Mercurial > repos > ecology > timeseries_extraction

comparison timeseries_plot.xml @ 0:810820a0d45c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 21:23:21 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:810820a0d45c
1 <tool id="timeseries_extraction" name="NetCDF timeseries Extractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE@">
2 <description>Extract and plot time series</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>macros_timeseries.xml</import>
6 </macros>
7 <expand macro="edam_ontology"/>
8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
10 <requirement type="package" version="3">python</requirement>
11 <requirement type="package" version="1.6.0">netcdf4</requirement>
12 <requirement type="package" version="3.5.2">matplotlib</requirement>
13 <requirement type="package" version="2022.7.0">dask</requirement>
14 <requirement type="package" version="1.4.3">pandas</requirement>
15 <requirement type="package" version="1.6.1">cftime</requirement>
16 </requirements>
17 <command detect_errors="exit_code"><![CDATA[
18 mkdir output_dir &&
19 mkdir -p `pwd`/mlp_tmpdir &&
20 MPLCONFIGDIR=`pwd`/mlp_tmpdir &&
21 python '$__tool_directory__/timeseries.py' '$input' '$var'
22 --config '$series_customization'
23 --output timeseries.png
24 --save $timeseries_tabular
25 --verbose &&
26 mv timeseries.png $timeseries_plot
27 ]]></command>
28 <expand macro="config_series"/>
29 <inputs>
30 <param type="data" name="input" label="Input netcdf file" format="netcdf" help="Select the input netCDF file."/>
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."/>
32 <param name="var" type="select" label="Choose the variable to plot">
33 <options from_dataset="var_tab">
34 <column name="name" index="0"/>
35 <column name="value" index="0"/>
36 </options>
37 </param>
38 <conditional name="condi_datetime">
39 <param name="datetime" type="select" label="Datetime selection" help="Use this option to set the start and end values for plotting.">
40 <option value="no">No</option>
41 <option value="yes">Yes</option>
42 </param>
43 <when value="no"></when>
44 <when value="yes">
45 <param name="time_name" type="select" label="Choose the name for date and time values">
46 <options from_dataset="var_tab">
47 <column name="name" index="0"/>
48 <column name="value" index="0"/>
49 </options>
50 </param>
51 <param name="time_start_value" type="text" value="" label="Choose the beginning date/time to plot (YYY-MM-DD)"/>
52 <param name="time_end_value" type="text" value="" label="Choose the ending date/time to plot (YYYY-MM-DD)"/>
53 </when>
54 </conditional>
55 <param name="lat_value" type="float" optional="true" label="latitude value for limited geographical area" />
56 <param name="lat_name" type="select" label="Choose the name for latitudes" optional="true">
57 <options from_dataset="var_tab">
58 <column name="name" index="0"/>
59 <column name="value" index="0"/>
60 </options>
61 </param>
62 <param name="lon_value" type="float" optional="true" label="longitude value for limited geographical area " />
63 <param name="lon_name" type="select" label="Choose the name for longitudes" optional="true">
64 <options from_dataset="var_tab">
65 <column name="name" index="0"/>
66 <column name="value" index="0"/>
67 </options>
68 </param>
69 <section name="adv" title="Advanced Plotting Options" expanded="false">
70 <param name="plot_title" type="text" value="" label="Plot title" />
71 <param name="xlabel" type="text" value="" label="Label for x-axis" />
72 <param name="ylabel" type="text" value="" label="Label for y-axis" />
73 <param name="format_date" type="text" value="" label="format date/time for plotting" />
74 </section>
75 </inputs>
76 <outputs>
77 <data name="timeseries_tabular" format="tabular" label="Timeseries table"/>
78 <data name="timeseries_plot" format="png" label="Timeseries plot"/>
79 </outputs>
80 <tests>
81 <test>
82 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
83 <param name="var" value="chl"/>
84 <param name="var_tab" value="var_tab_dataset-ibi"/>
85 <param name="lon_value" value="-5.0"/>
86 <param name="lat_value" value="43.50"/>
87 <param name="lon_name" value="longitude"/>
88 <param name="lat_name" value="latitude"/>
89 <conditional name="condi_datetime">
90 <param name="datetime" value="no"/>
91 </conditional>
92 <section name="adv">
93 <param name="plot_title" value="Timeseries of Chlorophyll concentration"/>
94 <param name="format_date" value="%Y"/>
95 <param name="xlabel" value="Year"/>
96 <param name="ylabel" value="Chl"/>
97 </section>
98 <output name="timeseries_tabular" ftype="tabular" file="time_series_customized.tabular"/>
99 <output name="timeseries_plot" ftype="png" file="time_series_customized.png"/>
100 </test>
101 <test>
102 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
103 <param name="var" value="chl"/>
104 <param name="var_tab" value="var_tab_dataset-ibi"/>
105 <param name="lon_value" value="-7.0"/>
106 <param name="lat_value" value="44.75"/>
107 <param name="lon_name" value="longitude"/>
108 <param name="lat_name" value="latitude"/>
109 <conditional name="condi_datetime">
110 <param name="datetime" value="yes"/>
111 <param name="time_start_value" value="2010-12-15"/>
112 <param name="time_end_value" value="2013-12-31"/>
113 </conditional>
114 <output name="timeseries_tabular" ftype="tabular" file="time_series.tabular"/>
115 <output name="timeseries_plot" ftype="png" file="time_series.png"/>
116 </test>
117 </tests>
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>
119 <expand macro="citations"/>
120 </tool>