Mercurial > repos > ecology > harmonize_insitu_to_netcdf

annotate 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
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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">
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2 <description>and aggregator of in-situ marine physical and biogeochemical data</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">3.0</token>
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5 <token name="@VERSION_SUFFIX@">1</token>
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6 </macros>
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7 <requirements>
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8 <container type="docker">easyqcvbgc/qcv_ingester:@TOOL_VERSION@</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 export HOME=\$PWD &&
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13 #for $i, $infile in enumerate($infiles):
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14 cp '$infile' '/runtime/data-in/${infile.element_identifier}' &&
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15 #end for
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17 /app/launchers/start-app.sh GALAXY &&
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19 mkdir ./output/ &&
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20 cp /runtime/data-out/*.nc ./output/
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21 ]]></command>
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22 <inputs>
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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"/>
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24 </inputs>
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25 <outputs>
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26 <collection type="list" name="output_net" format="netcdf">
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27 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="./output/" visible="true"/>
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28 </collection>
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29 </outputs>
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30 <tests>
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31 <test expect_num_outputs="1">
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32 <param name="infiles" value="D6901758_001.nc,D6901758_002.nc,D6901758_003.nc,D6901758_004.nc,D6901758_005.nc"/>
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33 <output_collection name="output_net" type="list" count="1"/>
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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38 .. class:: infomark
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40 **What it does**
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41 General presentation
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42
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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.
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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.
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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.
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46 Coordinates and variables :
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47
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48 "lon" : ["longitude", "LONGITUDE", "LON", "lon"],
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49 "lat" : ["latitude", "LATITUDE", "LAT", "lat"],
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50 "time" : ["date", "time", "TIME", "JULD"],
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51 "time_qc" : ["date_qc", "time_qc", "TIME_QC", "JULD_QC"],
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52 "depth" : ["DEPTH", "depth"],
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53 "cycle_number" : ["CYCLE_NUMBER"],
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54 "ref_time" : ["REFERENCE_DATE_TIME"],
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55 "pos_qc" : ["POSITION_QC",]
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56
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57 --
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58
1
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59 "temperature" : ["TEMP", "TEMPERATURE", "t_an"],
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60 "salinity" : ["PSAL", "PRACTICAL_SALINITY", "s_an"],
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61 "oxygen" : ["DOXY", "o_an"],
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62 "oxygenSat" : ["O_an"],
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63 "pressure" : ["PRES"],
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64 "chlorophylle" : ["CHLA"],
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65 "nitrate" : ["NO3", "NITRATE", "n_an"],
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66 "bbp700" : ["BBP700"],
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67 "C1PHASE_DOXY" : ["C1PHASE_DOXY"],
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68 "C2PHASE_DOXY" : ["C2PHASE_DOXY"],
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69 "TEMP_DOXY" : ["TEMP_DOXY"],
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71 All variables are tagged with a suffix to indicate the state of the data (_raw, _dmadjusted, _rtadjusted)
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73 --
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75 Variables extracted from meta files are :
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77 LAUNCH_DATE
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78 PLATFORM_TYPE
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79 PI_NAME meta variables are stored as metadata
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81 --
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82
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83 Units :
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84
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85 "degree_east" : ["degree_east"],
2a6d823efa51 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
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86 "degree_north" : ["degree_north"],
2a6d823efa51 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
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87 "degree_celsius" : ["degree_celsius", "degree_Celsius"], # temperature
2a6d823efa51 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
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88 "psu" : ["psu", "practical_salinity_unit", "PSU"], # salinity
2a6d823efa51 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
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89 "micromol/l" : ["micromole.l-1", "micromole_per_liter", "μmol.l-1", "μmol/l", "μmol/L", "μmol.L-1"], # concentration liters
2a6d823efa51 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
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90 "mg/m3" : ["mg/m3",],
2a6d823efa51 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
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91 "micromole/kg" : ["micromole/kg",],
2a6d823efa51 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
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92 "m-1" : ["m-1"],
2a6d823efa51 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
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93 "decibar" : ["decibar", "dbar"], # pressure
2a6d823efa51 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
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94
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95 Arbitrarily,
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96
1
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97 dates are written following: "days decimal since 1950-01-01T00:00:00 in julian calendar"
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98 longitude is set between: -180° and 180°
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99 latitude is set between: -90° and 90°
0
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100
1
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101 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.
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102 If two argo trajectories are needed to process, this tool needs to be run 2 times.
0
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103
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104 **Input**
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105
1
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106 files in the input folder should be like:
0
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107
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108 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
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109
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110 **Output**
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111
1
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112 A concatenated and harmonized NetCDF file.
0
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113
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114 ]]></help>
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115 <citations>
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116 <citation type="bibtex">
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117 @Manual{,
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118 title = {QCV Ingester},
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119 author = {Pokapok},
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120 year = {2024},
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121 note = {https://gitlab.com/pokapok-projects/PKP8-OGI-BGC/qcv_ingester}
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122 </citation>
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123 </citations>
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124 </tool>