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comparison psy-maps.xml @ 0:db8d76da4174 draft

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planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
author climate
date Thu, 25 Apr 2019 18:11:49 -0400
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1 <tool id="psy_maps" name="map plot" version="1.2.0">
2 <description>gridded (lat/lon) netCDF data</description>
3 <requirements>
4 <requirement type="package" version="3">python</requirement>
5 <requirement type="package" version="1.2.0">psy-maps</requirement>
6 <requirement type="package" version="1.2.0">psy-reg</requirement>
7 <requirement type="package" version="1.2.2">psyplot-gui</requirement>
8 <requirement type="package" version="1.4.1">netcdf4</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 python3 '$__tool_directory__/psymap_simple.py'
12 '$ifilename' '$variable'
13 --proj '$adv.projection'
14 --cmap '$adv.colormap'
15 --output image.png
16 ]]></command>
17 <inputs>
18 <param name="ifilename" type="data" format="netcdf" label="input with geographical coordinates (netCDF format)"></param>
19 <param name="variable" type="text" value="TS" label="variable name as given in the netCDF file" />
20 <section name="adv" title="Advanced Options" expanded="false">
21 <param name="projection" type="select">
22 <option value="" selected="true">PlateCarree</option>
23 <option value="robin">Robinson</option>
24 <option value="moll">Mollweide</option>
25 <option value="geo">Geostationary</option>
26 <option value="northpole">NorthPolarStereo</option>
27 <option value="southpole">SouthPolarStereo</option>
28 <option value="ortho">Orthographic</option>
29 <option value="stereo">Stereographic</option>
30 <option value="near">NearsidePerspective</option>
31 </param>
32 <param name="colormap" type="select">
33 <option value="Accent">Accent</option>
34 <option value="Blues">Blues</option>
35 <option value="BrBG">BrBG</option>
36 <option value="BuGn">BuGn</option>
37 <option value="BuPu">BuPu</option>
38 <option value="CMRmap">CMRmap</option>
39 <option value="Dark2">Dark2</option>
40 <option value="GnBu">GnBu</option>
41 <option value="Greens">Greens</option>
42 <option value="Greys">Greys</option>
43 <option value="OrRd">OrRd</option>
44 <option value="Oranges">Oranges</option>
45 <option value="PRGn">PRGn</option>
46 <option value="Paired">Paired</option>
47 <option value="Pastel1">Pastel1</option>
48 <option value="Pastel2">Pastel2</option>
49 <option value="PiYG">PiYG</option>
50 <option value="PuBu">PuBu</option>
51 <option value="PuBuGn">PuBuGn</option>
52 <option value="PuOr">PuOr</option>
53 <option value="PuRd">PuRd</option>
54 <option value="Purples">Purples</option>
55 <option value="RdBu">RdBu</option>
56 <option value="RdGy">RdGy</option>
57 <option value="RdPu">RdPu</option>
58 <option value="RdYlBu">RdYlBu</option>
59 <option value="RdYlGn">RdYlGn</option>
60 <option value="Reds">Reds</option>
61 <option value="Set1">Set1</option>
62 <option value="Set2">Set2</option>
63 <option value="Set3">Set3</option>
64 <option value="Spectral">Spectral</option>
65 <option value="Wistia">Wistia</option>
66 <option value="YlGn">YlGn</option>
67 <option value="YlGnBu">YlGnBu</option>
68 <option value="YlOrBr">YlOrBr</option>
69 <option value="YlOrRd">YlOrRd</option>
70 <option value="afmhot">afmhot</option>
71 <option value="autumn">autumn</option>
72 <option value="binary">binary</option>
73 <option value="bone">bone</option>
74 <option value="brg">brg</option>
75 <option value="bwr">bwr</option>
76 <option value="cool">cool</option>
77 <option value="coolwarm">coolwarm</option>
78 <option value="copper">copper</option>
79 <option value="cubehelix">cubehelix</option>
80 <option value="flag">flag</option>
81 <option value="gist_earth">gist_earth</option>
82 <option value="gist_gray">gist_gray</option>
83 <option value="gist_heat">gist_heat</option>
84 <option value="gist_ncar">gist_ncar</option>
85 <option value="gist_rainbow">gist_rainbow</option>
86 <option value="gist_stern">gist_stern</option>
87 <option value="gist_yarg">gist_yarg</option>
88 <option value="gnuplot">gnuplot</option>
89 <option value="gnuplot2">gnuplot2</option>
90 <option value="gray">gray</option>
91 <option value="hot">hot</option>
92 <option value="hsv">hsv</option>
93 <option value="jet" selected="true">jet</option>
94 <option value="nipy_spectral">nipy_spectral</option>
95 <option value="ocean">ocean</option>
96 <option value="pink">pink</option>
97 <option value="prism">prism</option>
98 <option value="rainbow">rainbow</option>
99 <option value="seismic">seismic</option>
100 <option value="spring">spring</option>
101 <option value="summer">summer</option>
102 <option value="tab10">tab10</option>
103 <option value="tab20">tab20</option>
104 <option value="tab20b">tab20b</option>
105 <option value="tab20c">tab20c</option>
106 <option value="terrain">terrain</option>
107 <option value="winter">winter</option>
108 </param>
109 </section>
110 </inputs>
111 <outputs>
112 <data name="ofilename" format="png" from_work_dir="image.png"/>
113 </outputs>
114 <tests>
115 <test>
116 <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" />
117 <param name="variable" value="TS" />
118 <param name="adv.projection" value="" />
119 <param name="adv.colormap" value="jet" />
120 <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12.png" compare="sim_size" delta="500"/>
121 </test>
122 <test>
123 <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" />
124 <param name="variable" value="TS" />
125 <param name="adv.projection" value="ortho" />
126 <param name="adv.colormap" value="jet" />
127 <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12.png" compare="sim_size" delta="500"/>
128 </test>
129 </tests>
130 <help><![CDATA[
131
132 **Visualization on a map with psyplot**
133 =========================================
134
135 This tool wraps the functionality of ``psyplot.plot.mapplot``.
136
137
138 .. class:: infomark
139
140 The wrappers aims at providing the same functionality as ``psyplot.plot.mapplot`` but it has some limitations.
141 The input file must be in netCDF format and must contain 2D arrays with geographical coordinatates
142 (latitudes, longitudes) given in degrees.
143 TODO: Fill in help.
144
145 **What it does**
146 ----------------
147
148 This tools creates an image (png format) corresponding to the visualization on a geographical map of a variable extracted from a
149 netCDF file (input file). By default, the projection is ``PlateCarree`` and colormap is ``jet``. These settings can be changed in *Advanced settings*.
150
151
152 **Usage**
153
154 ::
155
156 usage: psymap_simple.py [-h] [--proj PROJ] [--cmap CMAP] [--output OUTPUT] [-v] input varname
157
158
159 Positional arguments:
160 ~~~~~~~~~~~~~~~~~~~~~
161
162 - **input**: input filename with geographical coordinates (netCDF format)
163 - **varname**: Specify which variable to plot (case sensitive)
164
165 Optional arguments:
166 ~~~~~~~~~~~~~~~~~~~~~
167
168 -h, --help show this help message and exit
169 --proj PROJ Specify the projection on which we draw
170 --cmap CMAP Specify which colormap to use for plotting
171 --output OUTPUT output filename to store resulting image (png format)
172 -v, --verbose switch on verbose mode
173
174 It uses psy-maps, a python package to generate plots. More information about
175 psyplot and psy-maps can be found at https://psyplot.readthedocs.io/projects/psy-maps/en/latest/
176
177 ]]></help>
178 <citations>
179 </citations>
180 </tool>