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planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit e8074c9f6817bba5ca6cb322434ca5e4412b34cf
author climate
date Fri, 27 Sep 2024 19:34:28 +0000
parents 7fa6bc1fb588
children
comparison
equal deleted inserted replaced
0:7fa6bc1fb588 1:eadc0e7f9abd
1 <tool id="c3s" name="Copernicus Climate Data Store" version="0.1.0"> 1 <tool id="c3s" name="Copernicus Climate Data Store" version="0.3.0" profile="23.0">
2 <description>for retrieveing climate data</description> 2 <description>for retrieving climate data</description>
3 <edam_topics>
4 <edam_topic>topic_3855</edam_topic>
5 <edam_topic>topic_3318</edam_topic>
6 </edam_topics>
7 <edam_operations>
8 <edam_operation>operation_2422</edam_operation>
9 <edam_operation>operation_3357</edam_operation>
10 <edam_operation>operation_0335</edam_operation>
11 </edam_operations>
3 <requirements> 12 <requirements>
4 <requirement type="package" version="3">python</requirement> 13 <requirement type="package" version="3.8">python</requirement>
5 <requirement type="package" version="0.5.1">cdsapi</requirement> 14 <requirement type="package" version="0.7.3">cdsapi</requirement>
6 <requirement type="package" version="1.9.9">cdo</requirement> 15 <requirement type="package" version="2.4.4">cdo</requirement>
7 <requirement type="package" version="1.34">tar</requirement> 16 <requirement type="package" version="1.34">tar</requirement>
8 <requirement type="package" version="6.0">unzip</requirement> 17 <requirement type="package" version="6.0">unzip</requirement>
9 </requirements> 18 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 19 <command detect_errors="exit_code"><![CDATA[
11 export HOME=`pwd` && 20 export HOME=`pwd` &&
12 #set $c3s_cds_apikey = $__user__.extra_preferences.get('c3s_account|c3s_cds_apikey', "") 21 #set $c3s_cds_apikey = $__user__.extra_preferences.get('c3s_account|c3s_cds_apikey', "")
13 #if $c3s_cds_apikey == "" 22 #if $c3s_cds_apikey == ""
14 echo "Error. Set your credentials via: User -> Preferences -> Manage Information" && 23 echo "Error. Set your credentials via: User -> Preferences -> Manage Information" &&
15 #else 24 #else
16 cp '$cds_key_file' .cdsapirc && 25 cp '$cds_key_file' .cdsapirc &&
17 #end if 26 #end if
18 #if str($is_file.has_req).strip() == 'yes' 27 #if str($is_file.has_req).strip() == 'yes'
19 python3 '$__tool_directory__/c3s_retrieve.py' 28 python3 '$__tool_directory__/c3s_retrieve.py'
20 --request '$is_file.api_req_file' --output request.txt && 29 --request '$is_file.api_req_file' --output request.txt &&
21 #else 30 #else
22 python3 '$__tool_directory__/c3s_retrieve.py' 31 python3 '$__tool_directory__/c3s_retrieve.py'
23 --request $req_from_paste --output request.txt && 32 --request $req_from_paste --output request.txt &&
24 #end if 33 #end if
25 bash $__tool_directory__/c3s.sh && 34 bash $__tool_directory__/c3s.sh &&
26 echo "C3S data retrieval is done" 35 echo "C3S data retrieval is done"
27 ]]></command> 36 ]]></command>
28 <configfiles> 37 <configfiles>
29 <configfile name="cds_key_file"><![CDATA[ 38 <configfile name="cds_key_file"><![CDATA[
30 #set $c3s_cds_apikey = $__user__.extra_preferences.get('c3s_account|c3s_cds_apikey', "") 39 #set $c3s_cds_apikey = $__user__.extra_preferences.get('c3s_account|c3s_cds_apikey', "")
31 url: https://cds.climate.copernicus.eu/api/v2 40 url: https://cds.climate.copernicus.eu/api
32 key: $c3s_cds_apikey 41 key: $c3s_cds_apikey
33 ]]></configfile> 42 ]]></configfile>
34 <configfile name="req_from_paste"><![CDATA[ 43 <configfile name="req_from_paste"><![CDATA[
35 #if str($is_file.has_req).strip() == 'no' 44 #if str($is_file.has_req).strip() == 'no'
36 $is_file.api_req_text 45 $is_file.api_req_text
50 <param name="api_req_text" type="text" label="Paste API Request" area="true" /> 59 <param name="api_req_text" type="text" label="Paste API Request" area="true" />
51 </when> 60 </when>
52 </conditional> 61 </conditional>
53 </inputs> 62 </inputs>
54 <outputs> 63 <outputs>
55 <data name="request" format="txt" from_work_dir="request.txt"/> 64 <data name="request" format="txt" from_work_dir="request.txt" label="${tool.name} on ${on_string}: request script"/>
56 <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/> 65 <data name="ofilename" format="netcdf" from_work_dir="tmp.nc" label="${tool.name} on ${on_string}: NC"/>
