Mercurial > repos > ecology > xarray_metadata_info
diff xarray_metadata_info.xml @ 4:9bbaab36a5d4 draft
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
| author | ecology |
|---|---|
| date | Thu, 20 Jan 2022 17:09:40 +0000 |
| parents | 663268794710 |
| children | 00de53d18b99 |
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--- a/xarray_metadata_info.xml Sun Jun 06 08:49:43 2021 +0000 +++ b/xarray_metadata_info.xml Thu Jan 20 17:09:40 2022 +0000 @@ -1,86 +1,86 @@ -<tool id="xarray_metadata_info" name="NetCDF xarray Metadata Info" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description>summarize content of a Netcdf file</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="edam_ontology"/> - <requirements> - <requirement type="package" version="3">python</requirement> - <requirement type="package" version="1.5.6">netcdf4</requirement> - <requirement type="package" version="@TOOL_VERSION@">xarray</requirement> - <requirement type="package" version="0.9.0">geopandas</requirement> - <requirement type="package" version="1.7.1">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 $ncdump -h inputfile) - -Then, a general tabular 'variables' summarize dimensions details inside each available variable. - - -The summary tabular file has the general structure : - - - Variable1 Var1_Number_of_Dim Dim1 Dim1_size ... DimN DimN_size - - VariableX VarX_Number_of_Dim DimX1 DimX1_size ... DimXN DimXN_size - - ... - - -**Input** - -A netcdf file (xxx.nc). - -**Outputs** - -An Information file. - -A summary tabular file. - - --------------------------------- - -The Netcdf Info tool use the netcdf functions : https://www.unidata.ucar.edu/software/netcdf/docs/index.html - -Run this tool before considering using Netcdf Read. - ]]></help> - <expand macro="citations"/> -</tool> +<tool id="xarray_metadata_info" name="NetCDF xarray Metadata Info" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>summarize content of a Netcdf file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edam_ontology"/> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">xarray</requirement> + <requirement type="package" version="3">python</requirement> + <requirement type="package" version="1.5.6">netcdf4</requirement> + <requirement type="package" version="0.9.0">geopandas</requirement> + <requirement type="package" version="1.7.1">shapely</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python3 '$__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> + <expand macro="citations"/> +</tool>