Mercurial > repos > ecology > xarray_coords_info
annotate xarray_coords_info.xml @ 1:6015f30a7258 draft
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 0c4e3e42ddfcc1d4a2c4085063cd6a3f5cb2bf37"
| author | ecology |
|---|---|
| date | Sun, 29 Aug 2021 16:46:54 +0000 |
| parents | fea8a53f8099 |
| children | 3e73f657a998 |
| rev | line source |
|---|---|
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6015f30a7258
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 0c4e3e42ddfcc1d4a2c4085063cd6a3f5cb2bf37"
ecology
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1 <tool id="xarray_coords_info" name="NetCDF xarray Coordinate Info" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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2 <description>Get values for each coordinate of a Netcdf file</description> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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3 <macros> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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4 <import>macros.xml</import> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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5 </macros> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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6 <expand macro="edam_ontology"/> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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7 <requirements> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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8 <requirement type="package" version="3">python</requirement> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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9 <requirement type="package" version="1.5.6">netcdf4</requirement> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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10 <requirement type="package" version="@TOOL_VERSION@">xarray</requirement> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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11 <requirement type="package" version="0.9.0">geopandas</requirement> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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12 <requirement type="package" version="1.7.1">shapely</requirement> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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13 </requirements> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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14 <command detect_errors="exit_code"><![CDATA[ |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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15 mkdir output_dir && |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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16 echo "Galaxy xarray version @TOOL_VERSION@" > output_dir/version.tabular && |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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17 python3 '$__tool_directory__/xarray_tool.py' '$input' --coords_info output_dir |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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18 ]]></command> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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19 <inputs> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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20 <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need to extract coordinate values."/> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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21 </inputs> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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22 <outputs> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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23 <collection type="list" name="output_dir" label="Coordinates"> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
parents:
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24 <discover_datasets pattern="__name_and_ext__" visible="true" directory="output_dir"/> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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25 </collection> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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26 </outputs> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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27 <tests> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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28 <test> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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29 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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30 <output_collection name="output_dir" type="list" count="5"> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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31 <element name="time" file="time.tabular" ftype="tabular"/> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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32 <element name="latitude" file="latitude.tabular" ftype="tabular"/> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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33 <element name="longitude" file="longitude.tabular" ftype="tabular"/> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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34 <element name="depth" file="depth.tabular" ftype="tabular"/> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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35 <element name="version" file="version.tabular" ftype="tabular"/> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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36 </output_collection> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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37 </test> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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38 </tests> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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39 <help><![CDATA[ |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
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40 **What it does** |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
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41 |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
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42 The tool will generate a collection containing one file per coordinate. Each file contains the values of the |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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43 corresponding coordinate. The output of this tool is usually used as input to other tools. |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
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44 |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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45 **Input** |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
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46 |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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47 A netcdf file (xxx.nc). |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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48 |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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49 -------------------------------- |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
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50 |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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51 ]]></help> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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52 <expand macro="citations"/> |
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fea8a53f8099
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
ecology
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53 </tool> |