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comparison xarray_metadata_info.xml @ 0:965fcab0cd9f draft

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"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
author ecology
date Mon, 18 May 2020 08:30:10 -0400
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1 <tool id="xarray_metadata_info" name="NetCDF xarray Metadata Info" version="0.15.1">
2 <description>summarize content of a Netcdf file</description>
3 <requirements>
4 <requirement type="package" version="3">python</requirement>
5 <requirement type="package" version="1.5.3">netcdf4</requirement>
6 <requirement type="package" version="0.15.1">xarray</requirement>
7 <requirement type="package" version="0.7.0">geopandas</requirement>
8 <requirement type="package" version="1.7.0">shapely</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 python3 '$__tool_directory__/xarray_tool.py' '$input' --info '$info' --summary '$output'
12 ]]></command>
13 <inputs>
14 <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need information about."/>
15 </inputs>
16 <outputs>
17 <data name="output" format="tabular" label="Metadata infos from ${input.name}" from_work_dir="variables.tabular"/>
18 <data name="info" label="info file" format="txt"/>
19 </outputs>
20 <tests>
21 <test>
22 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
23 <param name="output" value="Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab"/>
24 <output name="info" value="info_file.txt">
25 <assert_contents>
26 <has_text_matching expression="depth\s+=\s+1"/>
27 <has_text_matching expression="latitude\s+=\s+97"/>
28 <has_text_matching expression="longitude\s+=\s+103"/>
29 <has_text_matching expression="time\s+=\s+145"/>
30 </assert_contents>
31 </output>
32 <output name="output" ftype="tabular" file="Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab">
33 <assert_contents>
34 <has_text_matching expression="VariableName\tNumberOfDimensions\tDim0Name\tDim0Size\tDim1Name\tDim1Size\tDim2Name\tDim2Size\tDim3Name\tDim3Size"/>
35 <has_text_matching expression="phy\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/>
36 <has_text_matching expression="chl\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/>
37 <has_text_matching expression="nh4\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/>
38 <has_text_matching expression="time\t1\ttime\t145"/>
39 <has_text_matching expression="longitude\t1\tlongitude\t103"/>
40 <has_text_matching expression="latitude\t1\tlatitude\t97"/>
41 <has_text_matching expression="depth\t1\tdepth\t1"/>
42 </assert_contents>
43 </output>
44 </test>
45 </tests>
46 <help><![CDATA[
47 **What it does**
48
49 First the tool will give general information about the input in a 'info file' output. (command $ncdump -h inputfile)
50
51 Then, a general tabular 'variables' summarize dimensions details inside each available variable.
52
53
54 The summary tabular file has the general structure :
55
56
57 Variable1 Var1_Number_of_Dim Dim1 Dim1_size ... DimN DimN_size
58
59 VariableX VarX_Number_of_Dim DimX1 DimX1_size ... DimXN DimXN_size
60
61 ...
62
63
64 **Input**
65
66 A netcdf file (xxx.nc).
67
68 **Outputs**
69
70 An Information file.
71
72 A summary tabular file.
73
74
75 --------------------------------
76
77 The Netcdf Info tool use the netcdf functions : https://www.unidata.ucar.edu/software/netcdf/docs/index.html
78
79 Run this tool before considering using Netcdf Read.
80 ]]></help>
81
82 </tool>