Mercurial > repos > ecology > timeseries_extraction
diff timeseries_plot.xml @ 0:810820a0d45c draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
| author | ecology |
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| date | Sun, 31 Jul 2022 21:23:21 +0000 |
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--- /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>