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