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"planemo upload for repository https://gitlab.com/eetun-tiimi/EODIE commit c4a5672398bc878dd2bc0bf4f3a26f59b3f6395c"
author climate
date Thu, 30 Dec 2021 15:24:09 +0000
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-1:000000000000 0:81b0ca76435d
1 <tool id="eodie" name="EODIE" version="@VERSION@" profile="20.09">
2 <description>converts simple features data between file formats</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam_ontology"/>
7 <requirements>
8 <requirement type="package" version="@VERSION@">eodie</requirement>
9 <requirement type="package" version="3.9">python</requirement>
10 <requirement type="package" version="1.8">shapely</requirement>
11 <requirement type="package" version="1.2">rasterio</requirement>
12 <requirement type="package" version="0.16">rasterstats</requirement>
13 <requirement type="package" version="1.8">fiona</requirement>
14 <requirement type="package" version="1.21">numpy</requirement>
15 <requirement type="package" version="3.4.0">gdal</requirement>
16 <requirement type="package" version="6.0">pyyaml</requirement>
17 <requirement type="package" version="6.0">unzip</requirement>
18 <requirement type="package" version="1.34">tar</requirement>
19 </requirements>
20 <command detect_errors="exit_code"><![CDATA[
21 mkdir -p work/data_collection work/results results_csv results_tiffs &&
22 cp '$config_tif' config_tif.yml &&
23 cp '$config_s2' config_s2.yml &&
24 cp '$config_ls8' config_ls8.yml &&
25 cp '$user_config' user_config.yml &&
26 cp '${input.extra_files_path}'/* work/ &&
27 cd work &&
28 ln -s '${input_type.input_file}' '${input_type.input_file.element_identifier}' &&
29 #if $input_type.input_file.is_of_type("zip")
30 unzip '$input_type.input_file' -d data_collection/ &&
31 #elif $input_type.input_file.is_of_type("tar")
32 tar -xf '$input_type.input_file' -C data_collection &&
33 #end if
34 #if str($input_type.platform) == 's2'
35 mkdir -p sentinel2_tiles_world &&
36 (cp '$input_type.s2_shp.extra_files_path'/shapefile.shp sentinel2_tiles_world/sentinel2_tiles_world.shp || true ) &&
37 (cp '$input_type.s2_shp.extra_files_path'/shapefile.shx sentinel2_tiles_world/sentinel2_tiles_world.shx || true ) &&
38 (cp '$input_type.s2_shp.extra_files_path'/shapefile.dbf sentinel2_tiles_world/sentinel2_tiles_world.dbf || true ) &&
39 (cp '$input_type.s2_shp.extra_files_path'/shapefile.prj sentinel2_tiles_world/sentinel2_tiles_world.prj || true ) &&
40 #elif str($input_type.platform) == 'ls8'
41 mkdir -p WRS2_descending &&
42 (cp '$input_type.ls8_shp.extra_files_path'/shapefile.shp WRS2_descending/WRS2_descending.shp || true ) &&
43 (cp '$input_type.ls8_shp.extra_files_path'/shapefile.shx WRS2_descending/WRS2_descending.shx || true ) &&
44 (cp '$input_type.ls8_shp.extra_files_path'/shapefile.dbf WRS2_descending/WRS2_descending.dbf || true ) &&
45 (cp '$input_type.ls8_shp.extra_files_path'/shapefile.prj WRS2_descending/WRS2_descending.prj || true ) &&
46 #end if
47
48 eodie_process.py
49 --platform $input_type.platform
50 #if str($input_type.platform) == 'tif'
51 --file ${input_type.input_file.element_identifier}
52 #else
53 --dir data_collection
54 --out ./results
55 #end if
56 --shp shapefile
57 #for $i, $s in enumerate( $adv_options.statistics )
58 #if str($i) == '0'
59 --statistics_out
60 --statistics
61 #end if
62 #if $s.stats_input.stats and str($s.stats_input.stats) != '':
63 #if str($s.stats_input.stats) == 'percentile':
64 '$s.stats_input.stats'_'$s.stats_input.p_value'
65 #else
66 '$s.stats_input.stats'
67 #end if
68 #end if
69 #end for
70 #if $adv_options.indices and str($adv_options.indices) != '':
71 --index
72 #for $idx in str($adv_options.indices).split(','):
73 '$idx'
74 #end for
75 #end if
76 #if $adv_options.start_date and str($adv_options.start_date) != '':
77 --start int($adv_options.start_date)
78 #end if
79 #if $adv_options.end_date and str($adv_options.end_date) != '':
80 --start int($adv_options.end_date)
81 #end if
82 $adv_options.exclude_border
