Mercurial > repos > ecology > copernicusmarine

annotate copernicusmarine.xml @ 2:a5b332a8f13b draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit fa49586ecc02936c00015c4368a3b5699295203c
author ecology
date Mon, 18 Nov 2024 10:38:59 +0000
parents c5357ce2123b
children
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1 <tool id="copernicusmarine" name="Copernicus Marine Data Store" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01" license="MIT">
0
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2 <description>retrieve marine data</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.3.3</token>
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5 <token name="@VERSION_SUFFIX@">1</token>
0
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">copernicusmarine</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import re
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12 #set $cmems_username = $__user__.extra_preferences.get('cmems_account|cmems_username', "")
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13 #set $cmems_password = $__user__.extra_preferences.get('cmems_account|cmems_password', "")
0
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15 #if $cmems_username == "" or $cmems_password == ""
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16 #set $cmems_username = os.getenv('CMEMS_USERNAME', '')
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17 #set $cmems_password = os.getenv('CMEMS_PASSWORD', '')
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19 echo "Using global ENVs" &&
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21 #if re.match(r"^(?=.*[a-z])(?=.*[A-Z])(?=.*\d).{8,}$", $cmems_password):
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22 echo "Password meets the required criteria" &&
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23 #else:
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24 echo "Password does not meet the required criteria" &&
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25 #end if
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27 #end if
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29 #if $cmems_username == ""
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30 echo 'Error. Set your CMEMS credentials via: User -> Preferences -> Manage Information' &&
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31 #end if
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33 #set $filename="config_file_with_my_command"
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34 echo -e '$input_text' > $filename --force-download --username $cmems_username --password $cmems_password &&
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36 python '$__tool_directory__/check.py' $filename
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37 ]]></command>
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38 <configfiles>
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39 <configfile name="cmems_credentials">
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40 #set $cmems_username = $__user__.extra_preferences.get('cmems_username', "")
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41 #set $cmems_password = $__user__.extra_preferences.get('cmems_password', "")
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42 cmems_username: $cmems_username
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43 cmems_password: $cmems_password
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44 </configfile>
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45 </configfiles>
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46 <inputs>
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47 <param name="input_text" label="Paste API Request" type="text" area="true">
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48 <sanitizer invalid_char="">
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49 <valid initial="string.letters,string.digits">
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50 <add value="_" />
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51 <add value="-" />
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52 <add value=" " />
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53 <add value=":" />
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54 <add value="." />
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55 <add value=" " />
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56 </valid>
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57 </sanitizer>
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58 <validator type="regex">[0-9a-zA-Z_:\-\. ]+</validator>
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59 </param>
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60 </inputs>
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61 <outputs>
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62 <data name="output_netcdf" label="Copernicus marine data" from_work_dir="./*.nc" format="netcdf"/>
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63 </outputs>
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64 <tests>
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65 <test expect_num_outputs="1">
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66 <param name="input_text" value="copernicusmarine subset --dataset-id cmems_mod_med_phy_my_4.2km-climatology_P1M-m --variable bottomT_avg --variable bottomT_std --variable mlotst_avg --variable mlotst_std --variable so_avg --variable so_std --variable thetao_avg --variable thetao_std --variable uo_avg --variable uo_std --variable vo_avg --variable vo_std --variable zos_avg --variable zos_std --start-datetime 1993-12-01T00:00:00 --end-datetime 1993-12-01T00:00:00 --minimum-longitude 10.283266521135577 --maximum-longitude 12.139348881644054 --minimum-latitude 38.461936025366256 --maximum-latitude 39.82957565942514 --minimum-depth 1.0182366371154785 --maximum-depth 1.0182366371154785"/>
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67 <output name="output_netcdf">
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68 <assert_contents>
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69 <has_text text="_NCProperties"/>
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70 </assert_contents>
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71 </output>
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 ============================
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76 Copernicus Marine Data Store
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77 ============================
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78
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79 ** Context **
2
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80
0
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81 This tool is a wrapper to retrieve data from the Copernicus Marine Environment Monitoring Service (CMEMS).
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82
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83 - It allows to retrieve data from the Copernicus Marine Service.
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84 - Any user willing to use this tool needs to `create a new account <https://data.marine.copernicus.eu/login>`_.
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85 - Set your Copernicus CMEMS API Key via: User > Preferences > Manage Information
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86 - Enter your username and password for Copernicus CMEMS
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87 - Compose your request directly on Copernicus Marine Data Store
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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88 - Choose there which data interest you click on the download button
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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89 - Then on the top right click again on the big download butto
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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90 - Log in
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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91 - Click on "Automate"
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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92 - You should have a pop-up window called "Automate download"
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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93 - Copy the ">_Command-Line Interface" proposed there
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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94 - Back on Galaxy paste it in the input field "Paste API Request".
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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95
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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96 For more information on the Command-Line Interface (CLI) go on `Copernicus Marine Toolbox CLI - Subset <https://help.marine.copernicus.eu/en/articles/7972861-copernicus-marine-toolbox-cli-subset>`
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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97
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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98 ** Input **
2
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99
0
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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100 Command line from the Copernicus marine services copy paste as a text.
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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101
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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102 ** Output **
2
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103
0
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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104 A netcdf file containing the the data chose by the user from the Copernicus Marine Data Store.
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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105
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106 ]]></help>
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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107 <citations>
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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108 <citation type="bibtex">
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109 @misc{Copernicus,
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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110 title={Copernicus Marine Data Store},
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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111 url={https://data.marine.copernicus.eu/products},
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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112 note={E.U. Copernicus Marine Service Information},
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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113 author={Copernicus, E.U.}
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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114 }
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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115 </citation>
482815be63e0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6
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116 </citations>
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117 </tool>