Mercurial > repos > ecology > tool_biogeochemical_calibration

annotate bgc_calib.xml @ 2:6f66f964d64c draft

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/ocean_data_view_manager commit 6ece1590d24793fc508b9237760827e79eb71c5d
author ecology
date Wed, 11 Jun 2025 18:23:33 +0000
parents e28357f3202c
children 689d7a46e359
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
1 <tool id="tool_biogeochemical_calibration" name="BioGeoChemical calibration" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
2 <description>for sensors according to Argo recommendations</description>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
3 <macros>
1
e28357f3202c planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit ced737b68c38210dc800fc8b5adf08c040c68db5
ecology
parents: 0
diff changeset
4 <token name="@VERSION@">1.0</token>
2
6f66f964d64c planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 6ece1590d24793fc508b9237760827e79eb71c5d
ecology
parents: 1
diff changeset
5 <token name="@VERSION_SUFFIX@">0.1</token>
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
6 </macros>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
7 <requirements>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
8 <container type="docker">easyqcvbgc/easy-qcv_calibration-methods_tool:@VERSION@</container>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
9 </requirements>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
11 export HOME=\$PWD &&
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
12 mkdir -p /runtime/config &&
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
13 mkdir -p '/runtime/data-in-raw/' &&
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
14 mkdir -p '/runtime/data-in-ref/' &&
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
15 mkdir -p '/runtime/data-out/' &&
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
16 mkdir -p ./outputs &&
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
17
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
18 #for $i, $infile in enumerate($input_raw):
2
6f66f964d64c planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 6ece1590d24793fc508b9237760827e79eb71c5d
ecology
parents: 1
diff changeset
19 cp '$infile' '/runtime/data-in-raw/${infile.element_identifier}.nc' &&
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
20 #end for
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
21 #if $input_ref:
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
22 #for $i, $infile in enumerate($input_ref):
2
6f66f964d64c planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 6ece1590d24793fc508b9237760827e79eb71c5d
ecology
parents: 1
diff changeset
23 cp '$infile' '/runtime/data-in-ref/${infile.element_identifier}' &&
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
24 #end for
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
25 #end if
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
26
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
27 #if $config.type == 'yes':
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
28 ## Write YAML content
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
29 cp '${config_file}' '/runtime/config/config_user_odv_tool.yml' &&
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
30 #end if
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
31
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
32 #set $mode="R_APP_CN"
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
33 /app/launchers/start-app.sh $mode &&
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
34
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
35 cp -r '/runtime/data-out/' './outputs/'
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
36 ]]></command>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
37 <configfiles>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
38 <configfile name="config_file">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
39 #if $config.type == 'yes':
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
40 #for $i, $file in enumerate($config.section_config):
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
41 default :
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
42 file_name_list_raw:
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
43 #for $i, $infile in enumerate($input_raw):
2
6f66f964d64c planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 6ece1590d24793fc508b9237760827e79eb71c5d
ecology
parents: 1
diff changeset
44 #set name_raw='${infile.element_identifier}.nc'
6f66f964d64c planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 6ece1590d24793fc508b9237760827e79eb71c5d
ecology
parents: 1
diff changeset
45 - ${name_raw}
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
46 #end for
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
47 param : nitrate
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
48 param_qc :
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
49 bad : '${param_qc_bad}'
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
50 to_be_replaced : '${param_qc_toreplaced}'
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
51 replaced_by : '${param_qc_replacedby}'
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
52 calib_configs :
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
53 - number : 1
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
54 method_raw :
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
55 name : method1
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
56 options :
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
57 bypass_P : '${file.bypass.p_value}'
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
58 P : '${file.bypass.p_value}'
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
59 multiple_linear_regression : '${file.regression.reg_value}'
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
60 single_favored : '${file.favored}'
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
61 method_ref :
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
62 name : '${file.method_ref.method_ref_name}'
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
63 reference :
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
64 name : '${file.method_ref.reference}'
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
65 #if '${file.method_ref.reference}' == 'woa':
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
66 resolution : '${file.method_ref.resolution}'
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
67 #end if
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
68 #end for
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
69 #end if
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
70 </configfile>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
71 </configfiles>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
72 <inputs>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
73 <param name="input_raw" type="data" format="netcdf" multiple="true" label="Input harmonized netcdf data" help="This netcdf should come from the ODV history manager or the QCV harmonizer."/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
74 <param name="input_ref" type="data" format="netcdf" optional="true" multiple="true" label="Input reference data" help="Comes from QCV harmonizer"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
75 <param name="param_qc_bad" type="text" optional="true" value="4" label="Bad data QC value"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
76 <param name="param_qc_toreplaced" type="text" optional="true" value="3" label="Nitrate QC value to be replaced"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
