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comparison xarray_coords_info.xml @ 0:fea8a53f8099 draft

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"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
author ecology
date Sun, 06 Jun 2021 08:50:43 +0000
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children 6015f30a7258
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-1:000000000000 0:fea8a53f8099
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>