Mercurial > repos > ecology > xarray_metadata_info

annotate xarray_metadata_info.xml @ 0:965fcab0cd9f draft

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"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
author ecology
date Mon, 18 May 2020 08:30:10 -0400
parents
children e8650cdf092f
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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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1 <tool id="xarray_metadata_info" name="NetCDF xarray Metadata Info" version="0.15.1">
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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2 <description>summarize content of a Netcdf file</description>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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3 <requirements>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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4 <requirement type="package" version="3">python</requirement>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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5 <requirement type="package" version="1.5.3">netcdf4</requirement>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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6 <requirement type="package" version="0.15.1">xarray</requirement>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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7 <requirement type="package" version="0.7.0">geopandas</requirement>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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8 <requirement type="package" version="1.7.0">shapely</requirement>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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9 </requirements>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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10 <command detect_errors="exit_code"><![CDATA[
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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11 python3 '$__tool_directory__/xarray_tool.py' '$input' --info '$info' --summary '$output'
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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12 ]]></command>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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13 <inputs>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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14 <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need information about."/>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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15 </inputs>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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16 <outputs>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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17 <data name="output" format="tabular" label="Metadata infos from ${input.name}" from_work_dir="variables.tabular"/>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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18 <data name="info" label="info file" format="txt"/>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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19 </outputs>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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20 <tests>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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21 <test>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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22 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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23 <param name="output" value="Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab"/>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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24 <output name="info" value="info_file.txt">
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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25 <assert_contents>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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26 <has_text_matching expression="depth\s+=\s+1"/>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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27 <has_text_matching expression="latitude\s+=\s+97"/>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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28 <has_text_matching expression="longitude\s+=\s+103"/>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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29 <has_text_matching expression="time\s+=\s+145"/>
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>
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>
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">
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>
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"/>
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"/>
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"/>
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"/>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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38 <has_text_matching expression="time\t1\ttime\t145"/>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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39 <has_text_matching expression="longitude\t1\tlongitude\t103"/>
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"/>
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"/>
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>
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>
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>
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>
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[
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**
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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48
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)
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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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.
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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52
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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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 :
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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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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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
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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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
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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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 ...
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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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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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**
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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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).
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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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**
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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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.
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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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.
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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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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965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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75 --------------------------------
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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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
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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78
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.
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>
965fcab0cd9f "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 812c1c92d6596722642515ba99c5efab113b6a68"
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81
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>