Mercurial > repos > ecology > tool_odv

annotate tool_odv.xml @ 5:418e44128024 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit bf6cd39b867fec1a8251ff9a4890f276799cdc0c
author ecology
date Mon, 21 Jul 2025 15:55:08 +0000
parents 197286c1fcce
children bdc969c006fe
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894b4a8a9a7b 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>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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3 <macros>
5
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4 <token name="@VERSION@">1.3</token>
4
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5 <token name="@VERSION_SUFFIX@">1</token>
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894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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6 </macros>
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7 <requirements>
5
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8 <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:oc@VERSION@</container>
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9 </requirements>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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10 <command detect_errors="exit_code"><![CDATA[
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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11 export HOME=\$PWD &&
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12 mkdir -p /runtime/config &&
894b4a8a9a7b 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/' &&
894b4a8a9a7b 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
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20 #set extension = $real_name.split('.')[-1]
197286c1fcce 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/${infile.element_identifier}" &&
197286c1fcce planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 03e7755bd0554044c4ca46c27007ee03a58b8d89
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23 #else
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24 cp '${infile.file_name}' "/runtime/data-in-raw/${infile.element_identifier}.nc" &&
197286c1fcce 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 $config.type == 'yes':
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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34 ## Write YAML content
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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35 cp '${config_file}' '/runtime/config/config_user_odv_tool.yml' &&
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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36 #end if
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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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' &&
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40 cp -r '/runtime/log/' './outputs/' &&
0
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41
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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42 cp -r '/runtime/data-out/' './outputs/'
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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43 ]]></command>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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44 <configfiles>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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45 <configfile name="config_file">
1
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46 #if $config.type == 'yes':
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47 default:
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48 file_name_list_raw:
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49 #for $i, $infile in enumerate($input_raw):
4
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50 #set real_name = $infile.element_identifier
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51 #set extension = $real_name.split('.')[-1]
197286c1fcce planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 03e7755bd0554044c4ca46c27007ee03a58b8d89
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52 #if $extension == 'nc':
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53 #set name_raw='${infile.element_identifier}'
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54 #else:
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55 #set name_raw='${infile.element_identifier}.nc'
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56 #end if
1
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57 #end for
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58 - ${name_raw}
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59 operator: '${config.operator}'
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60 QV:
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61 file_name_list_ref:
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62 #for $i, $infile in enumerate($input_ref):
4
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63 #set name_ref='${infile.element_identifier}'
1
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64 #end for
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65 - ${name_ref}
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66 odv_collection:
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67 name: "odv_collection.txt"
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68 qc_convention: '${config.qc_convention}'
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69 tool_option:
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70 subsetting: '${config.subsetting}'
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71 plt: '${config.plt}'
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72 #end if
0
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73 </configfile>
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74 </configfiles>
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75 <inputs>
1
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76 <param name="input_raw" type="data" format="netcdf" multiple="true" label="Input raw data"/>
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77 <param name="input_ref" type="data" format="netcdf" multiple="true" optional="true" label="Input reference data"/>
0
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78 <conditional name="config">
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79 <param name="type" type="select" label="Select if you want to write your own configuration file or not.">
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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80 <option value="no">No, I don't want to, I'll use the default one</option>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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81 <option value="yes">Yes, I to write my own configuration file</option>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
82 </param>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
83 <when value="yes">
894b4a8a9a7b 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="operator" type="text" value="Anonymous" label="Enter operator name"/>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
85 <param name="qc_convention" type="select" label="Enter QC convention for the ODV collection output (default: ARGO)">
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
86 <option value="ARGO">ARGO</option>
894b4a8a9a7b 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="ODV">ODV</option>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
88 <option value="GTSPP">GTSPP</option>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
89 <option value="SEADATANET">SEADATANET</option>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
90 <option value="ESEAS">ESEAS</option>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
91 <option value="WOD">WOD</option>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
92 <option value="WODSTATION">WODSTATION</option>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
93 <option value="WOCEBOTTLE">WOCEBOTTLE</option>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
94 <option value="WOCECTD">WOCECTD</option>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
95 <option value="QARTOD">QARTOD</option>
894b4a8a9a7b 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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96 <option value="BODC">BODC</option>
894b4a8a9a7b 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="PANGAEA">PANGAEA</option>
894b4a8a9a7b 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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98 <option value="SMHI">SMHI</option>
894b4a8a9a7b 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="OceanSITES">OceanSITES</option>
894b4a8a9a7b 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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100 <option value="IODE">IODE</option>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
101 </param>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
102 <param name="subsetting" type="float" min="-1" max="1" value="1" label="Enter subsetting (default: 1)"/>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
103 <param name="plt" type="float" min="0" max="1" value="0" label="Enter plt (default: 0 for QV, 1 for demo)"/>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
104 </when>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
105 <when value="no">
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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106 </when>
