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comparison xarray_select.xml @ 3:bf595d613af4 draft

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"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
author ecology
date Thu, 20 Jan 2022 17:07:19 +0000
parents 123a9a629bef
children b393815e4cb7
comparison
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2:123a9a629bef 3:bf595d613af4
1 <tool id="xarray_select" name="NetCDF xarray Selection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="xarray_select" name="NetCDF xarray Selection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>extracts variable values with custom conditions on dimensions</description> 2 <description>extracts variable values with custom conditions on dimensions</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/> 6 <expand macro="edam_ontology"/>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
8 <requirement type="package" version="3">python</requirement> 9 <requirement type="package" version="3">python</requirement>
9 <requirement type="package" version="1.5.6">netcdf4</requirement> 10 <requirement type="package" version="1.5.6">netcdf4</requirement>
10 <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
11 <requirement type="package" version="0.9.0">geopandas</requirement> 11 <requirement type="package" version="0.9.0">geopandas</requirement>
12 <requirement type="package" version="1.7.1">shapely</requirement> 12 <requirement type="package" version="1.7.1">shapely</requirement>
13 </requirements> 13 </requirements>
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 mkdir output_dir && 15 mkdir output_dir &&
16 #if $condi_source_coord.coord_source=="coord_from_file" 16 #if $condi_source_coord.coord_source=="coord_from_file"
17 echo "Galaxy xarray version @TOOL_VERSION@" > output_dir/version.tabular && 17 echo "Galaxy xarray version @TOOL_VERSION@"> output_dir/version.tabular &&
18 #end if 18 #end if
19 python '$__tool_directory__/xarray_tool.py' '$input' --select '$var' 19 python '$__tool_directory__/xarray_tool.py' '$input' --select '$var'
20 --verbose 20 --verbose
21 --filter 21 --filter
22 #for $i,$uc in enumerate($user_choice) 22 #for $i,$uc in enumerate($user_choice)
63 --lonname $condi_source_coord.condi_coord.lon_dim 63 --lonname $condi_source_coord.condi_coord.lon_dim
64 --lonvalE $condi_source_coord.condi_coord.lon_valE 64 --lonvalE $condi_source_coord.condi_coord.lon_valE
65 --lonvalW $condi_source_coord.condi_coord.lon_valW 65 --lonvalW $condi_source_coord.condi_coord.lon_valW
66 #end if 66 #end if
67 #end if 67 #end if
68 ]]></command> 68 ]]> </command>
69 <inputs> 69 <inputs>
70 <param type="data" name="input" label="Input netcdf file" format="netcdf"/> 70 <param type="data" name="input" label="Input netcdf file" format="netcdf"/>
71 <param type="data" label="Tabular of variables" name="var_tab" format="tabular" help="Select the tabular file which summarize the available variables and dimensions."/> 71 <param type="data" label="Tabular of variables" name="var_tab" format="tabular" help="Select the tabular file which summarize the available variables and dimensions."/>
72 72
73 <param name="var" type="select" label="Choose the variable to extract"> 73 <param name="var" type="select" label="Choose the variable to extract">
83 <option value="coord_from_file">Use coordinates from input file</option> 83 <option value="coord_from_file">Use coordinates from input file</option>
84 </param> 84 </param>
85 85
86 <when value="coord_from_file"> 86 <when value="coord_from_file">
87 <param type="data" label="Tabular of coord" name="coord_tabular" format="tabular" help="Format : Latitude Longitude"/> 87 <param type="data" label="Tabular of coord" name="coord_tabular" format="tabular" help="Format : Latitude Longitude"/>
88 <param name="lat_dim" type="select" label="Name of latitude coordinate" > 88 <param name="lat_dim" type="select" label="Name of latitude coordinate">
