Mercurial > repos > ecology > harmonize_insitu_to_netcdf
comparison bgc_harmonizer.xml @ 3:208f69b31088 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit e37c39bf8ca6e30268737dc1a91ed294b6dc095c
author | ecology |
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date | Fri, 27 Jun 2025 16:44:51 +0000 |
parents | 7536ba055525 |
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2:7536ba055525 | 3:208f69b31088 |
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1 <tool id="harmonize_insitu_to_netcdf" name="QCV harmonizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01" license="MIT"> | 1 <tool id="harmonize_insitu_to_netcdf" name="QCV harmonizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01" license="MIT"> |
2 <description>and aggregator of in-situ marine physical and biogeochemical data</description> | 2 <description>and aggregator of in-situ marine physical and biogeochemical data</description> |
3 <macros> | 3 <macros> |
4 <token name="@TOOL_VERSION@">2.0</token> | 4 <token name="@TOOL_VERSION@">3.0</token> |
5 <token name="@VERSION_SUFFIX@">1</token> | 5 <token name="@VERSION_SUFFIX@">1</token> |
6 </macros> | 6 </macros> |
7 <requirements> | 7 <requirements> |
8 <container type="docker">easyqcvbgc/qcv_ingester:@TOOL_VERSION@</container> | 8 <container type="docker">easyqcvbgc/qcv_ingester:@TOOL_VERSION@</container> |
9 </requirements> | 9 </requirements> |
18 | 18 |
19 mkdir ./output/ && | 19 mkdir ./output/ && |
20 cp /runtime/data-out/*.nc ./output/ | 20 cp /runtime/data-out/*.nc ./output/ |
21 ]]></command> | 21 ]]></command> |
22 <inputs> | 22 <inputs> |
23 <param name="infiles" type="data" format="netcdf" multiple="true" label="Input the NetCDF data files" help="This files can NetCDF raw Argo or Gliders data files following CMEMS convention."/> | 23 <param name="infiles" type="data" format="netcdf" multiple="true" label="Input the NetCDF data files" help="This files or collection of files can be NetCDF Argo, Gliders, CMEMS, WOA data files"/> |
24 </inputs> | 24 </inputs> |
25 <outputs> | 25 <outputs> |
26 <collection type="list" name="output_net" format="netcdf"> | 26 <collection type="list" name="output_net" format="netcdf"> |
27 <discover_datasets pattern="(?P<designation>.+)" directory="./output/" visible="true"/> | 27 <discover_datasets pattern="(?P<designation>.+)" directory="./output/" visible="true"/> |
28 </collection> | 28 </collection> |
38 .. class:: infomark | 38 .. class:: infomark |
39 | 39 |
40 **What it does** | 40 **What it does** |
41 General presentation | 41 General presentation |
42 | 42 |
43 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. | 43 The qcv-ingester 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 a concatenated single file with harmonized vocabulary needed for the project. |
44 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. | 44 Profiles are concatenated along the time dimension in the order given by the listing : For Argo data, if BGC data precede CORE profiles, all BGC data will precede CORE data. Use cycle_number variable to associate them again. |
45 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. | 45 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. |
46 | |
47 Coordinates and variables : | 46 Coordinates and variables : |
48 | 47 |
49 "lon" : ["longitude", "LONGITUDE", "LON", "lon"], | 48 "lon" : ["longitude", "LONGITUDE", "LON", "lon"], |
50 "lat" : ["latitude", "LATITUDE", "LAT", "lat"], | 49 "lat" : ["latitude", "LATITUDE", "LAT", "lat"], |
51 "time" : ["date", "time", "TIME", "JULD"], | 50 "time" : ["date", "time", "TIME", "JULD"], |