Mercurial > repos > climate > cdo_operations

comparison cdo_operations.xml @ 0:26eb6b5443c1 draft default tip

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"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo commit da614bb8e3e9b19a5167ff19b625a71d9976108a"
author climate
date Sat, 15 Jan 2022 23:19:24 +0000
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-1:000000000000 0:26eb6b5443c1
1 <tool id="cdo_operations" name="CDO Operations" profile="20.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Climate Data Manipulation Operators operations for standard processing of climate and NWP model output.</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>macros_operations.xml</import>
6 </macros>
7 <expand macro="edam_ontology"/>
8 <expand macro="cdo_requirements"/>
9 <expand macro="cdo_stdio"/>
10 <command detect_errors="exit_code"><![CDATA[
11 mkdir output_dir &&
12 cdo
13 #for $i, $cdo_option in enumerate( $section_option )
14 #if $cdo_option.option_type.add_opt == '-f'
15 $cdo_option.option_type.add_opt $cdo_option.option_type.output_format
16 #elif $cdo_option.option_type.add_opt == '-g'
17 $cdo_option.option_type.add_opt $cdo_option.option_type.grid
18 #elif $cdo_option.option_type.add_opt == '-gf'
19 $cdo_option.option_type.add_opt $cdo_option.option_type.gridfile
20 #elif $cdo_option.option_type.add_opt == '-m'
21 $cdo_option.option_type.add_opt $cdo_option.option_type.missval
22 #elif $cdo_option.option_type.add_opt == '--percentile'
23 $cdo_option.option_type.add_opt $cdo_option.option_type.percentile
24 #elif $cdo_option.option_type.add_opt == '--seed'
25 $cdo_option.option_type.add_opt $cdo_option.option_type.seed
26 #else
27 $cdo_option.option_type.add_opt
28 #end if
29 #end for
30 #for $i, $cdo_oper in enumerate( $section_operators )
31 #if $cdo_oper.operator.opt == 'duplicate'
32 -'$cdo_oper.operator.opt',$cdo_oper.operator.ndup
33 #elif $cdo_oper.operator.opt == 'addc' or $cdo_oper.operator.opt == 'subc' or $cdo_oper.operator.opt == 'mulc' or $cdo_oper.operator.opt == 'divc'
34 -'$cdo_oper.operator.opt',$cdo_oper.operator.const_value
35 #elif $cdo_oper.operator.opt == 'ens' or $cdo_oper.operator.opt == 'zon' or $cdo_oper.operator.opt == 'tim' or $cdo_oper.operator.opt == 'vert' or $cdo_oper.operator.opt == 'day' or $cdo_oper.operator.opt == 'year' or $cdo_oper.operator.opt == 'mon' or $cdo_oper.operator.opt == 'seas' or $cdo_oper.operator.opt == 'fld'
36 -'${cdo_oper.operator.opt}${cdo_oper.operator.stat}'
37 #elif $cdo_oper.operator.opt == 'sp2gp' or $cdo_oper.operator.opt == 'gp2sp'
38 #if $cdo_oper.operator.trunc > 0
39 -'$cdo_oper.operator.opt',$cdo_oper.operator.trunc
40 #else
41 -'$cdo_oper.operator.opt'
42 #end if
43 #elif $cdo_oper.operator.opt == 'collgrid'
44 #if str($cdo_oper.operator.nx)
45 #if str($cdo_oper.operator.names)
46 -'$cdo_oper.operator.opt',$cdo_oper.operator.nx,'$cdo_oper.operator.names'
47 #else
48 -'$cdo_oper.operator.opt',$cdo_oper.operator.nx
49 #end if
50 #else
51 -'$cdo_oper.operator.opt'
52 #end if
53 #elif $cdo_oper.operator.opt == 'distgrid'
54 -'$cdo_oper.operator.opt',$cdo_oper.operator.nx,$cdo_oper.operator.ny
55 #elif $cdo_oper.operator.opt == 'splitsel'
56 #if str($cdo_oper.operator.noffset)
57 #if str($cdo_oper.operator.nskip)
58 -'$cdo_oper.operator.opt',$cdo_oper.operator.nsets,$cdo_oper.operator.noffset,$cdo_oper.operator.nskip
59 #else
60 -'$cdo_oper.operator.opt',$cdo_oper.operator.nsets,$cdo_oper.operator.noffset
61 #end if
62 #else
63 -'$cdo_oper.operator.opt',$cdo_oper.operator.nsets
64 #end if
65 #elif $cdo_oper.operator.opt == 'select' or $cdo_oper.operator.opt == 'delete' or $cdo_oper.operator.opt == 'selname' or $cdo_oper.operator.opt == 'delname' or $cdo_oper.operator.opt == 'seltimestep' or $cdo_oper.operator.opt == 'sellonlatbox' or $cdo_oper.operator.opt == 'expr' or $cdo_oper.operator.opt == 'ml2pl' or $cdo_oper.operator.opt == 'ml2hl' or $cdo_oper.operator.opt == 'intlevel'
66 -'$cdo_oper.operator.opt','$cdo_oper.operator.params'
67 #elif $cdo_oper.operator.opt == 'setattribute'
68 -'$cdo_oper.operator.opt',FILE='$cdo_oper.operator.attr_file'
69 #else
70 -'$cdo_oper.operator.opt'
71 #end if
72 #if $cdo_oper.operator.opt == 'copy' or $cdo_oper.operator.opt == 'cat' or $cdo_oper.operator.opt == 'merge' or $cdo_oper.operator.opt == 'mergetime' or $cdo_oper.operator.opt == 'collgrid' or $cdo_oper.operator.opt == 'select' or $cdo_oper.operator.opt == 'delete' or $cdo_oper.operator.opt == 'replace'
73 #for $ifile in $cdo_oper.operator.add_file
