Mercurial > repos > ecology > harmonize_insitu_to_netcdf

annotate bgc_harmonizer.xml @ 3:208f69b31088 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit e37c39bf8ca6e30268737dc1a91ed294b6dc095c
author ecology
date Fri, 27 Jun 2025 16:44:51 +0000
parents 7536ba055525
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
1 <tool id="harmonize_insitu_to_netcdf" name="QCV harmonizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01" license="MIT">
1
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
2 <description>and aggregator of in-situ marine physical and biogeochemical data</description>
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
3 <macros>
3
208f69b31088 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit e37c39bf8ca6e30268737dc1a91ed294b6dc095c
ecology
parents: 2
diff changeset
4 <token name="@TOOL_VERSION@">3.0</token>
2
7536ba055525 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 38f258b108edc5aa9279cc7719adf4b86caeffa7
ecology
parents: 1
diff changeset
5 <token name="@VERSION_SUFFIX@">1</token>
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
6 </macros>
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
7 <requirements>
2
7536ba055525 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 38f258b108edc5aa9279cc7719adf4b86caeffa7
ecology
parents: 1
diff changeset
8 <container type="docker">easyqcvbgc/qcv_ingester:@TOOL_VERSION@</container>
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
9 </requirements>
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
11 export HOME=\$PWD &&
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
12
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
13 #for $i, $infile in enumerate($infiles):
1
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
14 cp '$infile' '/runtime/data-in/${infile.element_identifier}' &&
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
15 #end for
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
16
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
17 /app/launchers/start-app.sh GALAXY &&
2
7536ba055525 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 38f258b108edc5aa9279cc7719adf4b86caeffa7
ecology
parents: 1
diff changeset
18
7536ba055525 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 38f258b108edc5aa9279cc7719adf4b86caeffa7
ecology
parents: 1
diff changeset
19 mkdir ./output/ &&
7536ba055525 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 38f258b108edc5aa9279cc7719adf4b86caeffa7
ecology
parents: 1
diff changeset
20 cp /runtime/data-out/*.nc ./output/
7536ba055525 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 38f258b108edc5aa9279cc7719adf4b86caeffa7
ecology
parents: 1
diff changeset
21 ]]></command>
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
22 <inputs>
3
208f69b31088 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit e37c39bf8ca6e30268737dc1a91ed294b6dc095c
ecology
parents: 2
diff changeset
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"/>
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
24 </inputs>
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
25 <outputs>
2
7536ba055525 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 38f258b108edc5aa9279cc7719adf4b86caeffa7
ecology
parents: 1
diff changeset
26 <collection type="list" name="output_net" format="netcdf">
7536ba055525 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 38f258b108edc5aa9279cc7719adf4b86caeffa7
ecology
parents: 1
diff changeset
27 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="./output/" visible="true"/>
7536ba055525 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 38f258b108edc5aa9279cc7719adf4b86caeffa7
ecology
parents: 1
diff changeset
28 </collection>
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
29 </outputs>
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
30 <tests>
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
31 <test expect_num_outputs="1">
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
32 <param name="infiles" value="D6901758_001.nc,D6901758_002.nc,D6901758_003.nc,D6901758_004.nc,D6901758_005.nc"/>
2
7536ba055525 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 38f258b108edc5aa9279cc7719adf4b86caeffa7
ecology
parents: 1
diff changeset
33 <output_collection name="output_net" type="list" count="1"/>
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
34 </test>
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
35 </tests>
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
36 <help><![CDATA[
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
37
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
38 .. class:: infomark
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
39
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
40 **What it does**
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
41 General presentation
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
42
3
208f69b31088 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit e37c39bf8ca6e30268737dc1a91ed294b6dc095c
ecology
parents: 2
diff changeset
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.
208f69b31088 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit e37c39bf8ca6e30268737dc1a91ed294b6dc095c
ecology
parents: 2
diff changeset
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.
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
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.
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
46 Coordinates and variables :
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
47
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
48 "lon" : ["longitude", "LONGITUDE", "LON", "lon"],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
49 "lat" : ["latitude", "LATITUDE", "LAT", "lat"],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
50 "time" : ["date", "time", "TIME", "JULD"],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
51 "time_qc" : ["date_qc", "time_qc", "TIME_QC", "JULD_QC"],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
52 "depth" : ["DEPTH", "depth"],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
53 "cycle_number" : ["CYCLE_NUMBER"],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
54 "ref_time" : ["REFERENCE_DATE_TIME"],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
55 "pos_qc" : ["POSITION_QC",]
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
56
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
57 --
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
58
1
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
59 "temperature" : ["TEMP", "TEMPERATURE", "t_an"],
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
60 "salinity" : ["PSAL", "PRACTICAL_SALINITY", "s_an"],
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
61 "oxygen" : ["DOXY", "o_an"],
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
62 "oxygenSat" : ["O_an"],
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
63 "pressure" : ["PRES"],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
64 "chlorophylle" : ["CHLA"],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
65 "nitrate" : ["NO3", "NITRATE", "n_an"],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
66 "bbp700" : ["BBP700"],
1
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
67 "C1PHASE_DOXY" : ["C1PHASE_DOXY"],
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
68 "C2PHASE_DOXY" : ["C2PHASE_DOXY"],
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
69 "TEMP_DOXY" : ["TEMP_DOXY"],
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
70
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
71 All variables are tagged with a suffix to indicate the state of the data (_raw, _dmadjusted, _rtadjusted)
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
72
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
73 --
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
74
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
75 Variables extracted from meta files are :
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
76
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
77 LAUNCH_DATE
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
78 PLATFORM_TYPE
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
79 PI_NAME meta variables are stored as metadata
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
80
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
81 --
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
82
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
83 Units :
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
84
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
85 "degree_east" : ["degree_east"],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
86 "degree_north" : ["degree_north"],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
87 "degree_celsius" : ["degree_celsius", "degree_Celsius"], # temperature
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
88 "psu" : ["psu", "practical_salinity_unit", "PSU"], # salinity
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
89 "micromol/l" : ["micromole.l-1", "micromole_per_liter", "μmol.l-1", "μmol/l", "μmol/L", "μmol.L-1"], # concentration liters
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
90 "mg/m3" : ["mg/m3",],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
91 "micromole/kg" : ["micromole/kg",],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
92 "m-1" : ["m-1"],
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
93 "decibar" : ["decibar", "dbar"], # pressure
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
94
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
95 Arbitrarily,
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
96
1
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
97 dates are written following: "days decimal since 1950-01-01T00:00:00 in julian calendar"
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
98 longitude is set between: -180° and 180°
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
99 latitude is set between: -90° and 90°
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
100
1
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
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.
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
102 If two argo trajectories are needed to process, this tool needs to be run 2 times.
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
103
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
104 **Input**
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
105
1
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
106 files in the input folder should be like:
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
107
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
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
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
109
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
110 **Output**
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
111
1
f10c3f6ee575 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit d39442c4f2ee63f6f33f8aef5e6ac2f9d0c7bb3a
ecology
parents: 0
diff changeset
112 A concatenated and harmonized NetCDF file.
0
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
113
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
114 ]]></help>
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
115 <citations>
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
116 <citation type="bibtex">
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
117 @Manual{,
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
118 title = {QCV Ingester},
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
119 author = {Pokapok},
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
120 year = {2024},
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
121 note = {https://gitlab.com/pokapok-projects/PKP8-OGI-BGC/qcv_ingester}
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
122 </citation>
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
123 </citations>
15260949227d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 124fc5205762aaf4f7b39b09a85b5b3fb918370d
ecology
parents:
diff changeset
124 </tool>