Mercurial > repos > ecology > xarray_metadata_info
diff xarray_metadata_info.xml @ 0:965fcab0cd9f draft
"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 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xarray_metadata_info.xml Mon May 18 08:30:10 2020 -0400 @@ -0,0 +1,82 @@ +<tool id="xarray_metadata_info" name="NetCDF xarray Metadata Info" version="0.15.1"> + <description>summarize content of a Netcdf file</description> + <requirements> + <requirement type="package" version="3">python</requirement> + <requirement type="package" version="1.5.3">netcdf4</requirement> + <requirement type="package" version="0.15.1">xarray</requirement> + <requirement type="package" version="0.7.0">geopandas</requirement> + <requirement type="package" version="1.7.0">shapely</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python3 '$__tool_directory__/xarray_tool.py' '$input' --info '$info' --summary '$output' + ]]></command> + <inputs> + <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need information about."/> + </inputs> + <outputs> + <data name="output" format="tabular" label="Metadata infos from ${input.name}" from_work_dir="variables.tabular"/> + <data name="info" label="info file" format="txt"/> + </outputs> + <tests> + <test> + <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/> + <param name="output" value="Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab"/> + <output name="info" value="info_file.txt"> + <assert_contents> + <has_text_matching expression="depth\s+=\s+1"/> + <has_text_matching expression="latitude\s+=\s+97"/> + <has_text_matching expression="longitude\s+=\s+103"/> + <has_text_matching expression="time\s+=\s+145"/> + </assert_contents> + </output> + <output name="output" ftype="tabular" file="Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab"> + <assert_contents> + <has_text_matching expression="VariableName\tNumberOfDimensions\tDim0Name\tDim0Size\tDim1Name\tDim1Size\tDim2Name\tDim2Size\tDim3Name\tDim3Size"/> + <has_text_matching expression="phy\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/> + <has_text_matching expression="chl\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/> + <has_text_matching expression="nh4\t4\ttime\t145\tdepth\t1\tlatitude\t97\tlongitude\t103"/> + <has_text_matching expression="time\t1\ttime\t145"/> + <has_text_matching expression="longitude\t1\tlongitude\t103"/> + <has_text_matching expression="latitude\t1\tlatitude\t97"/> + <has_text_matching expression="depth\t1\tdepth\t1"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +First the tool will give general information about the input in a 'info file' output. (command $ncdump -h inputfile) + +Then, a general tabular 'variables' summarize dimensions details inside each available variable. + + +The summary tabular file has the general structure : + + + Variable1 Var1_Number_of_Dim Dim1 Dim1_size ... DimN DimN_size + + VariableX VarX_Number_of_Dim DimX1 DimX1_size ... DimXN DimXN_size + + ... + + +**Input** + +A netcdf file (xxx.nc). + +**Outputs** + +An Information file. + +A summary tabular file. + + +-------------------------------- + +The Netcdf Info tool use the netcdf functions : https://www.unidata.ucar.edu/software/netcdf/docs/index.html + +Run this tool before considering using Netcdf Read. + ]]></help> + +</tool>