Mercurial > repos > ecology > xarray_coords_info
comparison xarray_coords_info.xml @ 0:fea8a53f8099 draft
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
author | ecology |
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date | Sun, 06 Jun 2021 08:50:43 +0000 |
parents | |
children | 6015f30a7258 |
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1 <tool id="xarray_coords_info" name="NetCDF xarray Coordinate Info" version="@TOOL_VERSION+galaxy@VERSION_SUFFIX@"> | |
2 <description>Get values for each coordinate of a Netcdf file</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="edam_ontology"/> | |
7 <requirements> | |
8 <requirement type="package" version="3">python</requirement> | |
9 <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> | |
12 <requirement type="package" version="1.7.1">shapely</requirement> | |
13 </requirements> | |
14 <command detect_errors="exit_code"><![CDATA[ | |
15 mkdir output_dir && | |
16 echo "Galaxy xarray version @TOOL_VERSION@" > output_dir/version.tabular && | |
17 python3 '$__tool_directory__/xarray_tool.py' '$input' --coords_info output_dir | |
18 ]]></command> | |
19 <inputs> | |
20 <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need to extract coordinate values."/> | |
21 </inputs> | |
22 <outputs> | |
23 <collection type="list" name="output_dir" label="Coordinates"> | |
24 <discover_datasets pattern="__name_and_ext__" visible="true" directory="output_dir"/> | |
25 </collection> | |
26 </outputs> | |
27 <tests> | |
28 <test> | |
29 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/> | |
30 <output_collection name="output_dir" type="list" count="5"> | |
31 <element name="time" file="time.tabular" ftype="tabular"/> | |
32 <element name="latitude" file="latitude.tabular" ftype="tabular"/> | |
33 <element name="longitude" file="longitude.tabular" ftype="tabular"/> | |
34 <element name="depth" file="depth.tabular" ftype="tabular"/> | |
35 <element name="version" file="version.tabular" ftype="tabular"/> | |
36 </output_collection> | |
37 </test> | |
38 </tests> | |
39 <help><![CDATA[ | |
40 **What it does** | |
41 | |
42 The tool will generate a collection containing one file per coordinate. Each file contains the values of the | |
43 corresponding coordinate. The output of this tool is usually used as input to other tools. | |
44 | |
45 **Input** | |
46 | |
47 A netcdf file (xxx.nc). | |
48 | |
49 -------------------------------- | |
50 | |
51 ]]></help> | |
52 <expand macro="citations"/> | |
53 </tool> |