77 <param name="param_qc_replacedby" type="text" optional="true" value="1" label="QC value of replacement"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
78 <!--<param name="mode" type="select" label="Select in which mode you want to run the tool">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
79 <option value="R_APP_CN">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
80 QV that creates a odv collection with raw and ref files to qualify
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
81 </option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
82 <option value="DEMO">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
83 Valide with ODV demo that performes the demo
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
84 </option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
85 </param>-->
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
86 <conditional name="config">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
87 <param name="type" type="select" label="Select if you want to write your own configuration file or not.">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
88 <option value="no">No, I don't want to, I'll use the default one</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
89 <option value="yes">Yes, I to write my own configuration file</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
90 </param>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
91 <when value="yes">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
92 <repeat name="section_config" title="Configurations" min="0" max="10">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
93 <!--<param name="method_name" type="select" label="Enter methode name">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
94 <option value="method1">method1<option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
95 </param>-->
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
96 <conditional name="bypass">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
97 <param name="bypass_value" type="select" label="Bypass">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
98 <option value="0">The tool defines the P of reference for adjustment</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
99 <option value="1">The user defines P and chooses P below</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
100 </param>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
101 <when value="0">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
102 <param name="p_value" type="select" label="Fixed P_value">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
103 <option value="NULL">In this case the P value is NULL (no option)</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
104 </param>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
105 </when>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
106 <when value="1">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
107 <param name="p_value" type="integer" value="0" min="0" max="20000" label="Enter P_value"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
108 </when>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
109 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
110 <conditional name="regression">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
111 <param name="ml_regression" type="select" label="Enter multiple linear regression">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
112 <option value="0">Automatic choice of N</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
113 <option value="1">Single linear regression</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
114 <option value="N>1">N linear regressions</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
115 </param>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
116 <when value="0">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
117 <param name="reg_value" type="select" label="Regression choice">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
118 <option value="0">Automatic choice of N</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
119 </param>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
120 </when>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
121 <when value="1">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
122 <param name="reg_value" type="select" label="Regression choice">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
123 <option value="1">Single linear regression</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
124 </param>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
125 </when>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
126 <when value="N>1">
1
e28357f3202c planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit ced737b68c38210dc800fc8b5adf08c040c68db5
ecology
parents: 0
diff changeset
127 <param name="reg_value" type="integer" min="2" value="2" label="Regression choice, enter the N linear regressions"/>
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
128 </when>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
129 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
130 <param name="favored" type="boolean" label="Enter FALSE or TRUE to favored the single linear regression"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
131 <conditional name="method_ref">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
132 <param name="method_ref_name" type="select" label="Reference method">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
133 <option value="model">Model</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
134 <option value="clim">Climatology</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
135 </param>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
136 <when value="clim">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
137 <param name="reference" type="select" label="Reference">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
138 <option value="woa">WOA</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
139 </param>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
140 <param name="resolution" type="select" label="Resolution">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
141 <option value="annual">Annual</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
142 <option value="monthly">Monthly</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
143 <option value="seasonal">Seasonal</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
144 </param>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
145 </when>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
146 <when value="model">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
147 <param name="reference" type="select" label="Reference">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
148 <option value="canyon_b">CanyonB</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
149 <option value="canyon_med">Canyon Med</option>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
150 </param>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
151 </when>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
152 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
153 </repeat>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
154 </when>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
155 <when value="no">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
156 </when>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
157 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
158 </inputs>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
159 <outputs>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
160 <collection type="list" name="nc_files" label="BGC calibration netcdf collection">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
