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comparison bgc_harmonizer.xml @ 3:2e461a3ece09 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit e37c39bf8ca6e30268737dc1a91ed294b6dc095c
author ecology
date Fri, 27 Jun 2025 16:44:39 +0000
parents 71d66fc8087d
children
comparison
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2:71d66fc8087d 3:2e461a3ece09
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&lt;designation&gt;.+)" directory="./output/" visible="true"/> 27 <discover_datasets pattern="(?P&lt;designation&gt;.+)" 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"],