Mercurial > repos > ecology > harmonize_insitu_to_netcdf

annotate bgc_harmonizer.xml @ 0:2a6d823efa51 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
author ecology
date Thu, 05 Dec 2024 14:15:48 +0000
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children 2351461be706
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2a6d823efa51 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
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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 insitu marine physical and biogeochemical data</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.1</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <container type="docker">pokapok/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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12
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13 #for $i, $infile in enumerate($infiles):
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14 cp '$infile' '/runtime/data/original_data/work/ga_la_xy/${infile.element_identifier}' &&
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15 #end for
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16
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17 /app/launchers/start-app.sh GALAXY &&
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19 cp /runtime/data/harmonized_data/work/ga_la_xy_harm_agg.nc '$output_net'
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20 ]]></command>
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21 <inputs>
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22 <param name="infiles" type="data" format="netcdf" multiple="true" label="Input the netcdf data files" help="This files can netcdf raw Argo or Gliders datafiles following CMEMS convention."/>
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23 </inputs>
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24 <outputs>
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25 <data name="output_net" format="netcdf" from_work_dir="/runtime/data/harmonized_data/work/*.nc" label="${tool.name} netcdf data" />
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26 </outputs>
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27 <tests>
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28 <test expect_num_outputs="1">
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29 <param name="infiles" value="D6901758_001.nc,D6901758_002.nc,D6901758_003.nc,D6901758_004.nc,D6901758_005.nc"/>
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30 <output name="output_net">
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31 <assert_contents>
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32 <has_size value="427535" delta="0"/>
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33 </assert_contents>
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34 </output>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38
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39 .. class:: infomark
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40
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41 **What it does**
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42 General presentation
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43
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44 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.
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45 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.
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46 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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47
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48 Coordinates and variables :
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49
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50 "lon" : ["longitude", "LONGITUDE", "LON", "lon"],
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51 "lat" : ["latitude", "LATITUDE", "LAT", "lat"],
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52 "time" : ["date", "time", "TIME", "JULD"],
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53 "time_qc" : ["date_qc", "time_qc", "TIME_QC", "JULD_QC"],
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54 "depth" : ["DEPTH", "depth"],
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55 "cycle_number" : ["CYCLE_NUMBER"],
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56 "ref_time" : ["REFERENCE_DATE_TIME"],
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57 "pos_qc" : ["POSITION_QC",]
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58
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59 --
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61 "temperature" : ["TEMP", "TEMPERATURE"],
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62 "salinity" : ["PSAL", "PRACTICAL_SALINITY"],
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63 "oxygen" : ["DOXY"],
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64 "pressure" : ["PRES"],
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65 "chlorophylle" : ["CHLA"],
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66 "nitrate" : ["NO3", "NITRATE", "n_an"],
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67 "bbp700" : ["BBP700"],
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68
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69 All variables are tagged with a suffix to indicate the state of the data (_raw, _dmadjusted, _rtadjusted)
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71 --
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73 Variables extracted from meta files are :
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75 LAUNCH_DATE
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76 PLATFORM_TYPE
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77 PI_NAME meta variables are stored as metadata
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79 --
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81 Units :
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83 "degree_east" : ["degree_east"],
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84 "degree_north" : ["degree_north"],
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85 "degree_celsius" : ["degree_celsius", "degree_Celsius"], # temperature
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86 "psu" : ["psu", "practical_salinity_unit", "PSU"], # salinity
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87 "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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88 "mg/m3" : ["mg/m3",],
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89 "micromole/kg" : ["micromole/kg",],
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90 "m-1" : ["m-1"],
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91 "decibar" : ["decibar", "dbar"], # pressure
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92
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93 Arbitrarily,
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94
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95 dates are written following : "seconds since 1950-01-01T00:00:00 in julian calendar"
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96 longitude is set between : -180° and 180°
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97 latitude is set between : -90° and 90°
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98
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99 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.
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100
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101 **Input**
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102
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103 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 :
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104
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105 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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106
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107 paths of where are the data (volumes) containing configurations, listings and data. Paths are :
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108
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109 config path : where your textfile containing the list of files names is : it contains the listing cerb_listing.txt
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110 data_path : highest folder including all the files to harmonize written in the textfile listing
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111
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112 **Output**
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113
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114 A concatenated and harmonized netcdf file
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115
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116 ]]></help>
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117 <citations>
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118 <citation type="bibtex">
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119 @Manual{,
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120 title = {QCV Ingester},
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121 author = {Pokapok},
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122 year = {2024},
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123 note = {https://gitlab.com/pokapok-projects/PKP8-OGI-BGC/qcv_ingester}
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124 </citation>
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125 </citations>
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126 </tool>