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comparison xarray_metadata_info.xml @ 4:9bbaab36a5d4 draft

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"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
author ecology
date Thu, 20 Jan 2022 17:09:40 +0000
parents 663268794710
children 00de53d18b99
comparison
equal deleted inserted replaced
3:663268794710 4:9bbaab36a5d4
1 <tool id="xarray_metadata_info" name="NetCDF xarray Metadata Info" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="xarray_metadata_info" name="NetCDF xarray Metadata Info" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>summarize content of a Netcdf file</description> 2 <description>summarize content of a Netcdf file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/> 6 <expand macro="edam_ontology"/>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
8 <requirement type="package" version="3">python</requirement> 9 <requirement type="package" version="3">python</requirement>
9 <requirement type="package" version="1.5.6">netcdf4</requirement> 10 <requirement type="package" version="1.5.6">netcdf4</requirement>
10 <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
11 <requirement type="package" version="0.9.0">geopandas</requirement> 11 <requirement type="package" version="0.9.0">geopandas</requirement>
12 <requirement type="package" version="1.7.1">shapely</requirement> 12 <requirement type="package" version="1.7.1">shapely</requirement>
13 </requirements> 13 </requirements>
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 python3 '$__tool_directory__/xarray_tool.py' '$input' --info '$info' --summary '$output' 15 python3 '$__tool_directory__/xarray_tool.py' '$input' --info '$info' --summary '$output'
16 ]]></command> 16 ]]> </command>
17 <inputs> 17 <inputs>
18 <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need information about."/> 18 <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need information about."/>
19 </inputs> 19 </inputs>
20 <outputs> 20 <outputs>
21 <data name="output" format="tabular" label="Metadata infos from ${input.name}" from_work_dir="variables.tabular"/> 21 <data name="output" format="tabular" label="Metadata infos from ${input.name}" from_work_dir="variables.tabular"/>
22 <data name="info" label="info file" format="txt"/> 22 <data name="info" label="info file" format="txt"/>
23 </outputs> 23 </outputs>
24 <tests> 24 <tests>
25 <test> 25 <test>
26 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/> 26 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
27 <param name="output" value="Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab"/> 27 <param name="output" value="Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab"/>
28 <output name="info" value="info_file.txt"> 28 <output name="info" value="info_file.txt">
29 <assert_contents> 29 <assert_contents>
30 <has_text_matching expression="depth\s+=\s+1"/> 30 <has_text_matching expression="depth\s+=\s+1"/>
31 <has_text_matching expression="latitude\s+=\s+97"/> 31 <has_text_matching expression="latitude\s+=\s+97"/>
32 <has_text_matching expression="longitude\s+=\s+103"/> 32 <has_text_matching expression="longitude\s+=\s+103"/>
33 <has_text_matching expression="time\s+=\s+145"/> 33 <has_text_matching expression="time\s+=\s+145"/>
34 </assert_contents> 34 </assert_contents>
35 </output> 35 </output>
36 <output name="output" ftype="tabular" file="Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab"> 36 <output name="output" ftype="tabular" file="Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab">
37 <assert_contents> 37 <assert_contents>
38 <has_text_matching expression="VariableName\tNumberOfDimensions\tDim0Name\tDim0Size\tDim1Name\tDim1Size\tDim2Name\tDim2Size\tDim3Name\tDim3Size"/> 38 <has_text_matching expression="VariableName\tNumberOfDimensions\tDim0Name\tDim0Size\tDim1Name\tDim1Size\tDim2Name\tDim2Size\tDim3Name\tDim3Size"/>
39 <has_text_matching expression="phy\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/> 39 <has_text_matching expression="phy\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/>
40 <has_text_matching expression="chl\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/> 40 <has_text_matching expression="chl\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/>
41 <has_text_matching expression="nh4\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/> 41 <has_text_matching expression="nh4\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/>
42 <has_text_matching expression="time\t1\ttime\t145"/> 42 <has_text_matching expression="time\t1\ttime\t145"/>
43 <has_text_matching expression="longitude\t1\tlongitude\t103"/> 43 <has_text_matching expression="longitude\t1\tlongitude\t103"/>
44 <has_text_matching expression="latitude\t1\tlatitude\t97"/> 44 <has_text_matching expression="latitude\t1\tlatitude\t97"/>
45 <has_text_matching expression="depth\t1\tdepth\t1"/> 45 <has_text_matching expression="depth\t1\tdepth\t1"/>
46 </assert_contents> 46 </assert_contents>
47 </output> 47 </output>
48 </test> 48 </test>
49 </tests> 49 </tests>
50 <help><![CDATA[ 50 <help><![CDATA[
51 **What it does** 51 **What it does**
52 52
79 -------------------------------- 79 --------------------------------
80 80
81 The Netcdf Info tool use the netcdf functions : https://www.unidata.ucar.edu/software/netcdf/docs/index.html 81 The Netcdf Info tool use the netcdf functions : https://www.unidata.ucar.edu/software/netcdf/docs/index.html
82 82
83 Run this tool before considering using Netcdf Read. 83 Run this tool before considering using Netcdf Read.
84 ]]></help> 84 ]]> </help>
85 <expand macro="citations"/> 85 <expand macro="citations"/>
86 </tool> 86 </tool>