Mercurial > repos > ecology > tool_biogeochemical_calibration

annotate bgc_calib.xml @ 5:e3b3794bc806 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 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
author ecology
date Fri, 25 Jul 2025 09:44:10 +0000
parents c15538b093e0
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>
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4 <token name="@VERSION@">2.1</token>
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5 <token name="@VERSION_SUFFIX@">2</token>
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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:cm@VERSION@</container>
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9 </requirements>
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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
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11 export HOME=\$PWD &&
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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
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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]
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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" &&
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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_calibration.yml' &&
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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36 #end if
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37
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38 #if $dmfiller.dmfiller_value == 'yes':
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39 #for $i, $infile in enumerate($dmfiller.input_origin):
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40 #set real_name = $infile.element_identifier
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41 #set extension = $real_name.split('.')[-1]
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42 #if $extension == 'nc':
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43 cp '${infile.file_name}' "/runtime/data-in-origin/${infile.element_identifier}" &&
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44 #else
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45 cp '${infile.file_name}' "/runtime/data-in-origin/${infile.element_identifier}.nc" &&
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46 #end if
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47 #end for
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48 #if $dmfiller.input_histo:
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49 #for $j, $infile in enumerate($dmfiller.input_histo):
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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 $extension == 'csv':
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53 cp '${infile.file_name}' "/runtime/data-in-history/${infile.element_identifier}" &&
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54 #else
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55 cp '${infile.file_name}' "/runtime/data-in-history/${infile.element_identifier}.csv" &&
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56 #end if
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57 #end for
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58 #end if
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59 #end if
0
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60
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61 #set $mode="R_APP_CN"
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62 /app/launchers/start-app.sh $mode &&
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63 cp -r '/runtime/log/' './outputs/' &&
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64 cp -r '/runtime/data-out/' './outputs/'
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65 ]]></command>
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66 <configfiles>
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67 <configfile name="config_file">
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68 #if $config.type == 'yes':
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69 default :
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70 file_name_list_raw:
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71 #for $infile in $input_raw:
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72 #set real_name = $infile.element_identifier
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73 #set extension = $real_name.split('.')[-1]
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74 #if $extension == 'nc':
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75 - ${infile.element_identifier}
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76 #else
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77 - ${infile.element_identifier}.nc
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78 #end if
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79 #end for
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80 param : nitrate
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81 param_qc :
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82 bad : ${param_qc_bad}
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83 to_be_replaced : ${param_qc_toreplaced}
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
84 replaced_by : ${param_qc_replacedby}
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
85 #if $dmfiller.dmfiller_value == 'yes':
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
86 dmfiller :
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
87 active : TRUE
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
88 mandating_institution : ${dmfiller.mandating_institution}
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
89 dm_operator :
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
90 name : ${dmfiller.dm_operator_name}
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
91 orcid : ${dmfiller.orcid}
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
92 institution : ${dmfiller.institution}
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
93 contact_point :
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
94 name : ${dmfiller.contact_point}
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
95 orcid : ${dmfiller.orcid_contact}
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
96 institution : ${dmfiller.institution_contact}
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
97 file_name_list_history :
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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diff changeset
98 #if $dmfiller.input_histo
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ecology
parents: 4
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99 #for $infile in $dmfiller.input_histo:
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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diff changeset
100 - ${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
101 #end for
5
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
102 #end if
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
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103 #else:
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
104 dmfiller :
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
105 active : FALSE
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
106 #end if
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
107 calib_configs :
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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diff changeset
108 #set number = 1
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ecology
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109 #for $i, $file in enumerate($config.section_config):
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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110 #set number = $number + $i
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ecology
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111 - number : ${number}
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ecology
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112 method_raw :
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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113 name : method1
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ecology
parents: 4
diff changeset
114 options :
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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115 bypass_P : ${file.bypass.bypass_value}
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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116 P : ${file.bypass.p_value}
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ecology
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117 multiple_linear_regression : ${file.regression.reg_value}
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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118 #if $file.favored == 'false:'
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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119 single_favored : FALSE
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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120 #else
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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121 single_favored : TRUE
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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diff changeset
122 #end if
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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123 method_ref :
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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124 name : ${file.method_ref.method_ref_name}
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ecology
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diff changeset
125 reference :
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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126 name : ${file.method_ref.reference}
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ecology
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127 #if $file.method_ref.reference == 'woa':
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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128 resolution : ${file.method_ref.resolution}
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ecology
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129 #end if
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ecology
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130 #end for
0
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ecology
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131 #end if
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
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132 </configfile>
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ecology
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133 </configfiles>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
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134 <inputs>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
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135 <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
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136 <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
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137 <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
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138 <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
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139 <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
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140 <conditional name="config">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
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141 <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
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142 <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
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143 <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
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144 </param>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
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diff changeset
145 <when value="yes">
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ecology
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diff changeset
146 <repeat name="section_config" title="Configurations" min="0" max="10">
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ecology
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147 <!--<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
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148 <option value="method1">method1<option>
