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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/xarray_import_data commit 99843e9b86bfb355026559d36e29ed5a262aa9b0
author ecology
date Thu, 14 Aug 2025 08:54:07 +0000
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f1b185fc409a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/xarray_import_data commit 99843e9b86bfb355026559d36e29ed5a262aa9b0
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1 <tool id="xarray_import_data" name="Xarray Import Data" version="0.1.0" profile="22.05">
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2 <description>
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3 Import a dataset from an OPeNDAP URL and convert it to a local NetCDF file using xarray.
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="2025.4.0">xarray</requirement>
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7 <requirement type="package" version="3">python</requirement>
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8 <requirement type="package" version="1.6.0">netcdf4</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 python '$__tool_directory__/xarray_import_data.py' '$opendap_url' '$decode_times' '$decode_cf' '$output_dataset'
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12 ]]></command>
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13 <inputs>
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14 <param name="opendap_url" type="text" format="netcdf" label="OPeNDAP URL"
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15 help="OPeNDAP URL to a dataset, also see https://docs.xarray.dev/en/stable/user-guide/io.html#opendap"
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16 optional="false">
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17 <validator type="regex" message="Type a valid url">^(https:|http:|\.)\S*</validator>
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18 </param>
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19 <param name="decode_times" type="boolean" label="Decode times"
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20 help="If true, decode time variables to datetime objects. If false, keep them as raw data."
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21 checked="true" />
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22 <param name="decode_cf" type="boolean" label="Decode CF conventions"
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23 help="Whether to decode according to CF conventions"
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24 checked="true" />
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25 </inputs>
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26 <outputs>
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27 <data name="output_dataset" from_work_dir="xarray_imported_data" format="netcdf"
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28 label="xarray dataset" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="opendap_url"
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33 value="http://test.opendap.org:8080/opendap/catalog/data/nc/data.nc" />
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34 <output name="output_dataset" ftype="netcdf">
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35 <assert_contents>
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36 <has_size min="17K" max="18K" />
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37 </assert_contents>
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38 </output>
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42 ==================
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43 Xarray Import Data
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44 ==================
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45
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46 **What it does**
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47
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48 Open a dataset from an OPeNDAP URL and convert it to a NetCDF file using xarray and netcdf4.
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49
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50 |
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51
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52 **How to use it**
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53
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54 Pass a valid OPeNDAP URL to the `opendap_url` parameter. The tool will download the dataset and save it as a local NetCDF file.
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55
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56 For big datasets consider subsetting the dataset in the url using `<URL>?var_name1[start:step:end],var_name2[start:step:end]`
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57
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58 |
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59
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60 **Links**
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61 https://docs.xarray.dev/en/stable/user-guide/io.html#opendap
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62 https://www.opendap.org/
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63 ]]>
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64 </help>
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65 <citations>
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66 <citation type="doi">10.5334/jors.148</citation>
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67 </citations>
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68 </tool>