Mercurial > repos > ecology > tool_biogeochemical_calibration

annotate bgc_calib.xml @ 3:689d7a46e359 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 03e7755bd0554044c4ca46c27007ee03a58b8d89
author ecology
date Fri, 13 Jun 2025 14:11:41 +0000
parents 6f66f964d64c
children
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0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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1 <tool id="tool_biogeochemical_calibration" name="BioGeoChemical calibration" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT">
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2 <description>for sensors according to Argo recommendations</description>
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3 <macros>
1
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4 <token name="@VERSION@">1.0</token>
3
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5 <token name="@VERSION_SUFFIX@">1</token>
0
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6 </macros>
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7 <requirements>
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8 <container type="docker">easyqcvbgc/easy-qcv_calibration-methods_tool:@VERSION@</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 export HOME=\$PWD &&
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12 mkdir -p /runtime/config &&
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13 mkdir -p '/runtime/data-in-raw/' &&
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14 mkdir -p '/runtime/data-in-ref/' &&
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15 mkdir -p '/runtime/data-out/' &&
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16 mkdir -p ./outputs &&
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17
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18 #for $i, $infile in enumerate($input_raw):
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19 #set real_name = $infile.element_identifier
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20 #set extension = $real_name.split('.')[-1]
689d7a46e359 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 03e7755bd0554044c4ca46c27007ee03a58b8d89
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21 #if $extension == 'nc':
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22 cp '${infile.file_name}' "/runtime/data-in-raw/${infile.element_identifier}" &&
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23 #else
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24 cp '${infile.file_name}' "/runtime/data-in-raw/${infile.element_identifier}.nc" &&
689d7a46e359 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 03e7755bd0554044c4ca46c27007ee03a58b8d89
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25 #end if
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26 #end for
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27 #if $input_ref:
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28 #for $i, $infile in enumerate($input_ref):
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29 cp '$infile' '/runtime/data-in-ref/${infile.element_identifier}' &&
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30 #end for
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31 #end if
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32
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33 #if $config.type == 'yes':
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34 ## Write YAML content
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35 cp '${config_file}' '/runtime/config/config_user_odv_tool.yml' &&
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36 #end if
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37
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38 #set $mode="R_APP_CN"
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39 /app/launchers/start-app.sh $mode &&
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40
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41 cp -r '/runtime/data-out/' './outputs/'
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42 ]]></command>
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43 <configfiles>
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44 <configfile name="config_file">
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45 #if $config.type == 'yes':
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46 #for $i, $file in enumerate($config.section_config):
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47 default :
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48 file_name_list_raw:
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49 #for $i, $infile in enumerate($input_raw):
3
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50 #set real_name = $infile.element_identifier
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51 #set extension = $real_name.split('.')[-1]
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52 #if $extension == 'nc':
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53 #set name_raw='${infile.element_identifier}'
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54 #else:
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55 #set name_raw='${infile.element_identifier}.nc'
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56 #end if
2
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57 - ${name_raw}
0
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58 #end for
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59 param : nitrate
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60 param_qc :
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61 bad : '${param_qc_bad}'
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62 to_be_replaced : '${param_qc_toreplaced}'
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63 replaced_by : '${param_qc_replacedby}'
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64 calib_configs :
3
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65 - number : '${i}'
0
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66 method_raw :
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67 name : method1
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68 options :
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69 bypass_P : '${file.bypass.p_value}'
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70 P : '${file.bypass.p_value}'
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71 multiple_linear_regression : '${file.regression.reg_value}'
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72 single_favored : '${file.favored}'
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73 method_ref :
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74 name : '${file.method_ref.method_ref_name}'
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75 reference :
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76 name : '${file.method_ref.reference}'
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77 #if '${file.method_ref.reference}' == 'woa':
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78 resolution : '${file.method_ref.resolution}'
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79 #end if
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80 #end for
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81 #end if
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82 </configfile>
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83 </configfiles>
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84 <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
85 <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
86 <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
87 <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
88 <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
89 <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
90 <!--<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
91 <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
92 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
93 </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
94 <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
95 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
96 </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
97 </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
98 <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
99 <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
100 <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
101 <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
102 </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
103 <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
104 <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
105 <!--<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
106 <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
107 </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
108 <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
109 <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
110 <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
111 <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
112 </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
113 <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
114 <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
115 <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
116 </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
117 </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
118 <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
119 <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
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 </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
122 <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
123 <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
124 <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
125 <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
126 <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
127 </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
128 <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
129 <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
130 <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
131 </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
132 </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
133 <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
134 <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
135 <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
136 </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
137 </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
138 <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
