Mercurial > repos > ecology > xarray_coords_info
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xarray_coords_info.xml Sun Jun 06 08:50:43 2021 +0000 @@ -0,0 +1,53 @@ +<tool id="xarray_coords_info" name="NetCDF xarray Coordinate Info" version="@TOOL_VERSION+galaxy@VERSION_SUFFIX@"> + <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="3">python</requirement> + <requirement type="package" version="1.5.6">netcdf4</requirement> + <requirement type="package" version="@TOOL_VERSION@">xarray</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). + +-------------------------------- + + ]]></help> + <expand macro="citations"/> +</tool>