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comparison tool_odv.xml @ 3:07da6d3df8e7 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 6ece1590d24793fc508b9237760827e79eb71c5d
author ecology
date Wed, 11 Jun 2025 18:23:36 +0000
parents bdd2d93d99ce
children 5d257e0d5f09
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2:bdd2d93d99ce 3:07da6d3df8e7
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</token> 5 <token name="@VERSION_SUFFIX@">0.1</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}_${i}.nc' && 19 cp '$infile' '/runtime/data-in-raw/${infile.element_identifier}.nc' &&
20 #end for 20 #end for
21 #if $input_ref: 21 #if $input_ref:
22 #for $i, $infile in enumerate($input_ref): 22 #for $i, $infile in enumerate($input_ref):
23 cp '$infile' '/runtime/data-in-ref/${infile.element_identifier}_${i}' && 23 cp '$infile' '/runtime/data-in-ref/${infile.element_identifier}' &&
24 #end for 24 #end for
25 #end if 25 #end if
26 26
27 #if $config.type == 'yes': 27 #if $config.type == 'yes':
28 ## Write YAML content 28 ## Write YAML content
38 <configfile name="config_file"> 38 <configfile name="config_file">
39 #if $config.type == 'yes': 39 #if $config.type == 'yes':
40 default: 40 default:
41 file_name_list_raw: 41 file_name_list_raw:
42 #for $i, $infile in enumerate($input_raw): 42 #for $i, $infile in enumerate($input_raw):
43 #set name_raw='${infile.element_identifier}_${i}.nc' 43 #set name_raw='${infile.element_identifier}.nc'
44 #end for 44 #end for
45 - ${name_raw} 45 - ${name_raw}
46 operator: '${config.operator}' 46 operator: '${config.operator}'
47 QV: 47 QV:
48 file_name_list_ref: 48 file_name_list_ref:
49 #for $i, $infile in enumerate($input_ref): 49 #for $i, $infile in enumerate($input_ref):
50 #set name_ref='${infile.element_identifier}_${i}.nc' 50 #set name_ref='${infile.element_identifier}.nc'
51 #end for 51 #end for
52 - ${name_ref} 52 - ${name_ref}
53 odv_collection: 53 odv_collection:
54 name: "odv_collection.txt" 54 name: "odv_collection.txt"
55 qc_convention: '${config.qc_convention}' 55 qc_convention: '${config.qc_convention}'