Mercurial > repos > ecology > xarray_select
comparison xarray_select.xml @ 2:123a9a629bef draft
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
author | ecology |
---|---|
date | Sun, 06 Jun 2021 08:51:41 +0000 |
parents | 6baac361495b |
children | bf595d613af4 |
comparison
equal
deleted
inserted
replaced
1:6baac361495b | 2:123a9a629bef |
---|---|
1 <tool id="xarray_select" name="NetCDF xarray Selection" version="0.15.1"> | 1 <tool id="xarray_select" name="NetCDF xarray Selection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
2 <description>extracts variable values with custom conditions on dimensions</description> | 2 <description>extracts variable values with custom conditions on dimensions</description> |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="edam_ontology"/> | |
3 <requirements> | 7 <requirements> |
4 <requirement type="package" version="3">python</requirement> | 8 <requirement type="package" version="3">python</requirement> |
5 <requirement type="package" version="1.5.3">netcdf4</requirement> | 9 <requirement type="package" version="1.5.6">netcdf4</requirement> |
6 <requirement type="package" version="0.15.1">xarray</requirement> | 10 <requirement type="package" version="@TOOL_VERSION@">xarray</requirement> |
7 <requirement type="package" version="0.7.0">geopandas</requirement> | 11 <requirement type="package" version="0.9.0">geopandas</requirement> |
8 <requirement type="package" version="1.7.0">shapely</requirement> | 12 <requirement type="package" version="1.7.1">shapely</requirement> |
9 </requirements> | 13 </requirements> |
10 <command detect_errors="exit_code"><![CDATA[ | 14 <command detect_errors="exit_code"><![CDATA[ |
11 mkdir output_dir && | 15 mkdir output_dir && |
16 #if $condi_source_coord.coord_source=="coord_from_file" | |
17 echo "Galaxy xarray version @TOOL_VERSION@" > output_dir/version.tabular && | |
18 #end if | |
12 python '$__tool_directory__/xarray_tool.py' '$input' --select '$var' | 19 python '$__tool_directory__/xarray_tool.py' '$input' --select '$var' |
13 --verbose | 20 --verbose |
14 --filter | 21 --filter |
15 #for $i,$uc in enumerate($user_choice) | 22 #for $i,$uc in enumerate($user_choice) |
16 #if $uc.condi_between.comparator=="bi" | 23 #if $uc.condi_between.comparator=="bi" |
31 | 38 |
32 #if $condi_source_coord.coord_source=="coord_from_file" | 39 #if $condi_source_coord.coord_source=="coord_from_file" |
33 --coords '$coord_tabular' | 40 --coords '$coord_tabular' |
34 --latname '$condi_source_coord.lat_dim' --lonname '$condi_source_coord.lon_dim' | 41 --latname '$condi_source_coord.lat_dim' --lonname '$condi_source_coord.lon_dim' |
35 --outputdir output_dir | 42 --outputdir output_dir |
43 #if $condi_source_coord.tolerance | |
44 --tolerance '$condi_source_coord.tolerance' | |
45 #end if | |
36 #else | 46 #else |
37 --outfile 'final.tabular' | 47 --outfile 'final.tabular' |
38 #if $condi_source_coord.condi_coord.coord=='single' | 48 #if $condi_source_coord.condi_coord.coord=='single' |
39 --latname $condi_source_coord.condi_coord.lat_dim | 49 --latname $condi_source_coord.condi_coord.lat_dim |
40 --latvalN $condi_source_coord.condi_coord.lat_val | 50 --latvalN $condi_source_coord.condi_coord.lat_val |
41 --lonname $condi_source_coord.condi_coord.lon_dim | 51 --lonname $condi_source_coord.condi_coord.lon_dim |
42 --lonvalE $condi_source_coord.condi_coord.lon_val | 52 --lonvalE $condi_source_coord.condi_coord.lon_val |
53 #if $condi_source_coord.condi_coord.no_missing | |
54 --no_missing | |
55 #end if | |
56 #if $condi_source_coord.condi_coord.tolerance | |
57 --tolerance '$condi_source_coord.condi_coord.tolerance' | |
58 #end if | |
43 #elif $condi_source_coord.condi_coord.coord=='subregion' | 59 #elif $condi_source_coord.condi_coord.coord=='subregion' |
