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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xarray_metadata_info.xml	Mon May 18 08:30:10 2020 -0400
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+<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>