--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/timeseries_plot.xml	Sun Jul 31 21:23:21 2022 +0000
@@ -0,0 +1,120 @@
+<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>