44 --latname $condi_source_coord.condi_coord.lat_dim | 60 --latname $condi_source_coord.condi_coord.lat_dim |
45 --latvalN $condi_source_coord.condi_coord.lat_valN | 61 --latvalN $condi_source_coord.condi_coord.lat_valN |
46 --latvalS $condi_source_coord.condi_coord.lat_valS | 62 --latvalS $condi_source_coord.condi_coord.lat_valS |
47 --lonname $condi_source_coord.condi_coord.lon_dim | 63 --lonname $condi_source_coord.condi_coord.lon_dim |
77 <param name="lon_dim" type="select" label="Name of longitude coordinate" > | 93 <param name="lon_dim" type="select" label="Name of longitude coordinate" > |
78 <options from_dataset="var_tab"> | 94 <options from_dataset="var_tab"> |
79 <column name="value" index="0"/> | 95 <column name="value" index="0"/> |
80 </options> | 96 </options> |
81 </param> | 97 </param> |
98 <param type="float" name="tolerance" optional="true" label="Maximum distance between original and selected value for inexact matches e.g. abs(original, index) is lower or equal to tolerance"/> | |
82 </when> | 99 </when> |
83 | 100 |
84 <when value="coord_from_stdin"> | 101 <when value="coord_from_stdin"> |
85 <conditional name="condi_coord"> | 102 <conditional name="condi_coord"> |
86 <param name="coord" type="select" label="Geographical area" help="Use this option to get valid values at your custom coordinates."> | 103 <param name="coord" type="select" label="Geographical area" help="Use this option to get valid values at your custom coordinates."> |
99 <options from_dataset="var_tab"> | 116 <options from_dataset="var_tab"> |
100 <column name="value" index="0"/> | 117 <column name="value" index="0"/> |
101 </options> | 118 </options> |
102 </param> | 119 </param> |
103 <param name="lon_val" type="float" value="0" label="Longitude"/> | 120 <param name="lon_val" type="float" value="0" label="Longitude"/> |
121 <param name="no_missing" type="boolean" value="false" label="Do not handle null/missing values (only valid for single location and multiple columns)"/> | |
122 <param name="tolerance" type="float" optional="true" label="Maximum distance between original and selected value for inexact matches e.g. abs(original, index) is lower or equal to tolerance"/> | |
104 </when> | 123 </when> |
105 <when value="subregion"> | 124 <when value="subregion"> |
106 <param name="lat_dim" type="select" label="Name of latitude coordinate" > | 125 <param name="lat_dim" type="select" label="Name of latitude coordinate" > |
107 <options from_dataset="var_tab"> | 126 <options from_dataset="var_tab"> |
108 <column name="value" index="0"/> | 127 <column name="value" index="0"/> |
208 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/> | 227 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/> |
209 <param name="var" value="phy"/> | 228 <param name="var" value="phy"/> |
210 <param name="var_tab" value="var_tab_dataset-ibi"/> | 229 <param name="var_tab" value="var_tab_dataset-ibi"/> |
211 <conditional name="condi_source_coord"> | 230 <conditional name="condi_source_coord"> |
212 <param name="coord_source" value="coord_from_stdin"/> | 231 <param name="coord_source" value="coord_from_stdin"/> |
213 <conditional name="condi_coord"> | 232 <conditional name="condi_coord"> |
214 <param name="coord" value="single"/> | 233 <param name="coord" value="single"/> |
215 <param name="lat_dim" value="latitude"/> | 234 <param name="lat_dim" value="latitude"/> |
216 <param name="lat_val" value="44.0"/> | 235 <param name="lat_val" value="44.0"/> |
217 <param name="lon_dim" value="longitude"/> | 236 <param name="lon_dim" value="longitude"/> |
218 <param name="lon_val" value="-2.0"/> | 237 <param name="lon_val" value="-2.0"/> |
219 </conditional> | 238 </conditional> |
220 </conditional> | 239 </conditional> |
221 <output name="simpleoutput" value="Test1.tabular"> | 240 <output name="simpleoutput" value="Test1.tabular"> |
