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comparison bgc_calib.xml @ 2:6f66f964d64c 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 18:23:33 +0000
parents e28357f3202c
children 689d7a46e359
comparison
equal deleted inserted replaced
1:e28357f3202c 2:6f66f964d64c
1 <tool id="tool_biogeochemical_calibration" name="BioGeoChemical calibration" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT"> 1 <tool id="tool_biogeochemical_calibration" name="BioGeoChemical calibration" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT">
2 <description>for sensors according to Argo recommendations</description> 2 <description>for sensors according to Argo recommendations</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">1.0</token> 4 <token name="@VERSION@">1.0</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_calibration-methods_tool:@VERSION@</container> 8 <container type="docker">easyqcvbgc/easy-qcv_calibration-methods_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
39 #if $config.type == 'yes': 39 #if $config.type == 'yes':
40 #for $i, $file in enumerate($config.section_config): 40 #for $i, $file in enumerate($config.section_config):
41 default : 41 default :
42 file_name_list_raw: 42 file_name_list_raw:
43 #for $i, $infile in enumerate($input_raw): 43 #for $i, $infile in enumerate($input_raw):
44 #set name_raw='${infile.element_identifier}_${i}.nc' 44 #set name_raw='${infile.element_identifier}.nc'
45 - ${name_raw}
45 #end for 46 #end for
46 - ${name_raw}
47 param : nitrate 47 param : nitrate
48 param_qc : 48 param_qc :
49 bad : '${param_qc_bad}' 49 bad : '${param_qc_bad}'
50 to_be_replaced : '${param_qc_toreplaced}' 50 to_be_replaced : '${param_qc_toreplaced}'
51 replaced_by : '${param_qc_replacedby}' 51 replaced_by : '${param_qc_replacedby}'