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ecology
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diff changeset
149 </param>-->
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
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diff changeset
150 <conditional name="bypass">
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ecology
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diff changeset
151 <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
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152 <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
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153 <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
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diff changeset
154 </param>
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ecology
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diff changeset
155 <when value="0">
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ecology
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156 <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
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157 <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
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diff changeset
158 </param>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
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diff changeset
159 </when>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
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diff changeset
160 <when value="1">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
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161 <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
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diff changeset
162 </when>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
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163 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
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164 <conditional name="regression">
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ecology
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165 <param name="ml_regression" type="select" label="Enter multiple linear regression">
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ecology
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166 <option value="0">Automatic choice of N</option>
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ecology
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167 <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
168 <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
169 </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
170 <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
171 <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
172 <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
173 </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
174 </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
175 <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
176 <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
177 <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
178 </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
179 </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
180 <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
181 <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
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diff changeset
182 </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
183 </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
184 <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
185 <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
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diff changeset
186 <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
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187 <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
188 <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
189 </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
190 <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
191 <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:
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192 <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
193 </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
194 <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:
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195 <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
196 <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:
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197 <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
198 </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
199 </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
200 <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
201 <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
202 <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
203 <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
204 </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
205 </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
206 </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
207 </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
208 </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
209 <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
210 </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
211 </conditional>
5
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
212 <conditional name="dmfiller">
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
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213 <param name="dmfiller_value" type="select" label="Do you want to use the DMfiller option ?" help="To fill the ARGO BD files with DM adjustment according to argo recommendations (scientific calib coef, comment, equations)">
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
214 <option value="no">No, I don't want to</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
215 <option value="yes">Yes, I want to use it</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
216 </param>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
217 <when value="yes">
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
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218 <param name="input_origin" type="data" format="netcdf" multiple="true" label="Input original raw netcdf data" help="This netcdf should be te same ones than for the QCV harmonizer."/>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
219 <param name="input_histo" type="data" format="csv" optional="true" multiple="true" label="Input csv files" help="This csv should come from the ODV history manager tool."/>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
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220 <param name="mandating_institution" type="select" label="Data centres and institutions handling or managing Argo data" help="To know more about the institution go there https://vocab.nerc.ac.uk/collection/R04/current/">
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
221 <option value="LV">Laboratoire Océanographique de Villefranche</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
222 <option value="AO">Atlantic Oceanographic and Meteorological Laboratory (AOML)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
223 <option value="BO">British Oceanographic Data Centre (BODC)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
224 <option value="GE">Federal Maritime and Hydrographic Agency (BSH)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
225 <option value="HZ">China Second Institute of Oceanography (CSIO)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
226 <option value="CS">Commonwealth Scientific and Industrial Research Organisation (CSIRO)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
227 <option value="VL">Far Eastern Regional Hydrometeorological Research Institute of Vladivostock (FERHRI)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
228 <option value="GT">Global Telecommunication System (GTS)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
229 <option value="IN">Indian National Centre for Ocean Information Services (INCOIS)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
230 <option value="PL">Institute of Oceanology Polish Academy of Science (IOPAN)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
231 <option value="IF">French Research Institute for the Sustainable Exploration of the Sea (Ifremer),</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
232 <option value="CI">Institute of Ocean Sciences (IOS)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
233 <option value="JA">Japan Meteorological Agency (JMA)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
234 <option value="JM">Japan Agency for Marine-Earth Science and Technology (JAMSTEC)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
235 <option value="KM">Korean Meteorological Administration (KMA)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
236 <option value="KO">Korea Institute of Ocean Science and Technology (KORDI)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
237 <option value="MB">Monterey Bay Aquarium Research Institute (MBARI)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
238 <option value="ME">Marine Environmental Data Service (MEDS)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
239 <option value="NA">Naval Oceanographic Office (NAVO)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
240 <option value="NM">National Marine Data and Information Service (NMDIS)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
241 <option value="PM">Pacific Marine Environmental Laboratory (PMEL), a National Oceanic and Atmospheric Administration (NOAA) laboratory</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
242 <option value="RU">Russia</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
243 <option value="SI">Scripps Institution of Oceanography (SIO), a division of the University of California San Diego (UCSD)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
244 <option value="SP">Spain</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
245 <option value="UW">University of Washington (UW)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
246 <option value="WH">Woods Hole Oceanographic Institution (WHOI)</option>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
diff changeset
247 </param>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 4
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248 <param name="dm_operator_name" type="text" optional="false" label="Enter First_name Last_name of the dm operator" help="The dm operator is the person in charge of the dmqc of the float (write the name without accent like é or è...)"/>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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249 <param name="orcid" type="text" optional="false" label="Enter its orcid number"/>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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250 <param name="institution" type="text" optional="false" label="Enter its institution"/>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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251 <param name="contact_point" type="text" optional="false" label="Enter First_name Last_name of the contact point" help="This refers to the BGC contact point for the dac (write the name without accent like é or è...)"/>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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252 <param name="orcid_contact" type="text" optional="false" label="Enter the contact point's orcid number"/>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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253 <param name="institution_contact" type="text" optional="false" label="Enter the contact point's institution"/>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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254 </when>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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255 <when value="no">
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256 </when>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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257 </conditional>
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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258 </inputs>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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259 <outputs>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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260 <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
