Mercurial > repos > mnhn65mo > netcdf_handler
comparison netcdf_metadata_info.xml @ 0:8da8ec7da45f draft default tip
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| author | mnhn65mo |
|---|---|
| date | Thu, 02 Aug 2018 09:24:38 -0400 |
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| -1:000000000000 | 0:8da8ec7da45f |
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| 1 <tool id="netcdf-metadata_info" name="Netcdf Metadata Info" version="0.1.0"> | |
| 2 <description>summarize content of a nc file</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.1.6">netcdf-metadata-info</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 netcdf-metadata-info '$input' | |
| 8 && | |
| 9 while read -r l;do | |
| 10 a=\$(echo \$l | cut -d' ' -f1);echo \$l>dimensions_\$a | |
| 11 ;done <variables.tabular | |
| 12 && | |
| 13 rm dimensions_VariableName | |
| 14 && | |
| 15 for f in dimensions_*; do cat \$f | sed 's/ /\t\n/g' | sed '\$s/$/ /' >\$f.tabular ; done | |
| 16 && | |
| 17 for f in dimensions_*.tabular;do | |
| 18 awk 'NR % 2 != 0' \$f > \$f.2 | |
| 19 && | |
| 20 sed 1d \$f.2 > \$f | |
| 21 && | |
| 22 rm \$f.2 | |
| 23 ;done | |
| 24 && | |
| 25 ncdump -h '$input' > '$info' | |
| 26 ]]></command> | |
| 27 <inputs> | |
| 28 <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need information about."/> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <!-- | |
| 32 <data name="var_tabs" format="tabular"> | |
| 33 <discover_datasets pattern="__designation_and_ext__" visible="true"/> | |
| 34 <discover_datasets pattern="conda_activate.log" visible="false"/> | |
| 35 </data> | |
| 36 --> | |
| 37 <data name="output" format="tabular" label="Metadata infos from ${input.name}.Variables.tab" from_work_dir="variables.tabular"/> | |
| 38 <data name="info" label="info file" format="txt"/> | |
| 39 </outputs> | |
| 40 | |
| 41 <help><![CDATA[ | |
| 42 **What it does** | |
| 43 | |
| 44 First the tool will give general information about the input in a 'info file' output. (command $ncdump -h inputfile) | |
| 45 | |
| 46 Then, a general tabular 'variables' summarize dimensions details inside each available variable. | |
| 47 | |
| 48 | |
| 49 The summary tabular file has the general structure : | |
| 50 | |
| 51 | |
| 52 Variable1 Var1_Number_of_Dim Dim1 Dim1_size ... DimN DimN_size | |
| 53 | |
| 54 VariableX VarX_Number_of_Dim DimX1 DimX1_size ... DimXN DimXN_size | |
| 55 | |
| 56 ... | |
| 57 | |
| 58 | |
| 59 **Input** | |
| 60 | |
| 61 A netcdf file (xxx.nc). | |
| 62 | |
| 63 **Outputs** | |
| 64 | |
| 65 An Information file. | |
| 66 | |
| 67 A summary tabular file. | |
| 68 | |
| 69 | |
| 70 -------------------------------- | |
| 71 | |
| 72 The Netcdf Info tool use the netcdf functions : https://www.unidata.ucar.edu/software/netcdf/docs/index.html | |
| 73 | |
| 74 Run this tool before considering using Netcdf Read. | |
| 75 ]]></help> | |
| 76 | |
| 77 </tool> |