83 $adv_options.exclude_splitshp
84 --id '$identifier' &&
85
86 mv results/*.log '$logfile' &&
87 bash '$__tool_directory__/postprocess_csv.sh' 'results' '../results_csv' &&
88 ( mv results/*.tif ../results_tiffs/ || echo "No tiff files generated" ) &&
89 echo "EODIE data extractor is done"
90 ]]> </command>
91 <expand macro="configfiles"/>
92 <inputs>
93 <conditional name="input_type">
94 <param name="platform" type="select" label="Select platform of the input data">
95 <option value="s2">Sentinel 2</option>
96 <option value="ls8">Landsat 8</option>
97 <option value="tif">tiff file</option>
98 </param>
99 <when value="tif">
100 <param name='input_file' format="tiff" type="data" label="Individual input file"/>
101 </when>
102 <when value="ls8">
103 <param name="input_file" type="data" format='zip,tar' label="Landsat 8 input data (zip or tarball)" />
104 <param name="ls8_shp" type="data" format="shp" label="Landsat 8 tile shapefile" help="Provide the Landsat-8 tile shapefile"/>
105 </when>
106 <when value="s2">
107 <param name="input_file" type="data" format='zip,tar' label="Sentinel 2 input data (zip or tarball)" />
108 <param name="s2_shp" type="data" format="shp" label="Sentinel-2 tile shapefile" help="Provide the Sentinel-2 tile shapefile"/>
109 </when>
110 </conditional>
111 <param type="data" name="input" format="shp" label="Shapefile with polygons" help="Provide shapefile with polygons"/>
112 <param name="identifier" type="text" value="PlotID" label="Name of identifier" />
113 <section name="adv_options" title="Advanced options" expanded="false">
114 <param name="start_date" type="text" optional="true" label="Time frame start date (YYYYMMDD)">
115 <validator type="length" min="8" max="8" message="Please enter a date in the form of YYYYMMDD"/>
116 </param>
117 <param name="end_date" type="text" optional="true" label="Time frame end date (YYYYMMDD)">
118 <validator type="length" min="8" max="8" message="Please enter a date in the form of YYYYMMDD"/>
119 </param>
120 <repeat name="statistics" title="Compute statistics" min="0">
121 <conditional name="stats_input">
122 <param name="stats" label="Statistics" type="select">
123 <option value="mean">Mean</option>
124 <option value="sum">Sum</option>
125 <option value="min">Minimum</option>
126 <option value="max">Maximum</option>
127 <option value="std">Standard deviation</option>
128 <option value="median">Median</option>
129 <option value="majority">Majority</option>
130 <option value="minority">Minority</option>
131 <option value="unique">Unique</option>
132 <option value="range">Range</option>
133 <option value="percentile">Percentile</option>
134 </param>
135 <when value="mean"/>
136 <when value="sum"/>
137 <when value="min"/>
138 <when value="max"/>
139 <when value="std"/>
140 <when value="median"/>
141 <when value="majority"/>
142 <when value="minority"/>
143 <when value="unique"/>
144 <when value="range"/>
145 <when value="percentile">
146 <param name="p_value" type="integer" value="0" min="0" max="100" label="percentile value (if percentile selected)" />
147 </when>
148 </conditional>
149 </repeat>
150 <param name="indices" label="Indice to compute" type="select" multiple="true">
151 <option value="ndvi">ndvi</option>
152 <option value="rvi">rvi</option>
153 <option value="savi">savi</option>
154 <option value="nbr">nbr</option>
155 <option value="kndvi">kndvi</option>
156 <option value="ndmi">ndmi</option>
157 <option value="mndwi">mndwi</option>
158 <option value="evi">evi</option>
159 <option value="evi2">evi2</option>
160 <option value="dvi">dvi</option>
161 <option value="cvi">cvi</option>
162 <option value="mcar">mcar</option>
163 <option value="ndi45">ndi45</option>
164 <option value="tctb">tctb</option>
165 <option value="tctg">tctg</option>
166 <option value="tctw">tctw</option>
167 <option value="ndwi">ndwi</option>
168 <option value="B02">B02</option>
169 <option value="B03">B03</option>
170 <option value="B04">B04</option>
171 <option value="B05">B05</option>
172 <option value="B06">B06</option>