74 '${ifile}'
75 #end for
76 #elif $cdo_oper.operator.add_file and '$cdo_oper.operator.add_file' != '' and '$cdo_oper.operator.add_file' != 'None' and $cdo_oper.operator.add_file is not None
77 '$cdo_oper.operator.add_file'
78 #end if
79 #if $i == 0
80 #if $cdo_oper.operator.opt == 'splitcode' or $cdo_oper.operator.opt == 'splitparam' or $cdo_oper.operator.opt == 'splitname' or $cdo_oper.operator.opt == 'splitlevel' or $cdo_oper.operator.opt == 'splitgrid' or $cdo_oper.operator.opt == 'splitzaxis' or $cdo_oper.operator.opt == 'splittabnum' or $cdo_oper.operator.opt == 'splithour' or $cdo_oper.operator.opt == 'splitday' or $cdo_oper.operator.opt == 'splitseas' or $cdo_oper.operator.opt == 'splityear' or $cdo_oper.operator.opt == 'splityearmon' or $cdo_oper.operator.opt == 'splitmon'
81 #set output = 'output_dir/outfile_'
82 #else
83 #set output = 'output_dir/outfile.netcdf'
84 #end if
85 #end if
86 #end for
87 '${output}'
88 ]]> </command>
89 <inputs>
90 <repeat name="section_operators" title="CDO Operators" min="1" max="10">
91 <expand macro="cdo_operator"/>
92 </repeat>
93 <repeat name="section_option" title="CDO Options" min="0" max="5">
94 <expand macro="cdo_option"/>
95 </repeat>
96 </inputs>
97 <outputs>
98 <collection name="output_files" type="list" label="${tool.name} outfiles">
99 <discover_datasets pattern="__name__" directory="output_dir" visible="true" format="netcdf"/>
100 </collection>
101 </outputs>
102 <tests>
103 <test>
104 <conditional name="operator">
105 <param name="opt" value="select" />
106 <param name="params" value="name=Drops" />
107 <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
108 </conditional>
109 <output_collection name="output_files" type="list" count="1">
110 <element name="outfile.netcdf" ftype="netcdf" file="drops1.nc" compare="sim_size" delta="50"/>
111 </output_collection>
112 </test>
113 <test>
114 <conditional name="operator">
115 <param name="opt" value="copy" />
116 <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
117 </conditional>
118 <output_collection name="output_files" type="list" count="1">
119 <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_copy.nc" compare="sim_size" delta="50"/>
120 </output_collection>
121 </test>
122 <test>
123 <conditional name="operator">
124 <param name="opt" value="cat" />
125 <param name="add_file" value="drops1.nc,drops2.nc" ftype="netcdf" />
126 </conditional>
127 <output_collection name="output_files" type="list" count="1">
128 <element name="outfile.netcdf" ftype="netcdf" file="drops_cat.nc" compare="sim_size" delta="50"/>
129 </output_collection>
130 </test>
131 <test>
132 <conditional name="operator">
133 <param name="opt" value="splitname" />
134 <param name="add_file" value="lat_long.nc" ftype="netcdf" />
135 </conditional>
136 <output_collection name="output_files" type="list" count="2"/>
137 </test>
138 <test>
139 <conditional name="operator">
140 <param name="opt" value="replace" />
141 <param name="add_file" value="lat_long.nc,latitude_modified.nc" ftype="netcdf" />
142 </conditional>
143 <output_collection name="output_files" type="list" count="1">
144 <element name="outfile.netcdf" ftype="netcdf" file="lat_long_modified.nc" compare="sim_size" delta="50"/>
145 </output_collection>
146 </test>
147 <test>
148 <conditional name="operator">
149 <param name="opt" value="duplicate" />
150 <param name="ndup" value="3" ftype="integer" />
151 <param name="add_file" value="latitude.nc" ftype="netcdf" />
152 </conditional>
153 <output_collection name="output_files" type="list" count="1">
154 <element name="outfile.netcdf" ftype="netcdf" file="latitude3.nc" compare="sim_size" delta="50"/>
155 </output_collection>
156 </test>
157 <test>
158 <conditional name="operator">
159 <param name="opt" value="selname" />
160 <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
161 <param name="params" value="Drops" />
162 </conditional>
163 <output_collection name="output_files" type="list" count="1">
164 <element name="outfile.netcdf" ftype="netcdf" file="drops1.nc" compare="sim_size" delta="50"/>
165 </output_collection>
166 </test>
167 <test>
168 <conditional name="operator">
169 <param name="opt" value="seltimestep" />
170 <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
171 <param name="params" value="1,13,25" />
172 </conditional>
173 <output_collection name="output_files" type="list" count="1">
174 <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_timesteps.nc" compare="sim_size" delta="50"/>
175 </output_collection>
176 </test>
