annotate xarray_metadata_info.xml @ 5:00de53d18b99 draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7

<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="3.10">python</requirement>
        <requirement type="package" version="1.6.0">netcdf4</requirement>
        <requirement type="package" version="1.4.3">pandas</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python3 '$__tool_directory__/xarray_info.py' '$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>