Mercurial > repos > ecology > harmonize_insitu_to_netcdf

comparison bgc_harmonizer.xml @ 2:71d66fc8087d draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/bgc_ocean commit 38f258b108edc5aa9279cc7719adf4b86caeffa7
author ecology
date Wed, 11 Jun 2025 12:09:57 +0000
parents 2351461be706
children
comparison
equal deleted inserted replaced
1:2351461be706 2:71d66fc8087d
1 <tool id="harmonize_insitu_to_netcdf" name="QCV harmonizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01" license="MIT"> 1 <tool id="harmonize_insitu_to_netcdf" name="QCV harmonizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01" license="MIT">
2 <description>and aggregator of in-situ marine physical and biogeochemical data</description> 2 <description>and aggregator of in-situ marine physical and biogeochemical data</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.0</token> 4 <token name="@TOOL_VERSION@">2.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <container type="docker">pokapok/qcv_ingester:@TOOL_VERSION@</container> 8 <container type="docker">easyqcvbgc/qcv_ingester:@TOOL_VERSION@</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 export HOME=\$PWD && 11 export HOME=\$PWD &&
12 12
13 #for $i, $infile in enumerate($infiles): 13 #for $i, $infile in enumerate($infiles):
14 cp '$infile' '/runtime/data-in/${infile.element_identifier}' && 14 cp '$infile' '/runtime/data-in/${infile.element_identifier}' &&
15 #end for 15 #end for
16 16
17 /app/launchers/start-app.sh GALAXY && 17 /app/launchers/start-app.sh GALAXY &&
18 18
19 cp /runtime/data-out/*.nc '$output_net' 19 mkdir ./output/ &&
20 ]]></command> 20 cp /runtime/data-out/*.nc ./output/
21 ]]></command>
21 <inputs> 22 <inputs>
22 <param name="infiles" type="data" format="netcdf" multiple="true" label="Input the NetCDF data files" help="This files can NetCDF raw Argo or Gliders data files following CMEMS convention."/> 23 <param name="infiles" type="data" format="netcdf" multiple="true" label="Input the NetCDF data files" help="This files can NetCDF raw Argo or Gliders data files following CMEMS convention."/>
23 </inputs> 24 </inputs>
24 <outputs> 25 <outputs>
25 <data name="output_net" format="netcdf" label="${tool.name} NetCDF data" /> 26 <collection type="list" name="output_net" format="netcdf">
27 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="./output/" visible="true"/>
28 </collection>
26 </outputs> 29 </outputs>
27 <tests> 30 <tests>
28 <test expect_num_outputs="1"> 31 <test expect_num_outputs="1">
29 <param name="infiles" value="D6901758_001.nc,D6901758_002.nc,D6901758_003.nc,D6901758_004.nc,D6901758_005.nc"/> 32 <param name="infiles" value="D6901758_001.nc,D6901758_002.nc,D6901758_003.nc,D6901758_004.nc,D6901758_005.nc"/>
30 <output name="output_net"> 33 <output_collection name="output_net" type="list" count="1"/>
31 <assert_contents>
32 <has_size value="480666" delta="0"/>
33 </assert_contents>
34 </output>
35 </test> 34 </test>
36 </tests> 35 </tests>
37 <help><![CDATA[ 36 <help><![CDATA[
38 37
39 .. class:: infomark 38 .. class:: infomark