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comparison xarray_mapplot.xml @ 0:d7479b6dfbe8 draft

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"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
author ecology
date Sun, 06 Jun 2021 08:51:12 +0000
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children dc05bf0af58f
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-1:000000000000 0:d7479b6dfbe8
1 <tool id="xarray_mapplot" name="NetCDF xarray map plotting" profile="20.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Visualize netCDF variables on a geographical map</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam_ontology"/>
7 <requirements>
8 <requirement type="package" version="3">python</requirement>
9 <requirement type="package" version="1.5.6">netcdf4</requirement>
10 <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
11 <requirement type="package" version="0.19.0">cartopy</requirement>
12 <requirement type="package" version="3.4.2">matplotlib</requirement>
13 <requirement type="package" version="1.2">cmcrameri</requirement>
14 </requirements>
15 <command detect_errors="exit_code"><![CDATA[
16 mkdir output_dir &&
17 mkdir -p `pwd`/mlp_tmpdir &&
18 MPLCONFIGDIR=`pwd`/mlp_tmpdir &&
19 echo "Galaxy xarray version @TOOL_VERSION@" > $version &&
20 python '$__tool_directory__/xarray_mapplot.py' '$input' '$var'
21 #if $condi_datetime.datetime=="yes"
22 --time="$condi_datetime.time_values"
23 #end if
24 --latitude='$lat_dim'
25 --longitude='$lon_dim'
26 #if $colorbar_label
27 --label='$colorbar_label'
28 #end if
29 #if $title
30 --title=$title
31 #end if
32 #if $cmap
33 --cmap='$cmap'
34 #end if
35 #if $proj
36 --proj='$proj'
37 #end if
38 #if $land
39 --land='$land'
40 #end if
41 #if $ocean
42 --ocean='$ocean'
43 #end if
44 #if $coastline
45 --coastline='$coastline'
46 #end if
47 #if $borders
48 --borders='$borders'
49 #end if
50 #if $threshold
51 --threshold='$threshold'
52 #end if
53 #if $range
54 --range='$range'
55 #end if
56 #if $xlim
57 --xlim='$xlim'
58 #end if
59 #if $ylim
60 --ylim='$ylim'
61 #end if
62 #if $shift
63 --shift
64 #end if
65 --output plot.png
66 --verbose &&
67 mv *.png output_dir
68 ]]></command>
69 <inputs>
70 <param type="data" name="input" label="Input netcdf file" format="netcdf"/>
71 <param type="data" label="Tabular of variables" name="var_tab" format="tabular" help="Select the tabular file which summarize the available variables and dimensions."/>
72 <param name="var" type="select" label="Choose the variable to plot">
73 <options from_dataset="var_tab">
74 <column name="name" index="0"/>
75 <column name="value" index="0"/>
76 </options>
77 </param>
78 <param name="lat_dim" type="select" label="Name of latitude coordinate" >
79 <options from_dataset="var_tab">
80 <column name="value" index="0"/>
81 </options>
82 </param>
83 <param name="lon_dim" type="select" label="Name of longitude coordinate" >
84 <options from_dataset="var_tab">
85 <column name="value" index="0"/>
86 </options>
87 </param>
88 <conditional name="condi_datetime">
89 <param name="datetime" type="select" label="Datetime selection" help="Use this option when your dataset contains multiple times/dates">
90 <option value="no">No</option>
91 <option value="yes">Yes</option>
92 </param>
93 <when value="no"></when>
94 <when value="yes">
95 <param type="data" label="Tabular of time values" name="time_tab" format="tabular" help="File containing time values."/>
96 <param name="time_values" type="select" multiple="true" label="Choose the times to plot">
97 <options from_dataset="time_tab">
98 <column name="name" index="1"/>
99 <column name="value" index="0"/>
100 </options>
101 </param>
102 </when>
103 </conditional>
104 <param name="xlim" type="text" optional="true" label="longitudes values 'lonW,lonE' for limited geographical area (optional and only available with some projections)" />
105 <param name="ylim" type="text" value="" optional="true" label="latitudes values 'latS,latN' for limited geographical area (optional and only available with some projections)" />
