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comparison xarray_select.xml @ 2:123a9a629bef draft

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"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
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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>