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261 <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
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262 </collection>
5
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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263 <collection type="list" name="tar_files" label="BGC calibration tar.gz collection">
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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264 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tar.gz" directory="./outputs" recurse="true" format="tar.gz"/>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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265 </collection>
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
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266 <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
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267 <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
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268 </collection>
5
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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269 <collection type="list" name="log_files" label="BGC calibration log files">
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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270 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.log" directory="./outputs" recurse="true" format="txt"/>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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271 </collection>
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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272 </outputs>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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273 <tests>
5
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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274 <test expect_num_outputs="4">
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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275 <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
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276 <conditional name="config">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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277 <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
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278 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
ecology
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279 <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
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280 <output_collection name="png_files" type="list" count="4"/>
5
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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281 <output_collection name="log_files" type="list" count="3"/>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
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282 <output_collection name="tar_files" type="list" count="0"/>
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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283 </test>
5
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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284 <test expect_num_outputs="4">
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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285 <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"/>
5
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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286 <conditional name="dmfiller">
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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287 <param name="dmfiller_value" value="no"/>
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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288 </conditional>
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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289 <conditional name="config">
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290 <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
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291 <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
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292 <conditional name="bypass">
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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293 <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
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294 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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295 <conditional name="regression">
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296 <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
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297 <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
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298 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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299 <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
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300 <conditional name="method_ref">
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301 <param name="method_ref_name" value="model"/>
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302 <param name="reference" value="canyon_b"/>
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303 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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304 </repeat>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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305 </conditional>
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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306 <output_collection name="nc_files" type="list" count="1"/>
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ecology
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307 <output_collection name="png_files" type="list" count="4"/>
5
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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308 <output_collection name="log_files" type="list" count="3"/>
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309 <output_collection name="tar_files" type="list" count="0"/>
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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310 </test>
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311 </tests>
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312 <help><![CDATA[
3
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313 ==========================
689d7a46e359 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 03e7755bd0554044c4ca46c27007ee03a58b8d89
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314 BioGeoChemical calibration
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315 ==========================
0
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316
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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317 **What it does**
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318
3
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319 This tool calibrates BioGeoChemical (BGC) data measured by ARGO or GLIDER network. The BGC variables managed by the tool for the moment are :
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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320
5
e3b3794bc806 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
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321 NITRATE using methods published in `archimer <https://archimer.ifremer.fr/doc/00350/46121/>`
3
689d7a46e359 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 03e7755bd0554044c4ca46c27007ee03a58b8d89
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322
0
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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323
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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324 **Input description**
0c59d92788ed planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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325
3
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326 - file_name_raw : nc file to be qualified
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327 - param_qc$bad : qc values to be removed from param before calibration
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328 - param_qc$to_be_replaced : raw qc values to be replaced for building the adjusted qc values
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329 - param_qc$replaced_by : good qc value replacing raw qc values for building adjusted qc values
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330 - method_raw$name which method/equation will be used for estimating the adjusted variable
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331 - method_raw$options :
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332 - bypass_P : 0 (tool defines the P of reference for adjustment ) OR 1 (user defines P and chooses P below)
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333 - P : NULL (if bypass_P = 0) OR numeric_values (if bypass_P = 1)
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334 - multiple_linear_regression : 0 (automatic choice of N) or 1 (single linear regression) or N>1 (N linear regressions)
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335 - single_favored : FALSE or TRUE to favored the single linear regression
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336 - method_ref$name : which kind of reference method (for example model or climatology) will be used by the method_raw for estimating the adjusted variable.
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337 - reference : which reference method like canyonb or woa will be used by the method_raw for estimating the adjusted variable.
0
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338
3
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339 If the list of raw file name is empty, the tool stops If the user makes an error in the file extension, tool changes it by itself. If the user misses the yaml configuration, tool uses its default config and upload available files in data-in-raw
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340
5
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341 compatibility matrix :
0
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342
5
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343 - variable / application mode / [method_raw.name, method_ref.name, reference]
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344 - nitrate / R_APP_CN / [method1, model, canyon_b] & [method1, model, canyon_med] & [method1, clim, woa]
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345
3
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346
0
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347 **Output**
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348
3
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349 - an extended nc file including the _adjusted and _adjusted_qc
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350 - figures helping to understand the adjustment
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351
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352 The folder where to write the ODV generic spreadsheet. the output folder is organized like this :
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353 - /<file_name_raw>_C<calib_configs$number>-<param>
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354 - /figures
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355 - <file_name_raw>_C<calib_configs$number>-<param>.nc
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356 - /BDfiles_from_<file_name_raw>_C<calib_configs$number>-<param>.tar.gz (when dmfiller=true)
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357
0
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358 ]]></help>
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359 <citations>
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360 <citation type="bibtex">
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361 @Manual{,
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362 title = {ODV tool},
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363 author = {Pokapok},
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364 year = {2024},
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365 note = {https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool}
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366 </citation>
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367 </citations>
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368 </tool>