139 <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
140 </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
141 </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
142 <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
143 <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
144 <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
145 <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
146 <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
147 </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
148 <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
149 <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
150 <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
151 </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
152 <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
153 <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
154 <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
155 <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
156 </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
157 </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
158 <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
159 <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
160 <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
161 <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
162 </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
163 </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
164 </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
165 </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
166 </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
167 <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:
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168 </when>
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169 </conditional>
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170 </inputs>
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171 <outputs>
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172 <collection type="list" name="nc_files" label="BGC calibration netcdf collection">
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173 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.nc" directory="./outputs" recurse="true" format="netcdf"/>
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174 </collection>
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175 <collection type="list" name="png_files" label="BGC calibration figure collection">
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176 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" directory="./outputs" recurse="true" format="png"/>
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177 </collection>
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178 </outputs>
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179 <tests>
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180 <test expect_num_outputs="2">
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181 <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"/>
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182 <conditional name="config">
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183 <param name="type" value="no"/>
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184 </conditional>
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185 <output_collection name="nc_files" type="list" count="1"/>
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186 <output_collection name="png_files" type="list" count="4"/>
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187
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188 </test>
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189 <test expect_num_outputs="2">
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190 <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"/>
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191 <conditional name="config">
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192 <param name="type" value="yes"/>
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193 <repeat name="section_config">
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194 <conditional name="bypass">
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195 <param name="bypass_value" value="0"/>
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196 </conditional>
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197 <conditional name="regression">
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198 <param name="ml_regression" value="0"/>
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199 <param name="reg_value" value="0"/>
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200 </conditional>
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201 <param name="favored" value="FALSE"/>
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202 <conditional name="method_ref">
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203 <param name="method_ref_name" value="model"/>
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204 <param name="reference" value="canyon_b"/>
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205 </conditional>
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206 </repeat>
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207 </conditional>
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208 <output_collection name="nc_files" type="list" count="1"/>
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209 <output_collection name="png_files" type="list" count="4"/>
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210 </test>
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211 </tests>
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212 <help><![CDATA[
3
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213 ==========================
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214 BioGeoChemical calibration
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215 ==========================
0
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216
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217 **What it does**
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218
3
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219 This tool calibrates BioGeoChemical (BGC) data measured by ARGO or GLIDER network. The BGC variables managed by the tool for the moment are :
0
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220
3
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221 - NITRATE using methods published in `archimer <https://archimer.ifremer.fr/doc/00350/46121/>`
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222
0
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223
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224 **Input description**
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225
3
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226 - file_name_raw : nc file to be qualified
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227 - param_qc$bad : qc values to be removed from param before calibration
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228 - param_qc$to_be_replaced : raw qc values to be replaced for building the adjusted qc values
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229 - param_qc$replaced_by : good qc value replacing raw qc values for building adjusted qc values
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230 - method_raw$name which method/equation will be used for estimating the adjusted variable
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231 - method_raw$options :
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232 - bypass_P : 0 (tool defines the P of reference for adjustment ) OR 1 (user defines P and chooses P below)
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233 - P : NULL (if bypass_P = 0) OR numeric_values (if bypass_P = 1)
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234 - multiple_linear_regression : 0 (automatic choice of N) or 1 (single linear regression) or N>1 (N linear regressions)
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235 - single_favored : FALSE or TRUE to favored the single linear regression
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236 - method_ref$name : which kind of reference method (for example model or climatology) will be used by the method_raw for estimating the adjusted variable.
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237 - reference : which reference method like canyonb or woa will be used by the method_raw for estimating the adjusted variable.
0
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238
3
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239 If the list of raw file name is empty, the tool stops If the user makes an error in the file extension, tool changes it by itself. If the user misses the yaml configuration, tool uses its default config and upload available files in data-in-raw
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240
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241 compatibility matrix
0
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242
3
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243 - variable / application mode / [method_raw.name, method_ref.name, reference]
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244 - nitrate / R_APP_CN / [method1, model, canyon_b] & [method1, model, canyon_med] & [method1, clim, woa]
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245
0
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246 **Output**
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247
3
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248 - an extended nc file including the _adjusted and _adjusted_qc
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249 - figures helping to understand the adjustment
0
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250
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251 ]]></help>
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252 <citations>
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253 <citation type="bibtex">
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254 @Manual{,
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255 title = {ODV tool},
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256 author = {Pokapok},
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257 year = {2024},
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258 note = {https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool}
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259 </citation>
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260 </citations>
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261 </tool>