<tool id="timeseries_extraction" name="NetCDF timeseries Extractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE@">
    <description>Extract and plot time series</description>
    <macros>
        <import>macros.xml</import>
        <import>macros_timeseries.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
        <requirement type="package" version="3">python</requirement>
        <requirement type="package" version="1.6.0">netcdf4</requirement>
        <requirement type="package" version="3.5.2">matplotlib</requirement>
        <requirement type="package" version="2022.7.0">dask</requirement>
        <requirement type="package" version="1.4.3">pandas</requirement>
        <requirement type="package" version="1.6.1">cftime</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    mkdir output_dir &&
    mkdir -p `pwd`/mlp_tmpdir &&
    MPLCONFIGDIR=`pwd`/mlp_tmpdir &&
    python '$__tool_directory__/timeseries.py' '$input' '$var'
    --config '$series_customization' 
         --output timeseries.png
	 --save $timeseries_tabular
         --verbose &&
    mv timeseries.png $timeseries_plot
    ]]></command>
    <expand macro="config_series"/>
    <inputs>
        <param type="data" name="input" label="Input netcdf file" format="netcdf"  help="Select the input netCDF file."/>
        <param type="data" label="Tabular of variables" name="var_tab" format="tabular" help="Select the tabular file which summarize the available variables and dimensions."/>
        <param name="var" type="select" label="Choose the variable to plot">
            <options from_dataset="var_tab">
                <column name="name" index="0"/>
                <column name="value" index="0"/>
            </options>
        </param>
        <conditional name="condi_datetime">
            <param name="datetime" type="select" label="Datetime selection" help="Use this option to set the start and end values for plotting.">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"></when>
            <when value="yes">
                <param name="time_name" type="select" label="Choose the name for date and time values">
                    <options from_dataset="var_tab">
                        <column name="name" index="0"/>
                        <column name="value" index="0"/>
                    </options>
                </param>
		<param name="time_start_value" type="text" value="" label="Choose the beginning date/time to plot (YYY-MM-DD)"/>
		<param name="time_end_value" type="text" value="" label="Choose the ending date/time to plot (YYYY-MM-DD)"/>
            </when>
        </conditional>
        <param name="lat_value" type="float" optional="true" label="latitude value for limited geographical area" />
        <param name="lat_name" type="select" label="Choose the name for latitudes" optional="true">
            <options from_dataset="var_tab">
                <column name="name" index="0"/>
                <column name="value" index="0"/>
            </options>
        </param>
        <param name="lon_value" type="float" optional="true" label="longitude value for limited geographical area " />
        <param name="lon_name" type="select" label="Choose the name for longitudes" optional="true">
            <options from_dataset="var_tab">
                <column name="name" index="0"/>
                <column name="value" index="0"/>
            </options>
        </param>
        <section name="adv" title="Advanced Plotting Options" expanded="false">
            <param name="plot_title" type="text" value="" label="Plot title" />
            <param name="xlabel" type="text" value="" label="Label for x-axis" />
            <param name="ylabel" type="text" value="" label="Label for y-axis" />
            <param name="format_date" type="text" value="" label="format date/time for plotting" />
        </section>
    </inputs>
    <outputs>
        <data name="timeseries_tabular" format="tabular" label="Timeseries table"/>
        <data name="timeseries_plot" format="png" label="Timeseries plot"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
            <param name="var" value="chl"/>
            <param name="var_tab" value="var_tab_dataset-ibi"/>
            <param name="lon_value" value="-5.0"/>
            <param name="lat_value" value="43.50"/>
            <param name="lon_name" value="longitude"/>
            <param name="lat_name" value="latitude"/>
            <conditional name="condi_datetime">
                <param name="datetime" value="no"/>
            </conditional>                    
            <section name="adv">
                <param name="plot_title" value="Timeseries of Chlorophyll concentration"/>
                <param name="format_date" value="%Y"/>
                <param name="xlabel" value="Year"/>
                <param name="ylabel" value="Chl"/>
            </section>
            <output name="timeseries_tabular" ftype="tabular" file="time_series_customized.tabular"/>
            <output name="timeseries_plot" ftype="png" file="time_series_customized.png"/>
        </test>
        <test>
            <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
            <param name="var" value="chl"/>
            <param name="var_tab" value="var_tab_dataset-ibi"/>
            <param name="lon_value" value="-7.0"/>
            <param name="lat_value" value="44.75"/>
            <param name="lon_name" value="longitude"/>
            <param name="lat_name" value="latitude"/>
            <conditional name="condi_datetime">
                <param name="datetime" value="yes"/>
                <param name="time_start_value" value="2010-12-15"/>
                <param name="time_end_value" value="2013-12-31"/>
            </conditional>                    
            <output name="timeseries_tabular" ftype="tabular" file="time_series.tabular"/>
            <output name="timeseries_plot" ftype="png" file="time_series.png"/>
        </test>
    </tests>
    <help><![CDATA[ Extracts time series for a given variable in a .csv format file. This file can be used to plot the timeseries easily. ]]></help> 
    <expand macro="citations"/>
</tool>