Mercurial > repos > ecology > tool_odv

annotate tool_odv.xml @ 4:5d257e0d5f09 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 14:11:44 +0000
parents 07da6d3df8e7
children
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28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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1 <tool id="tool_odv" name="ODV collection manager" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT">
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2 <description>tool for qualificiation and validation</description>
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3 <macros>
2
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4 <token name="@VERSION@">1.2</token>
4
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5 <token name="@VERSION_SUFFIX@">1</token>
0
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6 </macros>
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7 <requirements>
1
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8 <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:@VERSION@</container>
0
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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 &&
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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13 mkdir -p '/runtime/data-in-raw/' &&
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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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
1
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18 #for $i, $infile in enumerate($input_raw):
4
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19 #set real_name = $infile.element_identifier
5d257e0d5f09 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 03e7755bd0554044c4ca46c27007ee03a58b8d89
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20 #set extension = $real_name.split('.')[-1]
5d257e0d5f09 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/${infile.element_identifier}" &&
5d257e0d5f09 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 03e7755bd0554044c4ca46c27007ee03a58b8d89
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23 #else
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24 cp '${infile.file_name}' "/runtime/data-in-raw/${infile.element_identifier}.nc" &&
5d257e0d5f09 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
1
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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}' &&
1
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30 #end for
0
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31 #end if
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32
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33 #if $config.type == 'yes':
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34 ## Write YAML content
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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35 cp '${config_file}' '/runtime/config/config_user_odv_tool.yml' &&
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36 #end if
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37
1
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38 /app/launchers/start-app.sh &&
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39 cp '/runtime/data-out/odv_collection.txt' '$output' &&
0
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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">
1
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45 #if $config.type == 'yes':
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46 default:
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47 file_name_list_raw:
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48 #for $i, $infile in enumerate($input_raw):
4
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49 #set real_name = $infile.element_identifier
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50 #set extension = $real_name.split('.')[-1]
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51 #if $extension == 'nc':
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52 #set name_raw='${infile.element_identifier}'
5d257e0d5f09 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 03e7755bd0554044c4ca46c27007ee03a58b8d89
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53 #else:
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54 #set name_raw='${infile.element_identifier}.nc'
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55 #end if
1
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56 #end for
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57 - ${name_raw}
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58 operator: '${config.operator}'
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59 QV:
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60 file_name_list_ref:
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61 #for $i, $infile in enumerate($input_ref):
4
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62 #set name_ref='${infile.element_identifier}'
1
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63 #end for
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64 - ${name_ref}
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65 odv_collection:
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66 name: "odv_collection.txt"
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67 qc_convention: '${config.qc_convention}'
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68 tool_option:
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69 subsetting: '${config.subsetting}'
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70 plt: '${config.plt}'
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71 #end if
0
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72 </configfile>
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73 </configfiles>
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74 <inputs>
1
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75 <param name="input_raw" type="data" format="netcdf" multiple="true" label="Input raw data"/>
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76 <param name="input_ref" type="data" format="netcdf" multiple="true" optional="true" label="Input reference data"/>
0
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77 <conditional name="config">
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78 <param name="type" type="select" label="Select if you want to write your own configuration file or not.">
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79 <option value="no">No, I don't want to, I'll use the default one</option>
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80 <option value="yes">Yes, I to write my own configuration file</option>
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81 </param>
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82 <when value="yes">
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ecology
parents:
diff changeset
83 <param name="operator" type="text" value="Anonymous" label="Enter operator name"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
84 <param name="qc_convention" type="select" label="Enter QC convention for the ODV collection output (default: ARGO)">
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
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85 <option value="ARGO">ARGO</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
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86 <option value="ODV">ODV</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
87 <option value="GTSPP">GTSPP</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
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88 <option value="SEADATANET">SEADATANET</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
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89 <option value="ESEAS">ESEAS</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
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90 <option value="WOD">WOD</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
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91 <option value="WODSTATION">WODSTATION</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
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92 <option value="WOCEBOTTLE">WOCEBOTTLE</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
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93 <option value="WOCECTD">WOCECTD</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
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94 <option value="QARTOD">QARTOD</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
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95 <option value="BODC">BODC</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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96 <option value="PANGAEA">PANGAEA</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
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97 <option value="SMHI">SMHI</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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98 <option value="OceanSITES">OceanSITES</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
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99 <option value="IODE">IODE</option>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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100 </param>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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101 <param name="subsetting" type="float" min="-1" max="1" value="1" label="Enter subsetting (default: 1)"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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102 <param name="plt" type="float" min="0" max="1" value="0" label="Enter plt (default: 0 for QV, 1 for demo)"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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103 </when>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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104 <when value="no">
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105 </when>
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106 </conditional>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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107 </inputs>
