annotate bgc_harmonizer.xml @ 0:15260949227d draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d

<tool id="harmonize_insitu_to_netcdf" name="QCV harmonizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01" license="MIT">
    <description>and aggregator of insitu marine physical and biogeochemical data</description>
    <macros>
        <token name="@TOOL_VERSION@">1.1</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <container type="docker">pokapok/qcv_ingester:@TOOL_VERSION@</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        export HOME=\$PWD &&

        #for $i, $infile in enumerate($infiles):
            cp '$infile' '/runtime/data/original_data/work/ga_la_xy/${infile.element_identifier}' &&
        #end for

        /app/launchers/start-app.sh GALAXY &&
        
        cp /runtime/data/harmonized_data/work/ga_la_xy_harm_agg.nc '$output_net'
    ]]></command>
    <inputs>
        <param name="infiles" type="data" format="netcdf" multiple="true" label="Input the netcdf data files" help="This files can netcdf raw Argo or Gliders datafiles following CMEMS convention."/>
    </inputs>
    <outputs>
        <data name="output_net" format="netcdf" from_work_dir="/runtime/data/harmonized_data/work/*.nc" label="${tool.name} netcdf data" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="infiles" value="D6901758_001.nc,D6901758_002.nc,D6901758_003.nc,D6901758_004.nc,D6901758_005.nc"/>
            <output name="output_net">
                <assert_contents>
            	    <has_size value="427535" delta="0"/>
            	</assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**
General presentation

The cerb_harmonizer tool aggregates and harmonizes marine in-situ data following the needs of the UseCase 2.1-BCG - Fair-Ease. It converts files of individual or already aggregated data profiles into concatened single file with harmonized vocabullary needed for the project.
Profiles are concatenated along the time dimension in the order given by the lising : if BGC data preceed CORE profiles, all BGC data will preceed CORE data. Use cycle_number variable to associate them again.
Vocabulary translations are below. On the left, the writing of each variable in the output file, on the right, all possible translations found over data exploration.

Coordinates and variables :

    "lon" : ["longitude", "LONGITUDE", "LON", "lon"],
    "lat" : ["latitude", "LATITUDE", "LAT", "lat"],
    "time" : ["date", "time", "TIME", "JULD"],
    "time_qc" : ["date_qc", "time_qc", "TIME_QC", "JULD_QC"],
    "depth" : ["DEPTH", "depth"],
    "cycle_number" : ["CYCLE_NUMBER"],
    "ref_time" : ["REFERENCE_DATE_TIME"],
    "pos_qc" : ["POSITION_QC",]

--

    "temperature" : ["TEMP", "TEMPERATURE"],
    "salinity" : ["PSAL", "PRACTICAL_SALINITY"],
    "oxygen" : ["DOXY"],
    "pressure" : ["PRES"],
    "chlorophylle" : ["CHLA"],
    "nitrate" : ["NO3", "NITRATE", "n_an"],
    "bbp700" : ["BBP700"],

All variables are tagged with a suffix to indicate the state of the data (_raw, _dmadjusted, _rtadjusted)

--

Variables extracted from meta files are :

    LAUNCH_DATE
    PLATFORM_TYPE
    PI_NAME meta variables are stored as metadata

--

Units :

    "degree_east" : ["degree_east"],
    "degree_north" : ["degree_north"],
    "degree_celsius" : ["degree_celsius", "degree_Celsius"], # temperature
    "psu" : ["psu", "practical_salinity_unit", "PSU"], # salinity
    "micromol/l" : ["micromole.l-1", "micromole_per_liter", "μmol.l-1", "μmol/l", "μmol/L", "μmol.L-1"], # concentration liters
    "mg/m3" : ["mg/m3",],
    "micromole/kg" : ["micromole/kg",],
    "m-1" : ["m-1"],
    "decibar" : ["decibar", "dbar"], # pressure

Arbitrarily,

    dates are written following : "seconds since 1950-01-01T00:00:00 in julian calendar"
    longitude is set between : -180° and 180°
    latitude is set between : -90° and 90°

WARNING : This application works only platform by platform. For example, it is possible to aggregate and harmonize a whole argo trajectory but one at a time. If two argo trajectories are needed to process, this tool needs to be run 2 times.

**Input**

a list of files in a txt file named cerb_listing.txt copntaining only filenames without paths. The tool will find the files automatically. A listing example here :

BD6901580_003.nc BD6901580_004.nc BD6901580_005.nc BD6901580_006.nc D6901580_003.nc D6901580_004.nc D6901580_005.nc D6901580_006.nc 6901580_meta.nc

paths of where are the data (volumes) containing configurations, listings and data. Paths are :

    config path : where your textfile containing the list of files names is : it contains the listing cerb_listing.txt
    data_path : highest folder including all the files to harmonize written in the textfile listing

**Output**

A concatenated and harmonized netcdf file

    ]]></help>
    <citations>
        <citation type="bibtex">
            @Manual{,
            title = {QCV Ingester},
            author = {Pokapok},
            year = {2024},
            note = {https://gitlab.com/pokapok-projects/PKP8-OGI-BGC/qcv_ingester}
        </citation>    
    </citations>
</tool>