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ecology
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107 </conditional>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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108 </inputs>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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109 <outputs>
894b4a8a9a7b 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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110 <data name="output" format="txt" label="ODV tool output"/>
894b4a8a9a7b 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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111 <collection type="list" name="files" label="ODV tool collection">
894b4a8a9a7b 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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112 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="./outputs" recurse="true" format="txt"/>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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diff changeset
113 </collection>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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114 </outputs>
894b4a8a9a7b 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 <tests>
894b4a8a9a7b 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 <test expect_num_outputs="2">
894b4a8a9a7b 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_raw" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool/-/raw/7b3557c89438b7347c601d6959af354103b167a1/galaxy_tool/test-data/data_raw.nc"/>
894b4a8a9a7b 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 <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"/>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
119 <conditional name="config">
894b4a8a9a7b 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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120 <param name="type" value="no"/>
894b4a8a9a7b 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 </conditional>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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diff changeset
122 <output name="output">
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ecology
parents:
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123 <assert_contents>
2
e47dfd67f2b5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit ced737b68c38210dc800fc8b5adf08c040c68db5
ecology
parents: 1
diff changeset
124 <has_n_lines n="26363"/>
0
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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125 </assert_contents>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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126 </output>
5
418e44128024 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit bf6cd39b867fec1a8251ff9a4890f276799cdc0c
ecology
parents: 4
diff changeset
127 <output_collection name="files" type="list" count="6"/>
0
894b4a8a9a7b 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>
894b4a8a9a7b 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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129 <test expect_num_outputs="2">
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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130 <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"/>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
131 <conditional name="config">
894b4a8a9a7b 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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132 <param name="type" value="yes"/>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
133 <param name="operator" value="anonymous"/>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
134 <param name="qc_convention" value="ARGO"/>
894b4a8a9a7b 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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135 <param name="subsetting" value="1"/>
894b4a8a9a7b 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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136 <param name="plt" value="0"/>
894b4a8a9a7b 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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137 </conditional>
894b4a8a9a7b 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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138 <output name="output">
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ecology
parents:
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139 <assert_contents>
2
e47dfd67f2b5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit ced737b68c38210dc800fc8b5adf08c040c68db5
ecology
parents: 1
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140 <has_n_lines n="17952"/>
0
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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141 </assert_contents>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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142 </output>
5
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ecology
parents: 4
diff changeset
143 <output_collection name="files" type="list" count="6"/>
0
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
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144 </test>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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145 </tests>
894b4a8a9a7b 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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146 <help><![CDATA[
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parents:
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147 ======================
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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148 ODV collection manager
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149 ======================
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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150
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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151 **What it does**
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152
894b4a8a9a7b 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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153 This tool present two type of actions :
894b4a8a9a7b 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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154
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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155 - 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.
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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parents:
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156
894b4a8a9a7b 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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157 **Input description**
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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158
894b4a8a9a7b 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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159 - file_name_raw : nc file to be qualified
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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160 - file_name_ref : nc file used for validation / comparison. noted NULL if no files
5
418e44128024 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit bf6cd39b867fec1a8251ff9a4890f276799cdc0c
ecology
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161 - operator : (optional) name of the person working on dataset qualification / validation
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162 - odv_collection$name : name of the odv collection created by the tool (by default = odv_collection.txt)
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163 - odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw (by default = ARGO)
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164 - tool_option$subsetting : 1 apply a subsetting to ref data searching the smallest box (by default) / 0 no subsetting / -1 apply an inverse subsetting
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165 - tool_option$plt : figure option to see the subsetted box (0 - by default - or 1) - default name *subset_box.png*
0
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166
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167 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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168
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169 **Output**
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170
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171 This tool creates a single generic ODV spreadsheet following ODV user’s guide
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172
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173 ]]></help>
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174 <citations>
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175 <citation type="bibtex">
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176 @Manual{,
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177 title = {ODV tool},
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178 author = {Pokapok},
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179 year = {2024},
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180 note = {https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool}
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181 </citation>
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182 </citations>
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183 </tool>