annotate copernicusmarine.xml @ 3:87ae77f2bd5a draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit ecc01d1975d2a603ece634c6cfe2d9591b307cc8

<tool id="copernicusmarine" name="Copernicus Marine Data Store" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01" license="MIT">
    <description>retrieve marine data</description>
    <macros>
        <token name="@TOOL_VERSION@">1.3.3</token>
        <token name="@VERSION_SUFFIX@">2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">copernicusmarine</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        bash '$cmems_credentials' &&
        
        echo -e '$input_text' > config_file_with_my_command &&
        python '$__tool_directory__/check.py' 'config_file_with_my_command'
    ]]></command>
    <configfiles>
        <configfile name="cmems_credentials">
#import os 
#set $cmems_username = $__user__.extra_preferences.get('cmems_username', "")
#set $cmems_password = $__user__.extra_preferences.get('cmems_password', "")
#if $cmems_username == "" or $cmems_password == ""
    #set $cmems_username = os.getenv('CMEMS_USERNAME', '')
    #set $cmems_password = os.getenv('CMEMS_PASSWORD', '')
#end if
export cmems_username='$cmems_username'
export cmems_password='$cmems_password'
        </configfile>
    </configfiles>
    <inputs>
        <param name="input_text" label="Paste API Request" type="text" area="true">
            <sanitizer invalid_char="">
                <valid initial="string.letters,string.digits">
                    <add value="_" />
                    <add value="-" />
                    <add value=" " />
                    <add value=":" />
                    <add value="." />
                    <add value=" " />
                </valid>
            </sanitizer>
            <validator type="regex">[0-9a-zA-Z_:\-\. ]+</validator>
        </param>
    </inputs>
    <outputs>
        <data name="output_netcdf" label="Copernicus marine data" from_work_dir="./*.nc" format="netcdf"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <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"/>
            <output name="output_netcdf">
                <assert_contents>
                    <has_text text="_NCProperties"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
============================
Copernicus Marine Data Store
============================

** Context **
        
This tool is a wrapper to retrieve data from the Copernicus Marine Environment Monitoring Service (CMEMS).

- It allows to retrieve data from the Copernicus Marine Service.
- Any user willing to use this tool needs to `create a new account <https://data.marine.copernicus.eu/login>`_.
- Set your Copernicus CMEMS API Key via: User > Preferences > Manage Information
- Enter your username and password for Copernicus CMEMS
- Compose your request directly on Copernicus Marine Data Store 
    - Choose there which data interest you click on the download button
    - Then on the top right click again on the big download butto
    - Log in
    - Click on "Automate"
    - You should have a pop-up window called "Automate download"
    - Copy the ">_Command-Line Interface" proposed there
- Back on Galaxy paste it in the input field "Paste API Request".

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>`

** Input **
        
Command line from the Copernicus marine services copy paste as a text.

** Output **
        
A netcdf file containing the the data chose by the user from the Copernicus Marine Data Store.

    ]]></help>
    <citations>
        <citation type="bibtex"> 
        @misc{Copernicus, 
        title={Copernicus Marine Data Store}, 
        url={https://data.marine.copernicus.eu/products}, 
        note={E.U. Copernicus Marine Service Information}, 
        author={Copernicus, E.U.} 
        }
        </citation>
    </citations>
</tool>