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108 <outputs>
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ecology
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109 <data name="output" format="txt" label="ODV tool output"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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110 <collection type="list" name="files" label="ODV tool collection">
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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111 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="./outputs" recurse="true" format="txt"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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112 </collection>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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113 </outputs>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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114 <tests>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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115 <test expect_num_outputs="2">
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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116 <param name="input_raw" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool/-/raw/7b3557c89438b7347c601d6959af354103b167a1/galaxy_tool/test-data/data_raw.nc"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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117 <param name="input_ref" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool/-/raw/7b3557c89438b7347c601d6959af354103b167a1/galaxy_tool/test-data/data_ref.nc"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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118 <conditional name="config">
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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119 <param name="type" value="no"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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120 </conditional>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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121 <output name="output">
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ecology
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122 <assert_contents>
2
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ecology
parents: 1
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123 <has_n_lines n="26363"/>
0
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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124 </assert_contents>
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125 </output>
1
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ecology
parents: 0
diff changeset
126 <output_collection name="files" type="list" count="3"/>
0
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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127 </test>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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128 <test expect_num_outputs="2">
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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129 <param name="input_raw" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool/-/raw/7b3557c89438b7347c601d6959af354103b167a1/galaxy_tool/test-data/data_raw.nc"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
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130 <conditional name="config">
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ecology
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131 <param name="type" value="yes"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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132 <param name="operator" value="anonymous"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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133 <param name="qc_convention" value="ARGO"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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134 <param name="subsetting" value="1"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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135 <param name="plt" value="0"/>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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136 </conditional>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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137 <output name="output">
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ecology
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138 <assert_contents>
2
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ecology
parents: 1
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139 <has_n_lines n="17952"/>
0
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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140 </assert_contents>
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141 </output>
1
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ecology
parents: 0
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142 <output_collection name="files" type="list" count="3"/>
0
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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143 </test>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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144 </tests>
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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145 <help><![CDATA[
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146 ======================
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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147 ODV collection manager
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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148 ======================
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149
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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150 **What it does**
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151
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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152 This tool present two type of actions :
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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153
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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154 - qualificiation & validation : the tool merges various datasets with a common vocabulary and creates a single generic ODV spreadsheet following ODV user’s guide (v5.7.0) in an automatic way.
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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155
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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156 **Input description**
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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157
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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158 - file_name_raw : nc file to be qualified
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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159 - file_name_ref : nc file used for validation / comparison. noted NULL if no files
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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160 - odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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161 - tool_option$subsetting : 1 apply a subbsetting to ref data searching the smallest box (default) / 0 no subsetting / -1 apply an inverse subseting
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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162 - tool_option$plt : figure option to see the subseted box (0 or 1) - default name subset_box.png
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163
28400e1abee0 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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164 with default values different from NULL :
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165
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166 - odv_collection$name : odv_collection.txt
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167 - odv_collection$qc_convention : ARGO
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168 - tool_action :
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169 - tool_option$subsetting :
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170 - tool_option$plt :
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171
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172 If the list of raw file name is empty, tool stops If the user make an error in the file extension, tool changes it by itself. If the user miss the yaml configuration, tool uses its default config and upload file in data-in-raw and data-in-ref
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173
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174 **Output**
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175
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176 This tool creates a single generic ODV spreadsheet following ODV user’s guide
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177
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178 ]]></help>
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179 <citations>
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180 <citation type="bibtex">
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181 @Manual{,
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182 title = {ODV tool},
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183 author = {Pokapok},
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184 year = {2024},
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185 note = {https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool}
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186 </citation>
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187 </citations>
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188 </tool>