Mercurial > repos > ecology > xarray_metadata_info
annotate xarray_metadata_info.xml @ 1:7edbe5ae8b72 draft
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit f1455c158011dc4aab0fd469cf794be6f4142992"
| author | ecology |
|---|---|
| date | Fri, 22 May 2020 05:18:55 -0400 |
| parents | 965fcab0cd9f |
| children | e8650cdf092f |
| rev | line source |
|---|---|
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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1 <tool id="xarray_metadata_info" name="NetCDF xarray Metadata Info" version="0.15.1"> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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2 <description>summarize content of a Netcdf file</description> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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3 <requirements> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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4 <requirement type="package" version="3">python</requirement> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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5 <requirement type="package" version="1.5.3">netcdf4</requirement> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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6 <requirement type="package" version="0.15.1">xarray</requirement> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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7 <requirement type="package" version="0.7.0">geopandas</requirement> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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8 <requirement type="package" version="1.7.0">shapely</requirement> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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9 </requirements> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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10 <command detect_errors="exit_code"><![CDATA[ |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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11 python3 '$__tool_directory__/xarray_tool.py' '$input' --info '$info' --summary '$output' |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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12 ]]></command> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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13 <inputs> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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14 <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need information about."/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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15 </inputs> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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16 <outputs> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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17 <data name="output" format="tabular" label="Metadata infos from ${input.name}" from_work_dir="variables.tabular"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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18 <data name="info" label="info file" format="txt"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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19 </outputs> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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20 <tests> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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21 <test> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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22 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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23 <param name="output" value="Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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24 <output name="info" value="info_file.txt"> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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25 <assert_contents> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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26 <has_text_matching expression="depth\s+=\s+1"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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27 <has_text_matching expression="latitude\s+=\s+97"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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28 <has_text_matching expression="longitude\s+=\s+103"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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29 <has_text_matching expression="time\s+=\s+145"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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30 </assert_contents> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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31 </output> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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32 <output name="output" ftype="tabular" file="Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab"> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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33 <assert_contents> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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34 <has_text_matching expression="VariableName\tNumberOfDimensions\tDim0Name\tDim0Size\tDim1Name\tDim1Size\tDim2Name\tDim2Size\tDim3Name\tDim3Size"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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35 <has_text_matching expression="phy\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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36 <has_text_matching expression="chl\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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37 <has_text_matching expression="nh4\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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38 <has_text_matching expression="time\t1\ttime\t145"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
ecology
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39 <has_text_matching expression="longitude\t1\tlongitude\t103"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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40 <has_text_matching expression="latitude\t1\tlatitude\t97"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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41 <has_text_matching expression="depth\t1\tdepth\t1"/> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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42 </assert_contents> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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43 </output> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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44 </test> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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45 </tests> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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46 <help><![CDATA[ |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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47 **What it does** |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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48 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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49 First the tool will give general information about the input in a 'info file' output. (command $ncdump -h inputfile) |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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50 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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51 Then, a general tabular 'variables' summarize dimensions details inside each available variable. |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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52 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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53 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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54 The summary tabular file has the general structure : |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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55 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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56 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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57 Variable1 Var1_Number_of_Dim Dim1 Dim1_size ... DimN DimN_size |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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58 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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59 VariableX VarX_Number_of_Dim DimX1 DimX1_size ... DimXN DimXN_size |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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60 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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61 ... |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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62 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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63 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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64 **Input** |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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65 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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66 A netcdf file (xxx.nc). |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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67 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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68 **Outputs** |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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69 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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70 An Information file. |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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71 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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72 A summary tabular file. |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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73 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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74 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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75 -------------------------------- |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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76 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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77 The Netcdf Info tool use the netcdf functions : https://www.unidata.ucar.edu/software/netcdf/docs/index.html |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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78 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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79 Run this tool before considering using Netcdf Read. |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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80 ]]></help> |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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81 |
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965fcab0cd9f
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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82 </tool> |