177 <test>
178 <conditional name="operator">
179 <param name="opt" value="sellonlatbox" />
180 <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
181 <param name="params" value="-10,10,60,70" />
182 </conditional>
183 <output_collection name="output_files" type="list" count="1">
184 <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_sellonlatbox.nc" compare="sim_size" delta="50"/>
185 </output_collection>
186 </test>
187 <test>
188 <conditional name="operator">
189 <param name="opt" value="invertlat" />
190 <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
191 </conditional>
192 <output_collection name="output_files" type="list" count="1">
193 <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_invertlat.nc" compare="sim_size" delta="50"/>
194 </output_collection>
195 </test>
196 <test>
197 <repeat name="section_operators">
198 <conditional name="operator">
199 <param name="opt" value="selname" />
200 <param name="params" value="Drops" />
201 </conditional>
202 </repeat>
203 <repeat name="section_operators">
204 <conditional name="operator">
205 <param name="opt" value="addc" />
206 <param name="const_value" value="10.5" />
207 <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
208 </conditional>
209 </repeat>
210 <output_collection name="output_files" type="list" count="1">
211 <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_addc.nc" compare="sim_size" delta="50"/>
212 </output_collection>
213 </test>
214 <test>
215 <conditional name="operator">
216 <param name="opt" value="expr" />
217 <param name="params" value="Drops2=1000*exp(1+Drops)" />
218 <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
219 </conditional>
220 <output_collection name="output_files" type="list" count="1">
221 <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_expr.nc" compare="sim_size" delta="50"/>
222 </output_collection>
223 </test>
224 <test>
225 <repeat name="section_operators">
226 <conditional name="operator">
227 <param name="opt" value="selname" />
228 <param name="params" value="CLEAR_SKY_BHI" />
229 </conditional>
230 </repeat>
231 <repeat name="section_operators">
232 <conditional name="operator">
233 <param name="opt" value="tim" />
234 <param name="stat" value="avg" />
235 <param name="add_file" value="timeseries.nc" ftype="netcdf" />
236 </conditional>
237 </repeat>
238 <output_collection name="output_files" type="list" count="1">
239 <element name="outfile.netcdf" ftype="netcdf" file="timeseries_timavg.nc" compare="sim_size" delta="50"/>
240 </output_collection>
241 </test>
242 <test>
243 <repeat name="section_operators">
244 <conditional name="operator">
245 <param name="opt" value="sub" />
246 <param name="add_file" value="timeseries.nc" ftype="netcdf" />
247 </conditional>
248 </repeat>
249 <repeat name="section_operators">
250 <conditional name="operator">
251 <param name="opt" value="addc" />
252 <param name="const_value" value="10.5" />
253 <param name="add_file" value="timeseries.nc" ftype="netcdf" />
254 </conditional>
255 </repeat>
256 <output_collection name="output_files" type="list" count="1">
257 <element name="outfile.netcdf" ftype="netcdf" file="timeseries_sub.nc" compare="sim_size" delta="50"/>
258 </output_collection>
259 </test>
260 <test>
261 <repeat name="section_operators">
262 <conditional name="operator">
263 <param name="opt" value="sellonlatbox" />
264 <param name="params" value="-10,10,60,70" />
265 </conditional>
266 </repeat>
267 <repeat name="section_operators">
268 <conditional name="operator">
269 <param name="opt" value="setattribute" />
270 <param name="attr_file" value="attributes.txt" />
271 <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
272 </conditional>
273 </repeat>
274 <output_collection name="output_files" type="list" count="1">
275 <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_sellonlatbox_units.nc" compare="sim_size" delta="50"/>
276 </output_collection>
277 </test>
278 </tests>
279 <help><![CDATA[
280
281 **Climate Data Operators (CDO)**
282 =======================================================================================================
283
284 This tool is a wrapper to the Climate Data Operators (CDO) for all operators manipulating input files and creating a new output file.
285
286 - CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
287 - There are more than 600 operators available.
288
289 - `CDO online documentation <https://code.mpimet.mpg.de/projects/cdo/>`_.
290
291 ]]> </help>
292 <expand macro="citations"/>
293 </tool>