173 <option value="B07">B07</option>
174 <option value="B08">B08</option>
175 <option value="B8A">B8A</option>
176 <option value="B11">B11</option>
177 <option value="B12">B12</option>
178 </param>
179 <param name="exclude_splitshp" type="boolean" checked="false" label="exclude splitshp" help="Flag to indicate that splitshp has been run manually beforehand" truevalue="--exclude_splitshp" falsevalue="" />
180 <param name="exclude_border" type="boolean" checked="false" label="exclude border" help="Flag to indicate that border pixels (within the polygon) should be excluded from statistics calculations / array extraction" truevalue="--exclude_border" falsevalue="" />
181 <param name="geotiff_out" type="boolean" checked="false" label="generate geotiffs" help="flag to indicate that geotiffs shall be extracted" truevalue="--geotiff_out" falsevalue="" />
182 </section>
183 </inputs>
184 <outputs>
185 <data name="logfile" format="txt"/>
186 <collection name="csv_files" type="list" label="${tool.name} (statistics csv outputs)">
187 <discover_datasets pattern="__name__" directory="results_csv" visible="false" format="tabular"/>
188 </collection>
189 </outputs>
190 <tests>
191 <test>
192 <conditional name="input_type">
193 <param name="platform" value="tif" />
194 <param name="input_file" ftype="tiff" value="smaller_area_20100401.tif" />
195 </conditional>
196 <param name="input" value="test_polygons/test_polygons.html" ftype="shp">
197 <composite_data value="test_polygons/test_polygons.shp"/>
198 <composite_data value="test_polygons/test_polygons.shx"/>
199 <composite_data value="test_polygons/test_polygons.dbf"/>
200 <composite_data value="test_polygons/test_polygons.prj"/>
201 </param>
202 <param name="identifier" value="id"/>
203 <section name="adv_options">
204 <repeat name="statistics">
205 <conditional name="stats_input">
206 <param name="stats" value="mean"/>
207 </conditional>
208 </repeat>
209 <repeat name="statistics">
210 <conditional name="stats_input">
211 <param name="stats" value="percentile"/>
212 <param name="p_value" value="10"/>
213 </conditional>
214 </repeat>
215 <param name="exclude_splitshp" value="true"/>
216 </section>
217 <output file="20211213-104427.log" name="logfile" compare="sim_size" delta="100"/>
218 <output_collection name="csv_files" type="list" count="1">
219 <element name="testrgb_20100401__statistics.csv" ftype="tabular" file="testrgb_20100401__statistics.csv" compare="diff" lines_diff="1">
220 <assert_contents>
221 <has_text text="percentile_10" />
222 <has_text text="20508" />
223 <has_text text="12049" />
224 <has_text text="4508" />
225 <has_text text="110." />
226 <has_text text="147." />
227 <has_text text="32." />
228 <has_n_columns n="4" />
229 </assert_contents>
230 </element>
231
232
233 </output_collection>
234 </test>
235 <test>
236 <conditional name="input_type">
237 <param name="platform" value="ls8" />
238 <param name="input_file" ftype="tar" value="LS8.tar" />
239 <param name="ls8_shp" ftype="shp" value="WRS2_descending/WRS2_descending.html">
240 <composite_data value="WRS2_descending/WRS2_descending.shp"/>
241 <composite_data value="WRS2_descending/WRS2_descending.shx"/>
242 <composite_data value="WRS2_descending/WRS2_descending.dbf"/>
243 <composite_data value="WRS2_descending/WRS2_descending.prj"/>
244 </param>
245 </conditional>
246 <param name="input" value="test_parcels_32635/test_parcels_32635.html" ftype="shp">
247 <composite_data value="test_parcels_32635/test_parcels_32635.shp"/>
248 <composite_data value="test_parcels_32635/test_parcels_32635.shx"/>
249 <composite_data value="test_parcels_32635/test_parcels_32635.dbf"/>
250 <composite_data value="test_parcels_32635/test_parcels_32635.prj"/>
251 </param>
252 <param name="identifier" value="ID"/>
253 <section name="adv_options">
254 <repeat name="statistics">
255 <conditional name="stats_input">
256 <param name="stats" value="mean"/>
257 </conditional>
258 </repeat>
259 <repeat name="statistics">
260 <conditional name="stats_input">
