10 = Mean Temperature of Warmest Quarter
174
175 * BIO11 = Mean Temperature of Coldest Quarter
176
177 * BIO12 = Annual Precipitation
178
179 * BIO13 = Precipitation of Wettest Month
180
181 * BIO14 = Precipitation of Driest Month
182
183 * BIO15 = Precipitation Seasonality (Coefficient of Variation)
184
185 * BIO16 = Precipitation of Wettest Quarter
186
187 * BIO17 = Precipitation of Driest Quarter
188
189 * BIO18 = Precipitation of Warmest Quarter
190
191 * BIO19 = Precipitation of Coldest Quarter
192
193 |
194
195 **How to use it**
196
197 Simply select the variable to return and the resolution : 2.5, 5 or 10 minutes of a degree.
198
199 Available output format are : netcdf and grd (Native raster package format).
200
201 |
202
203 **Sources**
204
205 Worldclim : http://www.worldclim.org/
206
207 Raster package : https://cran.r-project.org/web/packages/raster/index.html
208
209 ]]></help>
210 </tool>