diff netcdf_metadata_info.xml @ 0:8da8ec7da45f draft default tip

Uploaded
author mnhn65mo
date Thu, 02 Aug 2018 09:24:38 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/netcdf_metadata_info.xml	Thu Aug 02 09:24:38 2018 -0400
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+<tool id="netcdf-metadata_info" name="Netcdf Metadata Info" version="0.1.0">
+    <description>summarize content of a nc file</description>
+    <requirements>
+        <requirement type="package" version="1.1.6">netcdf-metadata-info</requirement> 
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        netcdf-metadata-info '$input'
+        &&
+        while read -r l;do
+            a=\$(echo \$l | cut -d' ' -f1);echo \$l>dimensions_\$a
+        ;done <variables.tabular
+        &&
+        rm dimensions_VariableName 
+        &&
+        for f in dimensions_*; do cat \$f | sed 's/ /\t\n/g' | sed '\$s/$/ /' >\$f.tabular ; done
+        &&
+        for f in dimensions_*.tabular;do
+            awk 'NR % 2 != 0' \$f > \$f.2
+            &&
+            sed 1d \$f.2 > \$f 
+            &&
+            rm \$f.2
+        ;done
+        &&
+        ncdump -h '$input' > '$info'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need information about."/>
+    </inputs>
+    <outputs>
+<!--
+        <data name="var_tabs" format="tabular">
+            <discover_datasets pattern="__designation_and_ext__" visible="true"/>
+            <discover_datasets pattern="conda_activate.log" visible="false"/>
+        </data>
+-->
+        <data name="output" format="tabular" label="Metadata infos from ${input.name}.Variables.tab" from_work_dir="variables.tabular"/>
+        <data name="info" label="info file" format="txt"/>
+    </outputs>
+
+    <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>