57 </outputs> 66 </outputs>
58 <tests> 67 <tests>
59 <test> 68 <test>
60 <param name="api_req_file" value="input.txt" /> 69 <param name="api_req_file" value="input.txt" />
61 <output name="request" ftype="txt"> 70 <output name="request" ftype="txt">
62 <assert_contents> 71 <assert_contents>
63 <has_text text="dataset to retrieve: reanalysis-era5-single-levels-monthly-means" /> 72 <has_text text="dataset to retrieve: reanalysis-era5-single-levels-monthly-means" />
64 <has_text text="'format': 'netcdf'" /> 73 <has_text text="'data_format': 'netcdf'" />
65 <has_text text="'product_type': 'monthly_averaged_reanalysis'" /> 74 <has_text text="'product_type': 'monthly_averaged_reanalysis'" />
66 <has_text text="'variable': '2m_temperature'" /> 75 <has_text text="'variable': '2m_temperature'" />
67 <has_text text="'year': '2020'" /> 76 <has_text text="'year': '2020'" />
68 <has_text text="'month': '12'" /> 77 <has_text text="'month': '12'" />
69 <has_text text="'time': '00:00'" /> 78 <has_text text="'time': '00:00'" />
79 </test> 88 </test>
80 </tests> 89 </tests>
81 <help><![CDATA[ 90 <help><![CDATA[
82 91
83 **Copernicus Climate Data Store (C3S)** 92 **Copernicus Climate Data Store (C3S)**
84 ======================================================================================================= 93 =======================================
85 94
86 This tool is a wrapper to retrieve data from the Copernicus Climate Data Store. 95 This tool is a wrapper to retrieve data from the Copernicus Climate Data Store.
87 96
88 - It allows to retrieve data from the Copernicus climate Data Store. 97 - It allows to retrieve data from the Copernicus climate Data Store.
89 - Any user willing to use this tool needs to `create a new account <https://cds.climate.copernicus.eu/user/register?destination=%2F%23!%2Fhome>`_. 98 - Any user willing to use this tool needs to `create a new account <https://cds.climate.copernicus.eu/>`_.
90 - Set your CDS API Key via: User -> Preferences -> Manage Information" 99 - Set your CDS API Key via: User -> Preferences -> Manage Information"
91 - Documentation on where to get the CDS API key can be found `here <https://cds.climate.copernicus.eu/api-how-to>`_. 100 - Documentation on where to get the CDS API key can be found `here <https://cds.climate.copernicus.eu/how-to-api>`_.
92 - Compose your request directly on C3S and copy/paste it in the input field "Request" or save it in a file. 101 - Compose your request directly on C3S and extract the relevant information, which should be put in the input field "Request" or saved in a file. The format should be, for example::
93 - Be aware that for being able to download dataset from C3S, users also need to agree to their term of use (Licence to use Copernicus Products) on the C3S website. 102
103
104 import cdsapi
105
106 c = cdsapi.Client()
107 c.retrieve(
108 'reanalysis-era5-single-levels-monthly-means',
109 {
110 'data_format': 'netcdf',
111 'product_type': 'monthly_averaged_reanalysis',
112 'variable': '2m_temperature',
113 'year': '2020',
114 'month': '12',
115 'time': '00:00',
116 'area': [60, 10, 59.5, 10.5],
117 },
118 'download.nc')
119
120
121 - Be aware that for being able to download dataset from C3S, users also need to agree to licensing terms for each dataset of interest on the C3S website.
94 122
95 License: 123 License:
96 ~~~~~~~~ 124 ~~~~~~~~
97 125
98 Generated using Copernicus Climate Change Service information [2021] 126 Generated using Copernicus Climate Change Service information [2024]
99 Neither the European Commission nor ECMWF is responsible for any use 127 Neither the European Commission nor ECMWF is responsible for any use
100 that may be made of the Copernicus information or data it contains. 128 that may be made of the Copernicus information or data it contains.
101 ]]></help> 129 ]]></help>
102 <citations> 130 <citations>
103 131 <citation type="bibtex">
132 @misc{C3S2024,author={Copernicus Climate Change Service},year={2024}}</citation>
104 </citations> 133 </citations>
105 <edam_topics>
106 <edam_topic>topic_3855</edam_topic>
107 <edam_topic>topic_3318</edam_topic>
108 </edam_topics>
109 <edam_operations>
110 <edam_operation>operation_2422</edam_operation>
111 <edam_operation>operation_3357</edam_operation>
112 <edam_operation>operation_0335</edam_operation>
113 </edam_operations>
114 </tool> 134 </tool>