view xarray_coords_info.xml @ 2:3e73f657a998 draft

"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"

<tool id="xarray_coords_info" name="NetCDF xarray Coordinate Info" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Get values for each coordinate of a Netcdf file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
        <requirement type="package" version="3">python</requirement>
        <requirement type="package" version="1.5.6">netcdf4</requirement>
        <requirement type="package" version="0.9.0">geopandas</requirement>
        <requirement type="package" version="1.7.1">shapely</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir output_dir &&
        echo "Galaxy xarray version @TOOL_VERSION@"> output_dir/version.tabular &&
        python3 '$__tool_directory__/xarray_tool.py' '$input' --coords_info output_dir
    ]]>    </command>
    <inputs>
        <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need to extract coordinate values."/>
    </inputs>
    <outputs>
        <collection type="list" name="output_dir" label="Coordinates">
            <discover_datasets pattern="__name_and_ext__" visible="true" directory="output_dir"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
            <output_collection name="output_dir" type="list" count="5">
                <element name="time" file="time.tabular" ftype="tabular"/>
                <element name="latitude" file="latitude.tabular" ftype="tabular"/>
                <element name="longitude" file="longitude.tabular" ftype="tabular"/>
                <element name="depth" file="depth.tabular" ftype="tabular"/>
                <element name="version" file="version.tabular" ftype="tabular"/>
            </output_collection>
        </test>
    </tests>
    
    <help><![CDATA[
**What it does**

The tool will generate a collection containing one file per coordinate. Each file contains the values of the 
corresponding coordinate. The output of this tool is usually used as input to other tools.

**Input**

A netcdf file (xxx.nc).

**Outputs**

An output file is generated for each coordinate and each file contains the value of the corresponding coordinate.


--------------------------------

Run this tool before considering using Netcdf Xarray operation.
    ]]>    </help>
    <expand macro="citations"/>
</tool>