89 <options from_dataset="var_tab"> 89 <options from_dataset="var_tab">
90 <column name="value" index="0"/> 90 <column name="value" index="0"/>
91 </options> 91 </options>
92 </param> 92 </param>
93 <param name="lon_dim" type="select" label="Name of longitude coordinate" > 93 <param name="lon_dim" type="select" label="Name of longitude coordinate">
94 <options from_dataset="var_tab"> 94 <options from_dataset="var_tab">
95 <column name="value" index="0"/> 95 <column name="value" index="0"/>
96 </options> 96 </options>
97 </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"/> 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"/>
104 <option value="global">Whole available region</option> 104 <option value="global">Whole available region</option>
105 <option value="single">Single location</option> 105 <option value="single">Single location</option>
106 <option value="subregion">Sub-region extraction</option> 106 <option value="subregion">Sub-region extraction</option>
107 </param> 107 </param>
108 <when value="single"> 108 <when value="single">
109 <param name="lat_dim" type="select" label="Name of latitude coordinate" > 109 <param name="lat_dim" type="select" label="Name of latitude coordinate">
110 <options from_dataset="var_tab"> 110 <options from_dataset="var_tab">
111 <column name="value" index="0"/> 111 <column name="value" index="0"/>
112 </options> 112 </options>
113 </param> 113 </param>
114 <param name="lat_val" type="float" value="0" label="Latitude"/> 114 <param name="lat_val" type="float" value="0" label="Latitude"/>
115 <param name="lon_dim" type="select" label="Name of longitude coordinate" > 115 <param name="lon_dim" type="select" label="Name of longitude coordinate">
116 <options from_dataset="var_tab"> 116 <options from_dataset="var_tab">
117 <column name="value" index="0"/> 117 <column name="value" index="0"/>
118 </options> 118 </options>
119 </param> 119 </param>
120 <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)"/> 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"/> 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"/>
123 </when> 123 </when>
124 <when value="subregion"> 124 <when value="subregion">
125 <param name="lat_dim" type="select" label="Name of latitude coordinate" > 125 <param name="lat_dim" type="select" label="Name of latitude coordinate">
126 <options from_dataset="var_tab"> 126 <options from_dataset="var_tab">
127 <column name="value" index="0"/> 127 <column name="value" index="0"/>
128 </options> 128 </options>
129 </param> 129 </param>
130 <param name="lat_valN" type="float" value="0" label="Latitude North"/> 130 <param name="lat_valN" type="float" value="0" label="Latitude North"/>
131 <param name="lat_valS" type="float" value="0" label="Latitude South"/> 131 <param name="lat_valS" type="float" value="0" label="Latitude South"/>
132 <param name="lon_dim" type="select" label="Name of longitude coordinate" > 132 <param name="lon_dim" type="select" label="Name of longitude coordinate">
133 <options from_dataset="var_tab"> 133 <options from_dataset="var_tab">
134 <column name="value" index="0"/> 134 <column name="value" index="0"/>
135 </options> 135 </options>
136 </param> 136 </param>
137 <param name="lon_valE" type="float" value="0" label="Longitude East"/> 137 <param name="lon_valE" type="float" value="0" label="Longitude East"/>
222 <filter>condi_source_coord['coord_source'] == 'coord_from_stdin'</filter> 222 <filter>condi_source_coord['coord_source'] == 'coord_from_stdin'</filter>
223 </data> 223 </data>
224 </outputs> 224 </outputs>
225 <tests> 225 <tests>
226 <test> 226 <test>
227 <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"/>
228 <param name="var" value="phy"/> 228 <param name="var" value="phy"/>
229 <param name="var_tab" value="var_tab_dataset-ibi"/> 229 <param name="var_tab" value="var_tab_dataset-ibi"/>
230 <conditional name="condi_source_coord"> 230 <conditional name="condi_source_coord">
