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comparison xarray_coords_info.xml @ 2:3e73f657a998 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 17:07:54 +0000
parents 6015f30a7258
children 663e6f115a76
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1:6015f30a7258 2:3e73f657a998
1 <tool id="xarray_coords_info" name="NetCDF xarray Coordinate Info" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="xarray_coords_info" name="NetCDF xarray Coordinate Info" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Get values for each coordinate of a Netcdf file</description> 2 <description>Get values for each coordinate 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 mkdir output_dir && 15 mkdir output_dir &&
16 echo "Galaxy xarray version @TOOL_VERSION@" > output_dir/version.tabular && 16 echo "Galaxy xarray version @TOOL_VERSION@"> output_dir/version.tabular &&
17 python3 '$__tool_directory__/xarray_tool.py' '$input' --coords_info output_dir 17 python3 '$__tool_directory__/xarray_tool.py' '$input' --coords_info output_dir
18 ]]></command> 18 ]]> </command>
19 <inputs> 19 <inputs>
20 <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need to extract coordinate values."/> 20 <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need to extract coordinate values."/>
21 </inputs> 21 </inputs>
22 <outputs> 22 <outputs>
23 <collection type="list" name="output_dir" label="Coordinates"> 23 <collection type="list" name="output_dir" label="Coordinates">
24 <discover_datasets pattern="__name_and_ext__" visible="true" directory="output_dir"/> 24 <discover_datasets pattern="__name_and_ext__" visible="true" directory="output_dir"/>
25 </collection> 25 </collection>
26 </outputs> 26 </outputs>
27 <tests> 27 <tests>
28 <test> 28 <test>
29 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/> 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"> 30 <output_collection name="output_dir" type="list" count="5">
31 <element name="time" file="time.tabular" ftype="tabular"/> 31 <element name="time" file="time.tabular" ftype="tabular"/>
32 <element name="latitude" file="latitude.tabular" ftype="tabular"/> 32 <element name="latitude" file="latitude.tabular" ftype="tabular"/>
33 <element name="longitude" file="longitude.tabular" ftype="tabular"/> 33 <element name="longitude" file="longitude.tabular" ftype="tabular"/>
34 <element name="depth" file="depth.tabular" ftype="tabular"/> 34 <element name="depth" file="depth.tabular" ftype="tabular"/>
35 <element name="version" file="version.tabular" ftype="tabular"/> 35 <element name="version" file="version.tabular" ftype="tabular"/>
36 </output_collection> 36 </output_collection>
37 </test> 37 </test>
38 </tests> 38 </tests>
39
39 <help><![CDATA[ 40 <help><![CDATA[
40 **What it does** 41 **What it does**
41 42
42 The tool will generate a collection containing one file per coordinate. Each file contains the values of the 43 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 corresponding coordinate. The output of this tool is usually used as input to other tools.
44 45
45 **Input** 46 **Input**
46 47
47 A netcdf file (xxx.nc). 48 A netcdf file (xxx.nc).
48 49
50 **Outputs**
51
52 An output file is generated for each coordinate and each file contains the value of the corresponding coordinate.
53
54
49 -------------------------------- 55 --------------------------------
50 56
51 ]]></help> 57 Run this tool before considering using Netcdf Xarray operation.
58 ]]> </help>
52 <expand macro="citations"/> 59 <expand macro="citations"/>
53 </tool> 60 </tool>