Mercurial > repos > ecology > tool_odv

annotate tool_odv.xml @ 2:e47dfd67f2b5 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit ced737b68c38210dc800fc8b5adf08c040c68db5
author ecology
date Thu, 05 Jun 2025 16:48:36 +0000
parents 2af904e89d11
children 9b9f5e62fc91
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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>
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3 <macros>
2
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4 <token name="@VERSION@">1.2</token>
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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>
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7 <requirements>
1
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8 <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:@VERSION@</container>
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9 </requirements>
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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/' &&
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14 mkdir -p '/runtime/data-in-ref/' &&
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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 &&
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17
1
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18 #for $i, $infile in enumerate($input_raw):
2af904e89d11 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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19 cp '$infile' '/runtime/data-in-raw/${infile.element_identifier}_${i}.nc' &&
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20 #end for
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21 #if $input_ref:
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22 #for $i, $infile in enumerate($input_ref):
2af904e89d11 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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23 cp '$infile' '/runtime/data-in-ref/${infile.element_identifier}_${i}' &&
2af904e89d11 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 1e862e8c40fd4bfe034fc326df5c66247275768d
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24 #end for
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25 #end if
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27 #if $config.type == 'yes':
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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28 ## Write YAML content
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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29 cp '${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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30 #end if
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31
1
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32 /app/launchers/start-app.sh &&
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33 cp '/runtime/data-out/odv_collection.txt' '$output' &&
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34
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35 cp -r '/runtime/data-out/' './outputs/'
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36 ]]></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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37 <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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38 <configfile name="config_file">
1
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39 #if $config.type == 'yes':
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40 default:
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41 file_name_list_raw:
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42 #for $i, $infile in enumerate($input_raw):
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43 #set name_raw='${infile.element_identifier}_${i}.nc'
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44 #end for
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45 - ${name_raw}
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46 operator: '${config.operator}'
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47 QV:
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48 file_name_list_ref:
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49 #for $i, $infile in enumerate($input_ref):
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50 #set name_ref='${infile.element_identifier}_${i}.nc'
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51 #end for
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52 - ${name_ref}
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53 odv_collection:
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54 name: "odv_collection.txt"
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55 qc_convention: '${config.qc_convention}'
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56 tool_option:
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57 subsetting: '${config.subsetting}'
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58 plt: '${config.plt}'
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59 #end if
0
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60 </configfile>
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61 </configfiles>
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62 <inputs>
1
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63 <param name="input_raw" type="data" format="netcdf" multiple="true" label="Input raw data"/>
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64 <param name="input_ref" type="data" format="netcdf" multiple="true" optional="true" label="Input reference data"/>
0
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65 <conditional name="config">
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66 <param name="type" type="select" label="Select if you want to write your own configuration file or not.">
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67 <option value="no">No, I don't want to, I'll use the default one</option>
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68 <option value="yes">Yes, I to write my own configuration file</option>
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69 </param>
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70 <when value="yes">
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71 <param name="operator" type="text" value="Anonymous" label="Enter operator name"/>
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72 <param name="qc_convention" type="select" label="Enter QC convention for the ODV collection output (default: ARGO)">
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73 <option value="ARGO">ARGO</option>
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74 <option value="ODV">ODV</option>
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75 <option value="GTSPP">GTSPP</option>
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76 <option value="SEADATANET">SEADATANET</option>
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77 <option value="ESEAS">ESEAS</option>
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78 <option value="WOD">WOD</option>
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79 <option value="WODSTATION">WODSTATION</option>
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80 <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
81 <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
82 <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
83 <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
84 <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
85 <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
86 <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
87 <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
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88 </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
89 <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
90 <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
91 </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
92 <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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93 </when>
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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94 </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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95 </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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96 <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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97 <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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98 <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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99 <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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100 </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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101 </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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102 <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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103 <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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104 <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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105 <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:
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106 <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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107 <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
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108 </conditional>
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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109 <output name="output">
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110 <assert_contents>
2
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ecology
parents: 1
diff changeset
111 <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
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112 </assert_contents>
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113 </output>
1
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ecology
parents: 0
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114 <output_collection name="files" type="list" count="3"/>
0
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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115 </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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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
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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
parents:
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118 <conditional name="config">
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ecology
parents:
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119 <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:
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120 <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
121 <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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122 <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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123 <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
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124 </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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125 <output name="output">
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ecology
parents:
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126 <assert_contents>
2
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ecology
parents: 1
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127 <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
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128 </assert_contents>
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129 </output>
1
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ecology
parents: 0
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130 <output_collection name="files" type="list" count="3"/>
0
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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131 </test>
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132 </tests>
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133 <help><![CDATA[
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134 ======================
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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135 ODV collection manager
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136 ======================
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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137
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138 **What it does**
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139
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ecology
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140 This tool present two type of actions :
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141
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 - 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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143
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ecology
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144 **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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145
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ecology
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146 - file_name_raw : nc file to be qualified
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147 - file_name_ref : nc file used for validation / comparison. noted NULL if no files
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148 - odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw
894b4a8a9a7b planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 3bfe3bf761b2e95bc85e2936dee36f899a3e6393
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parents:
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149 - tool_option$subsetting : 1 apply a subbsetting to ref data searching the smallest box (default) / 0 no subsetting / -1 apply an inverse subseting
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 - tool_option$plt : figure option to see the subseted box (0 or 1) - default name subset_box.png
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151
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ecology
parents:
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152 with default values different from NULL :
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153
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154 - odv_collection$name : odv_collection.txt
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ecology
parents:
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155 - odv_collection$qc_convention : ARGO
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156 - tool_action :
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ecology
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157 - tool_option$subsetting :
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ecology
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158 - tool_option$plt :
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ecology
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159
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160 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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161
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162 **Output**
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163
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164 This tool creates a single generic ODV spreadsheet following ODV user’s guide
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165
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166 ]]></help>
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167 <citations>
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168 <citation type="bibtex">
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169 @Manual{,
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170 title = {ODV tool},
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171 author = {Pokapok},
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172 year = {2024},
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173 note = {https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool}
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174 </citation>
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175 </citations>
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176 </tool>