261 <param name="stats" value="median"/>
262 </conditional>
263 </repeat>
264 <repeat name="statistics">
265 <conditional name="stats_input">
266 <param name="stats" value="std"/>
267 </conditional>
268 </repeat>
269 <param name="indices" value="ndvi"/>
270 </section>
271 <output file="20211218-102629.log" name="logfile" compare="sim_size" delta="100"/>
272 <output_collection name="csv_files" type="list" count="1">
273 <element name="ndvi_20190628_189017_statistics.csv" ftype="tabular" file="ndvi_20190628_189017_statistics.csv" compare="diff" lines_diff="1">
274 <assert_contents>
275 <has_text text="count" />
276 <has_text text="32" />
277 <has_text text="81" />
278 <has_text text="48" />
279 <has_text text=".384" />
280 <has_text text=".304" />
281 <has_text text=".424" />
282 <has_text text=".387" />
283 <has_text text=".295" />
284 <has_text text=".432" />
285 <has_text text=".033" />
286 <has_text text=".078" />
287 <has_text text=".031" />
288 <has_n_columns n="5" />
289 </assert_contents>
290 </element>
291 </output_collection>
292 </test>
293 <test>
294 <conditional name="input_type">
295 <param name="platform" value="s2" />
296 <param name="input_file" ftype="tar" value="S2.tar" />
297 <param name="s2_shp" ftype="shp" value="sentinel2_tiles_world/sentinel2_tiles_world.html">
298 <composite_data value="sentinel2_tiles_world/sentinel2_tiles_world.shp"/>
299 <composite_data value="sentinel2_tiles_world/sentinel2_tiles_world.shx"/>
300 <composite_data value="sentinel2_tiles_world/sentinel2_tiles_world.dbf"/>
301 <composite_data value="sentinel2_tiles_world/sentinel2_tiles_world.prj"/>
302 </param>
303 </conditional>
304 <param name="input" value="test_parcels_32635/test_parcels_32635.html" ftype="shp">
305 <composite_data value="test_parcels_32635/test_parcels_32635.shp"/>
306 <composite_data value="test_parcels_32635/test_parcels_32635.shx"/>
307 <composite_data value="test_parcels_32635/test_parcels_32635.dbf"/>
308 <composite_data value="test_parcels_32635/test_parcels_32635.prj"/>
309 </param>
310 <param name="identifier" value="ID"/>
311 <section name="adv_options">
312 <repeat name="statistics">
313 <conditional name="stats_input">
314 <param name="stats" value="mean"/>
315 </conditional>
316 </repeat>
317 <repeat name="statistics">
318 <conditional name="stats_input">
319 <param name="stats" value="median"/>
320 </conditional>
321 </repeat>
322 <repeat name="statistics">
323 <conditional name="stats_input">
324 <param name="stats" value="std"/>
325 </conditional>
326 </repeat>
327 <param name="indices" value="ndvi"/>
328 </section>
329 <output file="20211217-210343.log" name="logfile" compare="sim_size" delta="100"/>
330 <output_collection name="csv_files" type="list" count="1">
331 <element name="ndvi_20200626_34VFN_statistics.csv" ftype="tabular" file="ndvi_20200626_34VFN_statistics.csv" compare="diff" lines_diff="1">
332 <assert_contents>
333 <has_text text="204" />
334 <has_text text="551" />
335 <has_text text="335" />
336 <has_text text=".321" />
337 <has_text text=".293" />
338 <has_text text=".661" />
339 <has_text text=".302" />
340 <has_text text=".294" />
341 <has_text text=".686" />
342 <has_text text=".091" />
343 <has_text text=".088" />
344 <has_text text=".091" />
345 <has_n_columns n="5" />
346 </assert_contents>
347 </element>
348 </output_collection>
349 </test>
350 </tests>
351 <help><![CDATA[
352
353 **EODIE - Earth Observation Data Information Extractor**
354 =======================================================================================================
355
356 Toolkit to extract object based timeseries from Earth Observation data such as Copernicus Sentinel 2, Landsat 8 and more generally geotiff files.
357
358 EODIE takes the objects in as polygons in a shapefile as well as the timeframe of interest and the features (eg vegetation indices) to be extracted.
359 The output is a per polygon timeseries of the selected features over the timeframe of interest.
360
361 ]]> </help>
362 <expand macro="citations" />
363 </tool>