| Previous changeset 1:bd153c794da1 (2024-02-08) |
|
Commit message:
planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit e8074c9f6817bba5ca6cb322434ca5e4412b34cf |
|
modified:
c3s.xml test-data/input.txt |
| b |
| diff -r bd153c794da1 -r 21e8386cf36f c3s.xml --- a/c3s.xml Thu Feb 08 17:58:54 2024 +0000 +++ b/c3s.xml Fri Sep 27 19:34:36 2024 +0000 |
| [ |
| @@ -1,9 +1,18 @@ -<tool id="c3s" name="Copernicus Climate Data Store" version="0.2.0"> +<tool id="c3s" name="Copernicus Climate Data Store" version="0.3.0" profile="23.0"> <description>for retrieving climate data</description> + <edam_topics> + <edam_topic>topic_3855</edam_topic> + <edam_topic>topic_3318</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_2422</edam_operation> + <edam_operation>operation_3357</edam_operation> + <edam_operation>operation_0335</edam_operation> + </edam_operations> <requirements> - <requirement type="package" version="3">python</requirement> - <requirement type="package" version="0.5.1">cdsapi</requirement> - <requirement type="package" version="1.9.9">cdo</requirement> + <requirement type="package" version="3.8">python</requirement> + <requirement type="package" version="0.7.3">cdsapi</requirement> + <requirement type="package" version="2.4.4">cdo</requirement> <requirement type="package" version="1.34">tar</requirement> <requirement type="package" version="6.0">unzip</requirement> </requirements> @@ -11,24 +20,24 @@ export HOME=`pwd` && #set $c3s_cds_apikey = $__user__.extra_preferences.get('c3s_account|c3s_cds_apikey', "") #if $c3s_cds_apikey == "" - echo "Error. Set your credentials via: User -> Preferences -> Manage Information" && + echo "Error. Set your credentials via: User -> Preferences -> Manage Information" && #else cp '$cds_key_file' .cdsapirc && #end if #if str($is_file.has_req).strip() == 'yes' python3 '$__tool_directory__/c3s_retrieve.py' - --request '$is_file.api_req_file' --output request.txt && + --request '$is_file.api_req_file' --output request.txt && #else python3 '$__tool_directory__/c3s_retrieve.py' - --request $req_from_paste --output request.txt && + --request $req_from_paste --output request.txt && #end if - bash $__tool_directory__/c3s.sh && + bash $__tool_directory__/c3s.sh && echo "C3S data retrieval is done" ]]></command> <configfiles> <configfile name="cds_key_file"><![CDATA[ #set $c3s_cds_apikey = $__user__.extra_preferences.get('c3s_account|c3s_cds_apikey', "") - url: https://cds.climate.copernicus.eu/api/v2 + url: https://cds.climate.copernicus.eu/api key: $c3s_cds_apikey ]]></configfile> <configfile name="req_from_paste"><![CDATA[ @@ -52,8 +61,8 @@ </conditional> </inputs> <outputs> - <data name="request" format="txt" from_work_dir="request.txt"/> - <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/> + <data name="request" format="txt" from_work_dir="request.txt" label="${tool.name} on ${on_string}: request script"/> + <data name="ofilename" format="netcdf" from_work_dir="tmp.nc" label="${tool.name} on ${on_string}: NC"/> </outputs> <tests> <test> @@ -61,7 +70,7 @@ <output name="request" ftype="txt"> <assert_contents> <has_text text="dataset to retrieve: reanalysis-era5-single-levels-monthly-means" /> - <has_text text="'format': 'netcdf'" /> + <has_text text="'data_format': 'netcdf'" /> <has_text text="'product_type': 'monthly_averaged_reanalysis'" /> <has_text text="'variable': '2m_temperature'" /> <has_text text="'year': '2020'" /> @@ -81,34 +90,45 @@ <help><![CDATA[ **Copernicus Climate Data Store (C3S)** -======================================================================================================= +======================================= This tool is a wrapper to retrieve data from the Copernicus Climate Data Store. - It allows to retrieve data from the Copernicus climate Data Store. -- Any user willing to use this tool needs to `create a new account <https://cds.climate.copernicus.eu/user/register?destination=%2F%23!%2Fhome>`_. +- Any user willing to use this tool needs to `create a new account <https://cds.climate.copernicus.eu/>`_. - Set your CDS API Key via: User -> Preferences -> Manage Information" -- Documentation on where to get the CDS API key can be found `here <https://cds.climate.copernicus.eu/api-how-to>`_. -- Compose your request directly on C3S and copy/paste it in the input field "Request" or save it in a file. -- 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. +- Documentation on where to get the CDS API key can be found `here <https://cds.climate.copernicus.eu/how-to-api>`_. +- 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:: + + + import cdsapi + + c = cdsapi.Client() + c.retrieve( + 'reanalysis-era5-single-levels-monthly-means', + { + 'data_format': 'netcdf', + 'product_type': 'monthly_averaged_reanalysis', + 'variable': '2m_temperature', + 'year': '2020', + 'month': '12', + 'time': '00:00', + 'area': [60, 10, 59.5, 10.5], + }, + 'download.nc') + + +- 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. License: ~~~~~~~~ -Generated using Copernicus Climate Change Service information [2021] +Generated using Copernicus Climate Change Service information [2024] Neither the European Commission nor ECMWF is responsible for any use that may be made of the Copernicus information or data it contains. ]]></help> <citations> - + <citation type="bibtex"> + @misc{C3S2024,author={Copernicus Climate Change Service},year={2024}}</citation> </citations> - <edam_topics> - <edam_topic>topic_3855</edam_topic> - <edam_topic>topic_3318</edam_topic> - </edam_topics> - <edam_operations> - <edam_operation>operation_2422</edam_operation> - <edam_operation>operation_3357</edam_operation> - <edam_operation>operation_0335</edam_operation> - </edam_operations> </tool> |
| b |
| diff -r bd153c794da1 -r 21e8386cf36f test-data/input.txt --- a/test-data/input.txt Thu Feb 08 17:58:54 2024 +0000 +++ b/test-data/input.txt Fri Sep 27 19:34:36 2024 +0000 |
| b |
| @@ -5,7 +5,7 @@ c.retrieve( 'reanalysis-era5-single-levels-monthly-means', { - 'format': 'netcdf', + 'data_format': 'netcdf', 'product_type': 'monthly_averaged_reanalysis', 'variable': '2m_temperature', 'year': '2020', |