Mercurial > repos > ecology > harmonize_insitu_to_netcdf
changeset 0:15260949227d draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
| author | ecology |
|---|---|
| date | Thu, 05 Dec 2024 14:16:02 +0000 |
| parents | |
| children | |
| files | bgc_harmonizer.xml test-data/D6901758_001.nc test-data/D6901758_002.nc test-data/D6901758_003.nc test-data/D6901758_004.nc test-data/D6901758_005.nc |
| diffstat | 6 files changed, 126 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bgc_harmonizer.xml Thu Dec 05 14:16:02 2024 +0000 @@ -0,0 +1,126 @@ +<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>