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comparison tool_odv.xml @ 4:5d257e0d5f09 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 03e7755bd0554044c4ca46c27007ee03a58b8d89
author ecology
date Fri, 13 Jun 2025 14:11:44 +0000
parents 07da6d3df8e7
children 991bed85aa21
comparison
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3:07da6d3df8e7 4:5d257e0d5f09
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@">1.2</token> 4 <token name="@VERSION@">1.2</token>
5 <token name="@VERSION_SUFFIX@">0.1</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:@VERSION@</container> 8 <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:@VERSION@</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
14 mkdir -p '/runtime/data-in-ref/' && 14 mkdir -p '/runtime/data-in-ref/' &&
15 mkdir -p '/runtime/data-out/' && 15 mkdir -p '/runtime/data-out/' &&
16 mkdir -p ./outputs && 16 mkdir -p ./outputs &&
17 17
18 #for $i, $infile in enumerate($input_raw): 18 #for $i, $infile in enumerate($input_raw):
19 cp '$infile' '/runtime/data-in-raw/${infile.element_identifier}.nc' && 19 #set real_name = $infile.element_identifier
20 #end for 20 #set extension = $real_name.split('.')[-1]
21 #if $extension == 'nc':
22 cp '${infile.file_name}' "/runtime/data-in-raw/${infile.element_identifier}" &&
23 #else
24 cp '${infile.file_name}' "/runtime/data-in-raw/${infile.element_identifier}.nc" &&
25 #end if
26 #end for
21 #if $input_ref: 27 #if $input_ref:
22 #for $i, $infile in enumerate($input_ref): 28 #for $i, $infile in enumerate($input_ref):
23 cp '$infile' '/runtime/data-in-ref/${infile.element_identifier}' && 29 cp '$infile' '/runtime/data-in-ref/${infile.element_identifier}' &&
24 #end for 30 #end for
25 #end if 31 #end if
38 <configfile name="config_file"> 44 <configfile name="config_file">
39 #if $config.type == 'yes': 45 #if $config.type == 'yes':
40 default: 46 default:
41 file_name_list_raw: 47 file_name_list_raw:
42 #for $i, $infile in enumerate($input_raw): 48 #for $i, $infile in enumerate($input_raw):
43 #set name_raw='${infile.element_identifier}.nc' 49 #set real_name = $infile.element_identifier
50 #set extension = $real_name.split('.')[-1]
51 #if $extension == 'nc':
52 #set name_raw='${infile.element_identifier}'
53 #else:
54 #set name_raw='${infile.element_identifier}.nc'
55 #end if
44 #end for 56 #end for
45 - ${name_raw} 57 - ${name_raw}
46 operator: '${config.operator}' 58 operator: '${config.operator}'
47 QV: 59 QV:
48 file_name_list_ref: 60 file_name_list_ref:
49 #for $i, $infile in enumerate($input_ref): 61 #for $i, $infile in enumerate($input_ref):
50 #set name_ref='${infile.element_identifier}.nc' 62 #set name_ref='${infile.element_identifier}'
51 #end for 63 #end for
52 - ${name_ref} 64 - ${name_ref}
53 odv_collection: 65 odv_collection:
54 name: "odv_collection.txt" 66 name: "odv_collection.txt"
55 qc_convention: '${config.qc_convention}' 67 qc_convention: '${config.qc_convention}'