231 <param name="coord_source" value="coord_from_stdin"/> 231 <param name="coord_source" value="coord_from_stdin"/>
232 <conditional name="condi_coord"> 232 <conditional name="condi_coord">
233 <param name="coord" value="single"/> 233 <param name="coord" value="single"/>
234 <param name="lat_dim" value="latitude"/> 234 <param name="lat_dim" value="latitude"/>
235 <param name="lat_val" value="44.0"/> 235 <param name="lat_val" value="44.0"/>
236 <param name="lon_dim" value="longitude"/> 236 <param name="lon_dim" value="longitude"/>
237 <param name="lon_val" value="-2.0"/> 237 <param name="lon_val" value="-2.0"/>
238 </conditional> 238 </conditional>
239 </conditional> 239 </conditional>
240 <output name="simpleoutput" value="Test1.tabular"> 240 <output name="simpleoutput" value="Test1.tabular">
241 <assert_contents> 241 <assert_contents>
242 <has_text_matching expression="0\t2002-12-15\t0.5"/> 242 <has_text_matching expression="0\t2002-12-15\t0.5"/>
243 <has_text_matching expression="144\t2014-12-15\t0.5"/> 243 <has_text_matching expression="144\t2014-12-15\t0.5"/>
244 </assert_contents> 244 </assert_contents>
245 </output> 245 </output>
246 </test> 246 </test>
247 <test> 247 <test>
248 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/> 248 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
249 <param name="var_tab" value="var_tab_dataset-ibi"/> 249 <param name="var_tab" value="var_tab_dataset-ibi"/>
250 <param name="var" value="nh4"/> 250 <param name="var" value="nh4"/>
251 251
252 <conditional name="condi_source_coord"> 252 <conditional name="condi_source_coord">
253 <param name="coord_source" value="coord_from_stdin"/> 253 <param name="coord_source" value="coord_from_stdin"/>
254 <conditional name="condi_coord"> 254 <conditional name="condi_coord">
255 <param name="coord" value="global"/> 255 <param name="coord" value="global"/>
256 </conditional> 256 </conditional>
257 </conditional> 257 </conditional>
258 <section name="time"> 258 <section name="time">
259 <conditional name="condi_datetime"> 259 <conditional name="condi_datetime">
260 <param name="datetime" value="yes"/> 260 <param name="datetime" value="yes"/>
261 <conditional name="condi_between"> 261 <conditional name="condi_between">
262 <param name="comparator" value="sl"/> 262 <param name="comparator" value="sl"/>
263 <param name="t1" value="2003-12-15" /> 263 <param name="t1" value="2003-12-15" />
264 <param name="t2" value="2004-12-15" /> 264 <param name="t2" value="2004-12-15" />
265 </conditional> 265 </conditional>
266 </conditional> 266 </conditional>
267 </section> 267 </section>
268 <repeat name="user_choice"> 268 <repeat name="user_choice">
269 <param name="dim" value="nh4"/> 269 <param name="dim" value="nh4"/>
270 <conditional name="condi_between"> 270 <conditional name="condi_between">
271 <param name="comparator" value="ge"/> 271 <param name="comparator" value="ge"/>
272 <param name="value" value="50."/> 272 <param name="value" value="50."/>
273 </conditional> 273 </conditional>
274 </repeat> 274 </repeat>
275 <output name="simpleoutput" value="Test2.tabular"> 275 <output name="simpleoutput" value="Test2.tabular">
276 <assert_contents> 276 <assert_contents>
277 <has_text_matching expression="0\t2003-12-15\t0.5"/> 277 <has_text_matching expression="0\t2003-12-15\t0.5"/>
278 <has_text_matching expression="23\t2004-12-15\t0.5"/> 278 <has_text_matching expression="23\t2004-12-15\t0.5"/>
279 </assert_contents> 279 </assert_contents>
280 </output> 280 </output>
281 </test> 281 </test>
282 </tests> 282 </tests>
283 <help><![CDATA[ 283 <help><![CDATA[
284 **What it does** 284 **What it does**
285 285
310 310
311 311
312 ------------------------------------------------- 312 -------------------------------------------------
313 313
314 The xarray select tool can be used after the xarray Info. 314 The xarray select tool can be used after the xarray Info.
315 ]]></help> 315 ]]> </help>
316 <expand macro="citations"/> 316 <expand macro="citations"/>
317 </tool> 317 </tool>