161 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.nc" directory="./outputs" recurse="true" format="netcdf"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
162 </collection>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
163 <collection type="list" name="png_files" label="BGC calibration figure collection">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
164 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" directory="./outputs" recurse="true" format="png"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
165 </collection>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
166 </outputs>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
167 <tests>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
168 <test expect_num_outputs="2">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
169 <param name="input_raw" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/3ae832154f55c76a7c95a5dc1e6bb19946917233/galaxy_tool/test-data/QCV_harmonizer_NetCDF_data_0_qced.nc"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
170 <conditional name="config">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
171 <param name="type" value="no"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
172 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
173 <output_collection name="nc_files" type="list" count="1"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
174 <output_collection name="png_files" type="list" count="4"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
175
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
176 </test>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
177 <test expect_num_outputs="2">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
178 <param name="input_raw" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/3ae832154f55c76a7c95a5dc1e6bb19946917233/galaxy_tool/test-data/QCV_harmonizer_NetCDF_data_0_qced.nc"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
179 <conditional name="config">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
180 <param name="type" value="yes"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
181 <repeat name="section_config">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
182 <conditional name="bypass">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
183 <param name="bypass_value" value="0"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
184 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
185 <conditional name="regression">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
186 <param name="ml_regression" value="0"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
187 <param name="reg_value" value="0"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
188 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
189 <param name="favored" value="FALSE"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
190 <conditional name="method_ref">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
191 <param name="method_ref_name" value="model"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
192 <param name="reference" value="canyon_b"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
193 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
194 </repeat>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
195 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
196 <output_collection name="nc_files" type="list" count="1"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
197 <output_collection name="png_files" type="list" count="4"/>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
198 </test>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
199 </tests>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
200 <help><![CDATA[
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
201 ======================
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
202 ODV collection manager
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
203 ======================
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
204
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
205 **What it does**
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
206
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
207 This tool present two type of actions :
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
208
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
209 - qualificiation & validation : the tool merges various datasets with a common vocabulary and creates a single generic ODV spreadsheet following ODV user’s guide (v5.7.0) in an automatic way.
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
210
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
211 **Input description**
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
212
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
213 - file_name_raw : nc file to be qualified
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
214 - file_name_ref : nc file used for validation / comparison. noted NULL if no files
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
215 - odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
216 - tool_option$subsetting : 1 apply a subbsetting to ref data searching the smallest box (default) / 0 no subsetting / -1 apply an inverse subseting
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
217 - tool_option$plt : figure option to see the subseted box (0 or 1) - default name subset_box.png
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
218
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
219 with default values different from NULL :
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
220
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
221 - odv_collection$name : odv_collection.txt
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
222 - odv_collection$qc_convention : ARGO
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
223 - tool_action :
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
224 - tool_option$subsetting :
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
225 - tool_option$plt :
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
226
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
227 If the list of raw file name is empty, tool stops If the user make an error in the file extension, tool changes it by itself. If the user miss the yaml configuration, tool uses its default config and upload file in data-in-raw and data-in-ref
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
228
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
229 **Output**
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
230
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
231 This tool creates a single generic ODV spreadsheet following ODV user’s guide
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
232
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
233 ]]></help>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
234 <citations>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
235 <citation type="bibtex">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
236 @Manual{,
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
237 title = {ODV tool},
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
238 author = {Pokapok},
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
239 year = {2024},
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
240 note = {https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool}
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
241 </citation>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
242 </citations>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
parents:
diff changeset
243 </tool>