annotate divandfull.xml @ 1:77787acbd793 draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit a7e53c429cf93485aba692b928defe6ee01633d6

<tool id="divand_full_analysis" name="DIVAnd" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description>Data-Interpolating Variational Analysis in n dimensions</description>
    <macros>
        <token name="@TOOL_VERSION@">0.1.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="1.8.5">julia</requirement>
        <requirement type="package" version="2.7.9">julia-divand</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    ## The HOME .julia folder is not writable inside the Docker container, so we need to set one that is writable. 
    export JULIA_DEPOT_PATH="\$PWD:\$JULIA_DEPOT_PATH" &&
    julia
        '$__tool_directory__/divandfull.jl'
        '$input_netcdf_identifier'
        '$longmin'
        '$longmax'
        '$latmin'
        '$latmax'
        '$startdate'
        '$enddate'
        '$varname'
        '$selmin'
        '$selmax'
        '$bathname'
    ]]></command>
    <inputs>
        <param name="input_netcdf_identifier" type="data" format="netcdf" label="Input your netcdf data"/>
        <param name="bathname" type="data" format="netcdf" label="Input your bathymetry netcdf file" help="for more info see below."/>
        <param name="longmin" type="float" min="-180" max="180" value="0" label="Longitude minimal"/>
        <param name="longmax" type="float" min="-180" max="180" value="0" label="Longitude maximal"/>
        <param name="latmin" type="float" min="-180" max="180" value="0" label="Latitude minimal"/>
        <param name="latmax" type="float" min="-180" max="180" value="0" label="Latitude maximal"/>
        <param name="startdate" type="text" value="yyyy-mm-dd" label="Input the starting date">
            <sanitizer invalid_char="">
                <valid initial="string.digits">
                    <add value="-"/>
                </valid>
            </sanitizer>
        </param>
        <param name="enddate" type="text" value="yyyy-mm-dd" label="Input the ending date">
            <sanitizer invalid_char="">
                <valid initial="string.digits">
                    <add value="-"/>
                </valid>
            </sanitizer>
        </param>
        <param name="varname" type="text" value="variable" label="Write the name of the variable of the analysis" help="Example: phosphate">
            <sanitizer invalid_char="">
                <valid initial="string.letters">
                    <add value="_"/>
                </valid>
            </sanitizer>
            <validator type="regex">[0-9a-zA-Z_]+</validator>
        </param>
        <param name="selmin" type="integer" min="0" max="100" optional="true" value="0" label="Minimum of the salinity"/>
        <param name="selmax" type="integer" min="0" max="100" optional="true" value="0" label="Maximum of the salinity"/>
    </inputs>
    <outputs>
        <data name="output_netcdf" label="DIVAnd netcdf output" from_work_dir="outputs_netcdf/*.nc" format="netcdf"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_netcdf_identifier" value="data_from_Eutrophication_Med_profiles_2022_unrestricted.nc"/>
            <param name="bathname" location="https://dox.ulg.ac.be/index.php/s/U0pqyXhcQrXjEUX/download"/>
            <param name="longmin" value="19.0"/>
            <param name="longmax" value="30.0"/>
            <param name="latmin" value="32.0"/>
            <param name="latmax" value="38.0"/>
            <param name="varname" value="phosphate"/>
            <param name="startdate" value="1950-01-01"/>
            <param name="enddate" value="2017-12-31"/>
            <param name="selmin" value="0"/>
            <param name="selmax" value="100"/>
            <output name="output_netcdf">
                <assert_contents>
            	    <has_size value="68291" delta="0"/>
            	</assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

This tool takes a observation netcdf file and create climatology 

**Input**

- An ocean observation netcdf file
- A bathymetry netcdf file, you can download it like this: download("https://dox.ulg.ac.be/index.php/s/U0pqyXhcQrXjEUX/download", "gebco_30sec_8.nc")
- Some complementary information for the tool to better understand your data and create your climatology on the right area: latitudes, longitudes, dates, and salinity.$

**Output**

One netcdf file containing the climatology created by DIVAnd.


**A bit of context**

DIVAnd (Data-Interpolating Variational Analysis in n dimensions) performs an n-dimensional variational analysis/gridding of
arbitrarily located observations. Observations will be interpolated/analyzed on a curvilinear grid in 1, 2, 3 or more dimensions.
In this sense it is a generalization of the original two-dimensional DIVA version (still available `here <https://github.com/gher-uliege/DIVA>`_ but
not further developed anymore).

The method bears some similarities and equivalences with Optimal Interpolation or Krigging in that it allows to create a smooth
and continous field from a collection of observations, observations which can be affected by errors. The analysis method is however
different in practise, allowing to take into account topological features, physical constraints etc in a natural way.
The method was initially developped with ocean data in mind, but it can be applied to any field where localized observations have
to be used to produce gridded fields which are "smooth".

DIVAndrun is the core analysis function in n dimensions. It does not know anything about the physical parameters or units you work with.
Coordinates can also be very general. The only constraint is that the metrics (pm,pn,po,...) when multiplied by the corresponding length
scales len lead to non-dimensional parameters. Furthermore the coordinates of the output grid (xi,yi,zi,...) need to have the same units
as the observation coordinates (x,y,z,...).

DIVAndfun is a version with a minimal set of parameters (the coordinates and values of observations, i.e. (x,f), the remaining parameters
being optional) and provides an interpolation function rather than an already gridded field.

diva3D is a higher-level function specifically designed for climatological analysis of data on Earth, using longitude/latitude/depth/time
coordinates and correlations length in meters. It makes the necessary preparation of metrics, parameter optimizations etc you normally would
program yourself before calling the analysis function DIVAndrun.

DIVAnd_heatmap can be used for additive data and produces Kernel Density Estimations.

DIVAndgo is only needed for very large problems when a call to DIVAndrun leads to memory or CPU time problems. This function tries to decide
which solver (direct or iterative) to use and how to make an automatic domain decomposition. Not all options from DIVAndrun are available.

If you want to try out multivariate approaches, you can look at DIVAnd_multivarEOF and DIVAnd_multivarJAC

If you want more informations about the functions and parameters see also the `documentations here <https://gher-uliege.github.io/DIVAnd.jl/latest/index.html>`_.

    ]]></help>
    <citations>
        <citation type="doi">doi:10.5194/gmd-7-225-2014</citation>
    </citations>
</tool>