Mercurial > repos > ecology > tool_odv

annotate tool_odv.xml @ 0:894b4a8a9a7b draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
author ecology
date Tue, 18 Mar 2025 11:19:39 +0000
parents
children 2af904e89d11
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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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1 <tool id="tool_odv" name="ODV collection manager" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT">
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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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>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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4 <token name="@VERSION@">0.2</token>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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5 <token name="@VERSION_SUFFIX@">0</token>
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>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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7 <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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8 <container type="docker">pokapok/qcv-odv-tool:@VERSION@</container>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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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 &&
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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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/' &&
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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15 mkdir -p '/runtime/data-out/' &&
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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16 mkdir -p ./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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17
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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18 cp '$input_raw' '/runtime/data-in-raw/${input_raw.element_identifier}' &&
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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19 #if $input_ref:
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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20 cp '$input_ref' '/runtime/data-in-ref/${input_ref.element_identifier}' &&
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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21 #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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22
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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23
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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24 #if $config.type == 'yes':
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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25 ## Write YAML content
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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26 cp '${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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27 #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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28
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29 /app/launchers/start-app.sh '$mode' &&
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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30
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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31 #if $mode == 'R_APP_QV':
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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32 cp '/runtime/data-out/odv_collection.txt' '$output' &&
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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33 #else:
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 cp '/runtime/data-out/demo_odv_collection.txt' '$output' &&
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 #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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36 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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37 ]]></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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38 <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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39 <configfile name="config_file">
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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40 #if $config.type == 'yes':
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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41 default:
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42 file_name_list_raw: '${input_raw.element_identifier}'
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 operator: '${config.operator}'
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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44 QV:
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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45 file_name_list_ref: '${input_ref.element_identifier}'
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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46 odv_collection:
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47 name: "odv_collection.txt"
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48 qc_convention: '${config.qc_convention}'
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49 tool_option:
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50 subsetting: '${config.subsetting}'
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51 plt: '${config.plt}'
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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52 #end if
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53 </configfile>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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54 </configfiles>
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55 <inputs>
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56 <param name="input_raw" type="data" format="netcdf" label="Input raw data"/>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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57 <param name="input_ref" type="data" format="netcdf" optional="true" label="Input reference data"/>
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58 <param name="mode" type="select" label="Select in which mode you want to run the tool">
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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59 <option value="R_APP_QV">QV that creates a odv collection with raw and ref files to qualify</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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60 <option value="DEMO">Valide with ODV demo that performes the demo</option>
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61 </param>
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62 <conditional name="config">
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63 <param name="type" type="select" label="Select if you want to write your own configuration file or not.">
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64 <option value="no">No, I don't want to, I'll use the default one</option>
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65 <option value="yes">Yes, I to write my own configuration file</option>
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66 </param>
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67 <when value="yes">
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68 <param name="operator" type="text" value="Anonymous" label="Enter operator name"/>
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69 <param name="qc_convention" type="select" label="Enter QC convention for the ODV collection output (default: ARGO)">
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70 <option value="ARGO">ARGO</option>
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71 <option value="ODV">ODV</option>
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72 <option value="GTSPP">GTSPP</option>
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73 <option value="SEADATANET">SEADATANET</option>
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74 <option value="ESEAS">ESEAS</option>
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75 <option value="WOD">WOD</option>
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76 <option value="WODSTATION">WODSTATION</option>
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77 <option value="WOCEBOTTLE">WOCEBOTTLE</option>
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78 <option value="WOCECTD">WOCECTD</option>
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79 <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:
diff changeset
80 <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:
diff changeset
81 <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:
diff changeset
82 <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:
diff changeset
83 <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:
diff changeset
84 <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
85 </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
86 <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
87 <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
88 </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
89 <when value="no">
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 </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
91 </conditional>
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 </inputs>
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 <outputs>
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 <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:
diff changeset
95 <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:
diff changeset
96 <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
parents:
diff changeset
97 </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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diff changeset
98 </outputs>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
99 <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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100 <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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diff changeset
101 <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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102 <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
103 <param name="mode" value="R_APP_QV"/>
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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104 <conditional name="config">
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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105 <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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106 </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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107 <output name="output">
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ecology
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108 <assert_contents>
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ecology
parents:
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109 <has_n_lines n="26377"/>
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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110 </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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111 </output>
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
112 <output_collection name="files" type="list" count="4"/>
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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113 </test>
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 <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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115 <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
116 <param name="mode" value="R_APP_QV"/>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
117 <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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118 <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
119 <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
120 <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:
diff changeset
121 <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:
diff changeset
122 <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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123 </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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124 <output name="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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125 <assert_contents>
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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126 <has_n_lines n="17966"/>
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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127 </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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128 </output>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
129 <output_collection name="files" type="list" count="4"/>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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130 </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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131 <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
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132 <param name="input_raw" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool/-/raw/dev_virginie/galaxy_tool/test-data/data_raw.nc?ref_type=heads"/>
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="mode" value="DEMO"/>
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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134 <conditional name="config">
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ecology
parents:
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135 <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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136 </conditional>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
137 <output name="output">
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ecology
parents:
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138 <assert_contents>
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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139 <has_n_lines n="17966"/>
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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140 </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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141 </output>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
ecology
parents:
diff changeset
142 <output_collection name="files" type="list" count="4"/>
894b4a8a9a7b 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>
894b4a8a9a7b 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>
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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145 <help><![CDATA[
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parents:
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146 ======================
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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147 ODV collection manager
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ecology
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148 ======================
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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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
ecology
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150 **What it does**
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151
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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152 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
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153
894b4a8a9a7b 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.
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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155 - history : the tool report in the input file the ODV history including the change of QC flag (not yet operational)
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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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
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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
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159 - file_name_raw : nc file to be qualified
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160 - file_name_ref : nc file used for validation / comparison. noted NULL if no files
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161 - odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw
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162 - tool_option$subsetting : 1 apply a subbsetting to ref data searching the smallest box (default) / 0 no subsetting / -1 apply an inverse subseting
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163 - tool_option$plt : figure option to see the subseted box (0 or 1) - default name subset_box.png
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164
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165 with default values different from NULL :
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166
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167 - odv_collection$name : odv_collection.txt
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168 - odv_collection$qc_convention : ARGO
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169 - tool_action :
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170 - tool_option$subsetting :
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171 - tool_option$plt :
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172
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173 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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174
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175 **Output**
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176
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177 This tool creates a single generic ODV spreadsheet following ODV user’s guide
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178
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179 ]]></help>
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180 <citations>
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181 <citation type="bibtex">
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182 @Manual{,
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183 title = {ODV tool},
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184 author = {Pokapok},
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185 year = {2024},
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186 note = {https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool}
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187 </citation>
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188 </citations>
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189 </tool>