106 <param name="shift" type="select" optional="true" display="radio" label="Shift longitudes [0,360] --> [-180,180]">
107 <option value="" selected="true">No</option>
108 <option value="Yes">Yes</option>
109 </param>
110 <param name="range" type="text" optional="true" label="Range of values for plotting e.g. minimum value abd maximum value (minval,maxval) (optional)" />
111 <param name="threshold" type="float" optional="true" label="Do not plot values below this threshold (optional)" />
112 <expand macro="customize_appearance_plots" />
113 <param name="proj" type="text" optional="true" label='Specify the projection (proj4) on which we draw e.g. {"proj":"PlateCarree"} with double quote (optional)'>
114 <sanitizer>
115 <valid initial="string.ascii_letters,string.digits,string.punctuation,string.whitespace">
116 <add value="{" />
117 <add value="}" />
118 </valid>
119 </sanitizer>
120 </param>
121
122 </inputs>
123 <outputs>
124 <data name="version" format="tabular" label="Tool version"/>
125 <collection type="list" name="output_dir" label="Map plots">
126 <discover_datasets pattern="__name_and_ext__" directory="output_dir"/>
127 </collection>
128 </outputs>
129 <tests>
130 <test>
131 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
132 <param name="var" value="nh4"/>
133 <param name="var_tab" value="var_tab_dataset-ibi"/>
134 <param name="lat_dim" value="latitude"/>
135 <param name="lon_dim" value="longitude"/>
136 <conditional name="condi_datetime">
137 <param name="datetime" value="yes"/>
138 <param name="time_tab" value="time.tabular"/>
139 <param name="time_values" value="50"/>
140 </conditional>
141 <param name="cmap" value="cm.devon_r"/>
142 <param name="proj" value='{"proj":"PlateCarree"}'/>
143 <param name="land" value="0.1"/>
144 <param name="ocean" value="0.1"/>
145 <param name="coastline" value="0.2"/>
146 <param name="borders" value="0.5"/>
147 <output_collection name="output_dir" type="list" count="1">
148 <element name="plot_time50" ftype='png' file="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time50.png"/>
149 </output_collection>
150 <output name="version" ftype='tabular' file="version.tabular"/>
151 </test>
152 <test>
153 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
154 <param name="var" value="chl"/>
155 <param name="var_tab" value="var_tab_dataset-ibi"/>
156 <param name="lat_dim" value="latitude"/>
157 <param name="lon_dim" value="longitude"/>
158 <conditional name="condi_datetime">
159 <param name="datetime" value="yes"/>
160 <param name="time_tab" value="time.tabular"/>
161 <param name="time_values" value="0,1"/>
162 </conditional>
163 <param name="cmap" value="Greens"/>
164 <param name="proj" value='{"proj":"PlateCarree"}'/>
165 <param name="land" value="0.1"/>
166 <param name="ocean" value="0.1"/>
167 <param name="coastline" value="0.2"/>
168 <param name="borders" value="0.5"/>
169 <output_collection name="output_dir" type="list" count="2">
170 <element name="plot_time0" ftype="png" file="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time0.png"/>
171 <element name="plot_time1" ftype="png" file="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time1.png"/>
172 </output_collection>
173 <output name="version" ftype="tabular" file="version.tabular"/>
174 </test>
175 </tests>
176 <help><![CDATA[
177 **What it does**
178
179 This tool plots a variable on a geographical map. It must be a 2D variable (latitude, longitude) and eventually with
180 and additional time dimension (specific time to plot should then be selected).
181
182 The appearance of plots can be customized with options as well at the projection.
183 The projection needs to be given as a PROJ dictionary such as:
184 - {"proj":"EquidistantConic", "central_longitude": 20.0, "central_latitude": 70.0 }
185 - {"proj":"AlbersEqualArea", "central_longitude": 20.0, "central_latitude": 70.0 }
186 - {"proj":"EuroPP"}
187
188 The output is a collection of plots (png format); one per selected times.
189
190 -------------------------------------------------
191
192 The xarray select tool can be used after the xarray Info and xarray coord.
193 ]]></help>
194 <expand macro="citations"/>
195 </tool>