Mercurial > repos > ecology > timeseries_extraction

annotate timeseries_plot.xml @ 0:dd19259f7da5 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
author ecology
date Sun, 31 Jul 2022 21:18:44 +0000
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dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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1 <tool id="timeseries_extraction" name="NetCDF timeseries Extractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE@">
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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2 <description>Extract and plot time series</description>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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3 <macros>
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4 <import>macros.xml</import>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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5 <import>macros_timeseries.xml</import>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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6 </macros>
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7 <expand macro="edam_ontology"/>
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8 <requirements>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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9 <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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10 <requirement type="package" version="3">python</requirement>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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11 <requirement type="package" version="1.6.0">netcdf4</requirement>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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12 <requirement type="package" version="3.5.2">matplotlib</requirement>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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13 <requirement type="package" version="2022.7.0">dask</requirement>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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14 <requirement type="package" version="1.4.3">pandas</requirement>
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15 <requirement type="package" version="1.6.1">cftime</requirement>
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16 </requirements>
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17 <command detect_errors="exit_code"><![CDATA[
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18 mkdir output_dir &&
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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19 mkdir -p `pwd`/mlp_tmpdir &&
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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20 MPLCONFIGDIR=`pwd`/mlp_tmpdir &&
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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21 python '$__tool_directory__/timeseries.py' '$input' '$var'
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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22 --config '$series_customization'
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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23 --output timeseries.png
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24 --save $timeseries_tabular
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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25 --verbose &&
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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26 mv timeseries.png $timeseries_plot
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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27 ]]></command>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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28 <expand macro="config_series"/>
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29 <inputs>
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30 <param type="data" name="input" label="Input netcdf file" format="netcdf" help="Select the input netCDF file."/>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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31 <param type="data" label="Tabular of variables" name="var_tab" format="tabular" help="Select the tabular file which summarize the available variables and dimensions."/>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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32 <param name="var" type="select" label="Choose the variable to plot">
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33 <options from_dataset="var_tab">
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34 <column name="name" index="0"/>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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35 <column name="value" index="0"/>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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36 </options>
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37 </param>
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38 <conditional name="condi_datetime">
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39 <param name="datetime" type="select" label="Datetime selection" help="Use this option to set the start and end values for plotting.">
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40 <option value="no">No</option>
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41 <option value="yes">Yes</option>
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42 </param>
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43 <when value="no"></when>
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44 <when value="yes">
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45 <param name="time_name" type="select" label="Choose the name for date and time values">
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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46 <options from_dataset="var_tab">
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47 <column name="name" index="0"/>
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48 <column name="value" index="0"/>
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49 </options>
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50 </param>
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51 <param name="time_start_value" type="text" value="" label="Choose the beginning date/time to plot (YYY-MM-DD)"/>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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52 <param name="time_end_value" type="text" value="" label="Choose the ending date/time to plot (YYYY-MM-DD)"/>
dd19259f7da5 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
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53 </when>
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54 </conditional>
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55 <param name="lat_value" type="float" optional="true" label="latitude value for limited geographical area" />
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56 <param name="lat_name" type="select" label="Choose the name for latitudes" optional="true">
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57 <options from_dataset="var_tab">
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58 <column name="name" index="0"/>
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59 <column name="value" index="0"/>
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60 </options>
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61 </param>
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62 <param name="lon_value" type="float" optional="true" label="longitude value for limited geographical area " />
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63 <param name="lon_name" type="select" label="Choose the name for longitudes" optional="true">
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64 <options from_dataset="var_tab">
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65 <column name="name" index="0"/>
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66 <column name="value" index="0"/>
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67 </options>
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68 </param>
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69 <section name="adv" title="Advanced Plotting Options" expanded="false">
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70 <param name="plot_title" type="text" value="" label="Plot title" />
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71 <param name="xlabel" type="text" value="" label="Label for x-axis" />
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72 <param name="ylabel" type="text" value="" label="Label for y-axis" />
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73 <param name="format_date" type="text" value="" label="format date/time for plotting" />
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74 </section>
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75 </inputs>
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76 <outputs>
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77 <data name="timeseries_tabular" format="tabular" label="Timeseries table"/>
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78 <data name="timeseries_plot" format="png" label="Timeseries plot"/>
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79 </outputs>
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80 <tests>
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81 <test>
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82 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
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83 <param name="var" value="chl"/>
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84 <param name="var_tab" value="var_tab_dataset-ibi"/>
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85 <param name="lon_value" value="-5.0"/>
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86 <param name="lat_value" value="43.50"/>
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87 <param name="lon_name" value="longitude"/>
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88 <param name="lat_name" value="latitude"/>
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89 <conditional name="condi_datetime">
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90 <param name="datetime" value="no"/>
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91 </conditional>
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92 <section name="adv">
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93 <param name="plot_title" value="Timeseries of Chlorophyll concentration"/>
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94 <param name="format_date" value="%Y"/>
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95 <param name="xlabel" value="Year"/>
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96 <param name="ylabel" value="Chl"/>
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97 </section>
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98 <output name="timeseries_tabular" ftype="tabular" file="time_series_customized.tabular"/>
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99 <output name="timeseries_plot" ftype="png" file="time_series_customized.png"/>
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100 </test>
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101 <test>
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102 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
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103 <param name="var" value="chl"/>
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104 <param name="var_tab" value="var_tab_dataset-ibi"/>
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105 <param name="lon_value" value="-7.0"/>
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106 <param name="lat_value" value="44.75"/>
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107 <param name="lon_name" value="longitude"/>
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108 <param name="lat_name" value="latitude"/>
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109 <conditional name="condi_datetime">
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110 <param name="datetime" value="yes"/>
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111 <param name="time_start_value" value="2010-12-15"/>
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112 <param name="time_end_value" value="2013-12-31"/>
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113 </conditional>
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114 <output name="timeseries_tabular" ftype="tabular" file="time_series.tabular"/>
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115 <output name="timeseries_plot" ftype="png" file="time_series.png"/>
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116 </test>
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117 </tests>
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118 <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>
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119 <expand macro="citations"/>
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120 </tool>