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comparison cads.xml @ 0:028c17cfb549 draft default tip

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"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
author climate
date Sat, 19 Jun 2021 18:35:18 +0000
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-1:000000000000 0:028c17cfb549
1 <tool id="cads" name="Copernicus Atmosphere Data Store" version="0.1.0" profile="20.05">
2 <description>for retrieving data from the Atmosphere Monitoring Service</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 $cads_apikey = $__user__.extra_preferences.get('cads_account|cads_apikey', "")
13 #if $cads_apikey == ''
14 echo 'Error. Set your CADS credentials via: User -> Preferences -> Manage Information' &&
15 echo 'Will try to use tool adsapirc file (used for testing)' &&
16 cp '$__tool_directory__/adsapirc.cfg' .cdsapirc &&
17 #else
18 cp '$cads_key_file' .cdsapirc &&
19 #end if
20
21 python3 '$__tool_directory__/cads_retrieve.py'
22 #if str($is_file.has_req).strip() == 'yes'
23 --request '$is_file.api_req_file'
24 #else
25 --request '$req_from_paste'
26 #end if
27 --output request.txt &&
28 bash '$__tool_directory__/cads.sh' &&
29 echo "Data retrieval from Copernicus Atmosphere Data Store is done"
30 ]]></command>
31 <configfiles>
32 <configfile name="cads_key_file"><![CDATA[
33 #set $cads_apikey = $__user__.extra_preferences.get('cads_account|cads_apikey', "")
34 url: https://ads.atmosphere.copernicus.eu/api/v2
35 key: $cads_apikey
36 ]]></configfile>
37 <configfile name="req_from_paste"><![CDATA[
38 #if str($is_file.has_req).strip() == 'no'
39 $is_file.api_req_text
40 #end if
41 ]]></configfile>
42 </configfiles>
43 <inputs>
44 <conditional name="is_file">
45 <param name="has_req" type="select" label="Provide CADS request">
46 <option value="no">paste as text</option>
47 <option value="yes" selected="true">give a filename</option>
48 </param>
49 <when value="yes">
50 <param name="api_req_file" type="data" label="API Request filename" format="txt"/>
51 </when>
52 <when value="no">
53 <param name="api_req_text" type="text" label="Paste API Request" area="true" />
54 </when>
55 </conditional>
56 </inputs>
57 <outputs>
58 <data name="request" format="txt" from_work_dir="request.txt"/>
59 <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/>
60 </outputs>
61 <tests>
62 <test>
63 <conditional name="is_file">
64 <param name="has_req" value="yes" />
65 <param name="api_req_file" ftype="txt" value="req.txt" />
66 </conditional>
67 <output name="request" value="req_out.txt" compare="sim_size" delta="10"/>
68 <output name="ofilename" ftype="netcdf" value="output.nc" compare="sim_size" delta="100"/>
69 </test>
70 <test>
71 <conditional name="is_file">
72 <param name="has_req" value="yes" />
73 <param name="api_req_file" ftype="txt" value="req-timeseries.txt" />
74 </conditional>
75 <output name="request" value="timeseries_out.txt" compare="sim_size" delta="10"/>
76 <output name="ofilename" ftype="netcdf" value="timeseries.nc" compare="sim_size" delta="100"/>
77 </test>
78 </tests>
79 <help><![CDATA[
80
81 **Copernicus Atmosphere Data Store (ADS)**
82 =======================================================================================================
83
84 This tool is a wrapper to retrieve data from the Copernicus Atmosphere Data Store.
85
86 - It allows to retrieve data from the Copernicus Atmosphere Monitoring Service.
87 - Any user willing to use this tool needs to `create a new account <https://ads.atmosphere.copernicus.eu/user/register?destination=/api-how-to|>`_.
88 - Set your CADS API Key via: User -> Preferences -> Manage Information"
89 - Documentation on where to get the CDS API key can be found `here <https://cds.climate.copernicus.eu/api-how-to>`_.
90 - Compose your request directly on Copernicus Atmosphere Data Store and copy/paste it in the input field "Request" or save it in a file.
91 - Be aware that for being able to download dataset from ADS, users also need to agree to their term of use (Licence to use Copernicus Products) on the ADS website.
92
93 License:
94 ~~~~~~~~
95
96 Generated using Copernicus Atmosphere Monitoring Service information [2021]
97 Neither the European Commission nor ECMWF is responsible for any use
98 that may be made of the Copernicus information or data it contains.
99 ]]></help>
100 <citations>
101 </citations>
102 <edam_topics>
103 <edam_topic>topic_3855</edam_topic>
104 <edam_topic>topic_3318</edam_topic>
105 </edam_topics>
106 <edam_operations>
107 <edam_operation>operation_2422</edam_operation>
108 <edam_operation>operation_3357</edam_operation>
109 <edam_operation>operation_0335</edam_operation>
110 </edam_operations>
111 </tool>