Mercurial > repos > ecology > tool_odv

annotate tool_odv.xml @ 6:bdc969c006fe draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
author ecology
date Fri, 25 Jul 2025 09:44:28 +0000
parents 418e44128024
children
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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>
5
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4 <token name="@VERSION@">1.3</token>
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5 <token name="@VERSION_SUFFIX@">2</token>
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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>
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10 <command detect_errors="exit_code"><![CDATA[
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11 export HOME=\$PWD &&
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12 mkdir -p /runtime/config &&
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/' &&
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16 mkdir -p ./outputs &&
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17
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18 #for $i, $infile in enumerate($input_raw):
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19 #set real_name = $infile.element_identifier
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20 #set extension = $real_name.split('.')[-1]
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21 #if $extension == 'nc':
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22 cp '${infile.file_name}' "/runtime/data-in-raw/${infile.element_identifier}" &&
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23 #else
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24 cp '${infile.file_name}' "/runtime/data-in-raw/${infile.element_identifier}.nc" &&
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25 #end if
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26 #end for
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27 #if $input_ref:
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28 #for $i, $infile in enumerate($input_ref):
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29 cp '$infile' '/runtime/data-in-ref/${infile.element_identifier}' &&
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30 #end for
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31 #end if
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33 #if $config.type == 'yes':
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34 ## Write YAML content
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35 cp '${config_file}' '/runtime/config/config_user_odv_manager.yml' &&
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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/' &&
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41
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42 cp -r '/runtime/data-out/' './outputs/'
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43 ]]></command>
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44 <configfiles>
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45 <configfile name="config_file">
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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 $infile in $input_raw:
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50 #set real_name = $infile.element_identifier
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51 #set extension = $real_name.split('.')[-1]
6
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52 #if $extension == 'nc':
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53 - ${infile.element_identifier}
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54 #else
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55 - ${infile.element_identifier}.nc
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56 #end if
1
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57 #end for
6
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58 operator: ${config.operator}
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59 QV:
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60 file_name_list_ref:
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61 #for $infile in $input_ref :
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62 - ${infile.element_identifier}
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63 #end for
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64 odv_collection:
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65 name: "odv_collection.txt"
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66 qc_convention: ${config.qc_convention}
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67 tool_option:
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68 subsetting: ${config.subsetting}
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69 plt: ${config.plt}
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70 #end if
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71 </configfile>
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72 </configfiles>
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73 <inputs>
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74 <param name="input_raw" type="data" format="netcdf" multiple="true" label="Input raw data"/>
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75 <param name="input_ref" type="data" format="netcdf" multiple="true" optional="true" label="Input reference data"/>
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76 <conditional name="config">
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77 <param name="type" type="select" label="Select if you want to write your own configuration file or not.">
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78 <option value="no">No, I don't want to, I'll use the default one</option>
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79 <option value="yes">Yes, I to write my own configuration file</option>
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80 </param>
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81 <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
82 <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
83 <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
84 <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
85 <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
86 <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
87 <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
88 <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
89 <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
90 <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
91 <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:
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92 <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
93 <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
94 <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
95 <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
96 <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
97 <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
98 <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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99 </param>
6
bdc969c006fe planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 5
diff changeset
100 <param name="subsetting" type="integer" min="-1" max="1" value="1" label="Enter subsetting (default: 1)"/>
bdc969c006fe planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 9439bd5028eacdaaaff42dd2e095cb6ddc5af56e
ecology
parents: 5
diff changeset
101 <param name="plt" type="integer" min="0" max="1" value="0" label="Enter plt (default: 0 for QV, 1 for demo)"/>
0
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 </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
103 <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:
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104 </when>
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ecology
parents:
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105 </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
106 </inputs>
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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107 <outputs>
6
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ecology
parents: 5
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108 <data name="output" format="txt" label="ODV collection manager output"/>
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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109 <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
110 <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
111 </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
112 </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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113 <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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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:
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116 <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
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:
diff changeset
118 <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
parents:
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119 </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
120 <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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121 <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
122 <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
parents:
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123 </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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124 </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
125 <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
parents:
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126 </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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127 <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
parents:
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128 <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
129 <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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130 <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
131 <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
132 <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
133 <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
134 <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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135 </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
136 <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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137 <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
138 <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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139 </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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140 </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
141 <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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142 </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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143 </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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144 <help><![CDATA[
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 ======================
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 ODV collection manager
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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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
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 **What it does**
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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
ecology
parents:
diff changeset
151 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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152
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 - 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
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
ecology
parents:
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155 **Input description**
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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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 - 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
ecology
parents:
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158 - 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
parents: 4
diff changeset
159 - operator : (optional) name of the person working on dataset qualification / validation
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
160 - odv_collection$name : name of the odv collection created by the tool (by default = odv_collection.txt)
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 - odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw (by default = ARGO)
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162 - tool_option$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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163 - tool_option$plt : figure option to see the subsetted box (0 - by default - or 1) - default name *subset_box.png*
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164
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165 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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166
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167 **Output**
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168
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169 This tool creates a single generic ODV spreadsheet following ODV user’s guide
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170
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171 ]]></help>
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172 <citations>
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173 <citation type="bibtex">
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174 @Manual{,
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175 title = {ODV tool},
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176 author = {Pokapok},
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177 year = {2024},
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178 note = {https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool}
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179 </citation>
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180 </citations>
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181 </tool>