Mercurial > repos > climate > c3s

annotate 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
parents
children bd153c794da1
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250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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1 <tool id="c3s" name="Copernicus Climate Data Store" version="0.1.0">
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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2 <description>for retrieveing climate data</description>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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3 <requirements>
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4 <requirement type="package" version="3">python</requirement>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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5 <requirement type="package" version="0.5.1">cdsapi</requirement>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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6 <requirement type="package" version="1.9.9">cdo</requirement>
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7 <requirement type="package" version="1.34">tar</requirement>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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8 <requirement type="package" version="6.0">unzip</requirement>
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9 </requirements>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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10 <command detect_errors="exit_code"><![CDATA[
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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11 export HOME=`pwd` &&
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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12 #set $c3s_cds_apikey = $__user__.extra_preferences.get('c3s_account|c3s_cds_apikey', "")
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13 #if $c3s_cds_apikey == ""
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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14 echo "Error. Set your credentials via: User -> Preferences -> Manage Information" &&
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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15 #else
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16 cp '$cds_key_file' .cdsapirc &&
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17 #end if
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18 #if str($is_file.has_req).strip() == 'yes'
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19 python3 '$__tool_directory__/c3s_retrieve.py'
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20 --request '$is_file.api_req_file' --output request.txt &&
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21 #else
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22 python3 '$__tool_directory__/c3s_retrieve.py'
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23 --request $req_from_paste --output request.txt &&
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24 #end if
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25 bash $__tool_directory__/c3s.sh &&
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26 echo "C3S data retrieval is done"
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27 ]]></command>
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28 <configfiles>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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29 <configfile name="cds_key_file"><![CDATA[
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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30 #set $c3s_cds_apikey = $__user__.extra_preferences.get('c3s_account|c3s_cds_apikey', "")
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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31 url: https://cds.climate.copernicus.eu/api/v2
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32 key: $c3s_cds_apikey
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33 ]]></configfile>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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34 <configfile name="req_from_paste"><![CDATA[
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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35 #if str($is_file.has_req).strip() == 'no'
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36 $is_file.api_req_text
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37 #end if
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38 ]]></configfile>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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39 </configfiles>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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40 <inputs>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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41 <conditional name="is_file">
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42 <param name="has_req" type="select" label="C3S request is a given as a filename">
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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43 <option value="yes" selected="true">yes</option>
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44 <option value="no">no</option>
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45 </param>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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46 <when value="yes">
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47 <param name="api_req_file" type="data" label="API Request filename" format="txt"/>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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48 </when>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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49 <when value="no">
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50 <param name="api_req_text" type="text" label="Paste API Request" area="true" />
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51 </when>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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52 </conditional>
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53 </inputs>
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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54 <outputs>
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55 <data name="request" format="txt" from_work_dir="request.txt"/>
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56 <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="api_req_file" value="input.txt" />
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61 <output name="request" ftype="txt">
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62 <assert_contents>
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63 <has_text text="dataset to retrieve: reanalysis-era5-single-levels-monthly-means" />
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64 <has_text text="'format': 'netcdf'" />
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65 <has_text text="'product_type': 'monthly_averaged_reanalysis'" />
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66 <has_text text="'variable': '2m_temperature'" />
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67 <has_text text="'year': '2020'" />
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68 <has_text text="'month': '12'" />
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69 <has_text text="'time': '00:00'" />
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70 <has_text text="'area': [" />
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71 <has_text text="60," />
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72 <has_text text="10," />
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73 <has_text text="59.5," />
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74 <has_text text="10.5," />
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75 <has_text text="]" />
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76 <has_text text="output filename: download.nc" />
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77 </assert_contents>
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78 </output>
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79 </test>
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80 </tests>
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81 <help><![CDATA[
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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82
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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83 **Copernicus Climate Data Store (C3S)**
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84 =======================================================================================================
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85
250554670f72 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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86 This tool is a wrapper to retrieve data from the Copernicus Climate Data Store.
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87
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88 - It allows to retrieve data from the Copernicus climate Data Store.
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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>`_.
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90 - Set your CDS API Key via: User -> Preferences -> Manage Information"
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91 - Documentation on where to get the CDS API key can be found `here <https://cds.climate.copernicus.eu/api-how-to>`_.
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92 - Compose your request directly on C3S and copy/paste it in the input field "Request" or save it in a file.
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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.
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94
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95 License:
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96 ~~~~~~~~
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97
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98 Generated using Copernicus Climate Change Service information [2021]
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99 Neither the European Commission nor ECMWF is responsible for any use
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100 that may be made of the Copernicus information or data it contains.
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101 ]]></help>
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102 <citations>
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103
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104 </citations>
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105 <edam_topics>
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106 <edam_topic>topic_3855</edam_topic>
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107 <edam_topic>topic_3318</edam_topic>
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108 </edam_topics>
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109 <edam_operations>
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110 <edam_operation>operation_2422</edam_operation>
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111 <edam_operation>operation_3357</edam_operation>
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112 <edam_operation>operation_0335</edam_operation>
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113 </edam_operations>
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114 </tool>