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comparison c3s.xml @ 0:250554670f72 draft

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"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
author climate
date Tue, 13 Apr 2021 18:32:45 +0000
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children bd153c794da1
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-1:000000000000 0:250554670f72
1 <tool id="c3s" name="Copernicus Climate Data Store" version="0.1.0">
2 <description>for retrieveing climate data</description>
3 <requirements>
4 <requirement type="package" version="3">python</requirement>
5 <requirement type="package" version="0.5.1">cdsapi</requirement>
6 <requirement type="package" version="1.9.9">cdo</requirement>
7 <requirement type="package" version="1.34">tar</requirement>
8 <requirement type="package" version="6.0">unzip</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 export HOME=`pwd` &&
12 #set $c3s_cds_apikey = $__user__.extra_preferences.get('c3s_account|c3s_cds_apikey', "")
13 #if $c3s_cds_apikey == ""
14 echo "Error. Set your credentials via: User -> Preferences -> Manage Information" &&
15 #else
16 cp '$cds_key_file' .cdsapirc &&
17 #end if
18 #if str($is_file.has_req).strip() == 'yes'
19 python3 '$__tool_directory__/c3s_retrieve.py'
20 --request '$is_file.api_req_file' --output request.txt &&
21 #else
22 python3 '$__tool_directory__/c3s_retrieve.py'
23 --request $req_from_paste --output request.txt &&
24 #end if
25 bash $__tool_directory__/c3s.sh &&
26 echo "C3S data retrieval is done"
27 ]]></command>
28 <configfiles>
29 <configfile name="cds_key_file"><![CDATA[
30 #set $c3s_cds_apikey = $__user__.extra_preferences.get('c3s_account|c3s_cds_apikey', "")
31 url: https://cds.climate.copernicus.eu/api/v2
32 key: $c3s_cds_apikey
33 ]]></configfile>
34 <configfile name="req_from_paste"><![CDATA[
35 #if str($is_file.has_req).strip() == 'no'
36 $is_file.api_req_text
37 #end if
38 ]]></configfile>
39 </configfiles>
40 <inputs>
41 <conditional name="is_file">
42 <param name="has_req" type="select" label="C3S request is a given as a filename">
43 <option value="yes" selected="true">yes</option>
44 <option value="no">no</option>
45 </param>
46 <when value="yes">
47 <param name="api_req_file" type="data" label="API Request filename" format="txt"/>
48 </when>
49 <when value="no">
50 <param name="api_req_text" type="text" label="Paste API Request" area="true" />
51 </when>
52 </conditional>
53 </inputs>
54 <outputs>
55 <data name="request" format="txt" from_work_dir="request.txt"/>
56 <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/>
57 </outputs>
58 <tests>
59 <test>
60 <param name="api_req_file" value="input.txt" />
61 <output name="request" ftype="txt">
62 <assert_contents>
63 <has_text text="dataset to retrieve: reanalysis-era5-single-levels-monthly-means" />
64 <has_text text="'format': 'netcdf'" />
65 <has_text text="'product_type': 'monthly_averaged_reanalysis'" />
66 <has_text text="'variable': '2m_temperature'" />
67 <has_text text="'year': '2020'" />
68 <has_text text="'month': '12'" />
69 <has_text text="'time': '00:00'" />
70 <has_text text="'area': [" />
71 <has_text text="60," />
72 <has_text text="10," />
73 <has_text text="59.5," />
74 <has_text text="10.5," />
75 <has_text text="]" />
76 <has_text text="output filename: download.nc" />
77 </assert_contents>
78 </output>
79 </test>
80 </tests>
81 <help><![CDATA[
82
83 **Copernicus Climate Data Store (C3S)**
84 =======================================================================================================
85
86 This tool is a wrapper to retrieve data from the Copernicus Climate Data Store.
87
88 - 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>`_.
90 - 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>`_.
92 - Compose your request directly on C3S and copy/paste it in the input field "Request" or save it in a file.
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.
94
95 License:
96 ~~~~~~~~
97
98 Generated using Copernicus Climate Change Service information [2021]
99 Neither the European Commission nor ECMWF is responsible for any use
100 that may be made of the Copernicus information or data it contains.
101 ]]></help>
102 <citations>
103
104 </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>