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comparison 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
comparison
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5:418e44128024 6:bdc969c006fe
1 <tool id="tool_odv" name="ODV collection manager" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT"> 1 <tool id="tool_odv" name="ODV collection manager" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT">
2 <description>tool for qualificiation and validation</description> 2 <description>tool for qualificiation and validation</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">1.3</token> 4 <token name="@VERSION@">1.3</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">2</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:oc@VERSION@</container> 8 <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:oc@VERSION@</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
30 #end for 30 #end for
31 #end if 31 #end if
32 32
33 #if $config.type == 'yes': 33 #if $config.type == 'yes':
34 ## Write YAML content 34 ## Write YAML content
35 cp '${config_file}' '/runtime/config/config_user_odv_tool.yml' && 35 cp '${config_file}' '/runtime/config/config_user_odv_manager.yml' &&
36 #end if 36 #end if
37 37
38 /app/launchers/start-app.sh && 38 /app/launchers/start-app.sh &&
39 cp '/runtime/data-out/odv_collection.txt' '$output' && 39 cp '/runtime/data-out/odv_collection.txt' '$output' &&
40 cp -r '/runtime/log/' './outputs/' && 40 cp -r '/runtime/log/' './outputs/' &&
44 <configfiles> 44 <configfiles>
45 <configfile name="config_file"> 45 <configfile name="config_file">
46 #if $config.type == 'yes': 46 #if $config.type == 'yes':
47 default: 47 default:
48 file_name_list_raw: 48 file_name_list_raw:
49 #for $i, $infile in enumerate($input_raw): 49 #for $infile in $input_raw:
50 #set real_name = $infile.element_identifier 50 #set real_name = $infile.element_identifier
51 #set extension = $real_name.split('.')[-1] 51 #set extension = $real_name.split('.')[-1]
52 #if $extension == 'nc': 52 #if $extension == 'nc':
53 #set name_raw='${infile.element_identifier}' 53 - ${infile.element_identifier}
54 #else: 54 #else
55 #set name_raw='${infile.element_identifier}.nc' 55 - ${infile.element_identifier}.nc
56 #end if 56 #end if
57 #end for 57 #end for
58 - ${name_raw} 58 operator: ${config.operator}
59 operator: '${config.operator}'
60 QV: 59 QV:
61 file_name_list_ref: 60 file_name_list_ref:
62 #for $i, $infile in enumerate($input_ref): 61 #for $infile in $input_ref :
63 #set name_ref='${infile.element_identifier}' 62 - ${infile.element_identifier}
64 #end for 63 #end for
65 - ${name_ref}
66 odv_collection: 64 odv_collection:
67 name: "odv_collection.txt" 65 name: "odv_collection.txt"
68 qc_convention: '${config.qc_convention}' 66 qc_convention: ${config.qc_convention}
69 tool_option: 67 tool_option:
70 subsetting: '${config.subsetting}' 68 subsetting: ${config.subsetting}
71 plt: '${config.plt}' 69 plt: ${config.plt}
72 #end if 70 #end if
73 </configfile> 71 </configfile>
74 </configfiles> 72 </configfiles>
75 <inputs> 73 <inputs>
76 <param name="input_raw" type="data" format="netcdf" multiple="true" label="Input raw data"/> 74 <param name="input_raw" type="data" format="netcdf" multiple="true" label="Input raw data"/>
77 <param name="input_ref" type="data" format="netcdf" multiple="true" optional="true" label="Input reference data"/> 75 <param name="input_ref" type="data" format="netcdf" multiple="true" optional="true" label="Input reference data"/>
97 <option value="PANGAEA">PANGAEA</option> 95 <option value="PANGAEA">PANGAEA</option>
98 <option value="SMHI">SMHI</option> 96 <option value="SMHI">SMHI</option>
99 <option value="OceanSITES">OceanSITES</option> 97 <option value="OceanSITES">OceanSITES</option>
100 <option value="IODE">IODE</option> 98 <option value="IODE">IODE</option>
101 </param> 99 </param>
102 <param name="subsetting" type="float" min="-1" max="1" value="1" label="Enter subsetting (default: 1)"/> 100 <param name="subsetting" type="integer" min="-1" max="1" value="1" label="Enter subsetting (default: 1)"/>
103 <param name="plt" type="float" min="0" max="1" value="0" label="Enter plt (default: 0 for QV, 1 for demo)"/> 101 <param name="plt" type="integer" min="0" max="1" value="0" label="Enter plt (default: 0 for QV, 1 for demo)"/>
104 </when> 102 </when>
105 <when value="no"> 103 <when value="no">
106 </when> 104 </when>
107 </conditional> 105 </conditional>
108 </inputs> 106 </inputs>
109 <outputs> 107 <outputs>
110 <data name="output" format="txt" label="ODV tool output"/> 108 <data name="output" format="txt" label="ODV collection manager output"/>
111 <collection type="list" name="files" label="ODV tool collection"> 109 <collection type="list" name="files" label="ODV tool collection">
112 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="./outputs" recurse="true" format="txt"/> 110 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="./outputs" recurse="true" format="txt"/>
113 </collection> 111 </collection>
114 </outputs> 112 </outputs>
115 <tests> 113 <tests>