222 <assert_contents> | 241 <assert_contents> |
223 <has_text_matching expression="0\t2002-12-15\t0.5"/> | 242 <has_text_matching expression="0\t2002-12-15\t0.5"/> |
224 <has_text_matching expression="144\t2014-12-15\t0.5"/> | 243 <has_text_matching expression="144\t2014-12-15\t0.5"/> |
230 <param name="var_tab" value="var_tab_dataset-ibi"/> | 249 <param name="var_tab" value="var_tab_dataset-ibi"/> |
231 <param name="var" value="nh4"/> | 250 <param name="var" value="nh4"/> |
232 | 251 |
233 <conditional name="condi_source_coord"> | 252 <conditional name="condi_source_coord"> |
234 <param name="coord_source" value="coord_from_stdin"/> | 253 <param name="coord_source" value="coord_from_stdin"/> |
235 <conditional name="condi_coord"> | 254 <conditional name="condi_coord"> |
236 <param name="coord" value="global"/> | 255 <param name="coord" value="global"/> |
237 </conditional> | 256 </conditional> |
238 </conditional> | 257 </conditional> |
239 <section name="time"> | 258 <section name="time"> |
240 <conditional name="condi_datetime"> | 259 <conditional name="condi_datetime"> |
241 <param name="datetime" value="yes"/> | 260 <param name="datetime" value="yes"/> |
242 <conditional name="condi_between"> | 261 <conditional name="condi_between"> |
247 </conditional> | 266 </conditional> |
248 </section> | 267 </section> |
249 <repeat name="user_choice"> | 268 <repeat name="user_choice"> |
250 <param name="dim" value="nh4"/> | 269 <param name="dim" value="nh4"/> |
251 <conditional name="condi_between"> | 270 <conditional name="condi_between"> |
252 <param name="comparator" value="ge"/> | 271 <param name="comparator" value="ge"/> |
253 <param name="value" value="50."/> | 272 <param name="value" value="50."/> |
254 </conditional> | 273 </conditional> |
255 </repeat> | 274 </repeat> |
256 <output name="simpleoutput" value="Test2.tabular"> | 275 <output name="simpleoutput" value="Test2.tabular"> |
257 <assert_contents> | 276 <assert_contents> |
258 <has_text_matching expression="0\t2003-12-15\t0.5"/> | 277 <has_text_matching expression="0\t2003-12-15\t0.5"/> |
259 <has_text_matching expression="23\t2004-12-15\t0.5"/> | 278 <has_text_matching expression="23\t2004-12-15\t0.5"/> |
260 </assert_contents> | 279 </assert_contents> |
261 </output> | 280 </output> |
262 </test> | 281 </test> |
263 </tests> | 282 </tests> |
264 <edam_topics> | |
265 <edam_topic>topic_0610</edam_topic> | |
266 <edam_topic>topic_3050</edam_topic> | |
267 </edam_topics> | |
268 <help><![CDATA[ | 283 <help><![CDATA[ |
269 **What it does** | 284 **What it does** |
270 | 285 |
271 This tool extracts variable values with custom conditions on dimensions. | 286 This tool extracts variable values with custom conditions on dimensions. |
272 | 287 |
282 | 297 |
283 A netcdf file (.nc). | 298 A netcdf file (.nc). |
284 | 299 |
285 Variable tabular file from 'Netcdf Metadate Info'. | 300 Variable tabular file from 'Netcdf Metadate Info'. |
286 | 301 |
287 Tabular file with coordinates and the following structure : 'lat' 'lon'. | 302 Tabular file with coordinates (only coordinates, no header!) and the following structure : 'lat' 'lon'. |
288 | 303 |
289 | 304 |
290 **Outputs** | 305 **Outputs** |
291 | 306 |
292 A single output with values for the wanted variable if there is only one coordinate. | 307 A single output with values for the wanted variable if there is only one coordinate. |
296 | 311 |
297 ------------------------------------------------- | 312 ------------------------------------------------- |
298 | 313 |
299 The xarray select tool can be used after the xarray Info. | 314 The xarray select tool can be used after the xarray Info. |
300 ]]></help> | 315 ]]></help> |
316 <expand macro="citations"/> | |
301 </tool> | 317 </tool> |