Mercurial > repos > ecology > harmonize_insitu_to_netcdf

comparison bgc_harmonizer.xml @ 1:f10c3f6ee575 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
author ecology
date Tue, 18 Mar 2025 18:16:09 +0000
parents 15260949227d
children 7536ba055525
comparison
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0:15260949227d 1:f10c3f6ee575
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 insitu 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@">1.1</token> 4 <token name="@TOOL_VERSION@">2.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <container type="docker">pokapok/qcv_ingester:@TOOL_VERSION@</container> 8 <container type="docker">pokapok/qcv_ingester:@TOOL_VERSION@</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 export HOME=\$PWD && 11 export HOME=\$PWD &&
12 12
13 #for $i, $infile in enumerate($infiles): 13 #for $i, $infile in enumerate($infiles):
14 cp '$infile' '/runtime/data/original_data/work/ga_la_xy/${infile.element_identifier}' && 14 cp '$infile' '/runtime/data-in/${infile.element_identifier}' &&
15 #end for 15 #end for
16 16
17 /app/launchers/start-app.sh GALAXY && 17 /app/launchers/start-app.sh GALAXY &&
18 18
19 cp /runtime/data/harmonized_data/work/ga_la_xy_harm_agg.nc '$output_net' 19 cp /runtime/data-out/*.nc '$output_net'
20 ]]></command> 20 ]]></command>
21 <inputs> 21 <inputs>
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."/> 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 data files following CMEMS convention."/>
23 </inputs> 23 </inputs>
24 <outputs> 24 <outputs>
25 <data name="output_net" format="netcdf" from_work_dir="/runtime/data/harmonized_data/work/*.nc" label="${tool.name} netcdf data" /> 25 <data name="output_net" format="netcdf" label="${tool.name} NetCDF data" />
26 </outputs> 26 </outputs>
27 <tests> 27 <tests>
28 <test expect_num_outputs="1"> 28 <test expect_num_outputs="1">
29 <param name="infiles" value="D6901758_001.nc,D6901758_002.nc,D6901758_003.nc,D6901758_004.nc,D6901758_005.nc"/> 29 <param name="infiles" value="D6901758_001.nc,D6901758_002.nc,D6901758_003.nc,D6901758_004.nc,D6901758_005.nc"/>
30 <output name="output_net"> 30 <output name="output_net">
31 <assert_contents> 31 <assert_contents>
32 <has_size value="427535" delta="0"/> 32 <has_size value="480666" delta="0"/>
33 </assert_contents> 33 </assert_contents>
34 </output> 34 </output>
35 </test> 35 </test>
36 </tests> 36 </tests>
37 <help><![CDATA[ 37 <help><![CDATA[
56 "ref_time" : ["REFERENCE_DATE_TIME"], 56 "ref_time" : ["REFERENCE_DATE_TIME"],
57 "pos_qc" : ["POSITION_QC",] 57 "pos_qc" : ["POSITION_QC",]
58 58
59 -- 59 --
60 60
61 "temperature" : ["TEMP", "TEMPERATURE"], 61 "temperature" : ["TEMP", "TEMPERATURE", "t_an"],
62 "salinity" : ["PSAL", "PRACTICAL_SALINITY"], 62 "salinity" : ["PSAL", "PRACTICAL_SALINITY", "s_an"],
63 "oxygen" : ["DOXY"], 63 "oxygen" : ["DOXY", "o_an"],
64 "oxygenSat" : ["O_an"],
64 "pressure" : ["PRES"], 65 "pressure" : ["PRES"],
65 "chlorophylle" : ["CHLA"], 66 "chlorophylle" : ["CHLA"],
66 "nitrate" : ["NO3", "NITRATE", "n_an"], 67 "nitrate" : ["NO3", "NITRATE", "n_an"],
67 "bbp700" : ["BBP700"], 68 "bbp700" : ["BBP700"],
69 "C1PHASE_DOXY" : ["C1PHASE_DOXY"],
70 "C2PHASE_DOXY" : ["C2PHASE_DOXY"],
71 "TEMP_DOXY" : ["TEMP_DOXY"],
68 72
69 All variables are tagged with a suffix to indicate the state of the data (_raw, _dmadjusted, _rtadjusted) 73 All variables are tagged with a suffix to indicate the state of the data (_raw, _dmadjusted, _rtadjusted)
70 74
71 -- 75 --
72 76
90 "m-1" : ["m-1"], 94 "m-1" : ["m-1"],
91 "decibar" : ["decibar", "dbar"], # pressure 95 "decibar" : ["decibar", "dbar"], # pressure
92 96
93 Arbitrarily, 97 Arbitrarily,
94 98
95 dates are written following : "seconds since 1950-01-01T00:00:00 in julian calendar" 99 dates are written following: "days decimal since 1950-01-01T00:00:00 in julian calendar"
96 longitude is set between : -180° and 180° 100 longitude is set between: -180° and 180°
97 latitude is set between : -90° and 90° 101 latitude is set between: -90° and 90°
98 102
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. 103 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.
104 If two argo trajectories are needed to process, this tool needs to be run 2 times.
100 105
101 **Input** 106 **Input**
102 107
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 : 108 files in the input folder should be like:
104 109
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 110 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
106 111
107 paths of where are the data (volumes) containing configurations, listings and data. Paths are :
108
109 config path : where your textfile containing the list of files names is : it contains the listing cerb_listing.txt
110 data_path : highest folder including all the files to harmonize written in the textfile listing
111
112 **Output** 112 **Output**
113 113
114 A concatenated and harmonized netcdf file 114 A concatenated and harmonized NetCDF file.
115 115
116 ]]></help> 116 ]]></help>
117 <citations> 117 <citations>
118 <citation type="bibtex"> 118 <citation type="bibtex">
119 @Manual{, 119 @Manual{,