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comparison psy-maps.xml @ 1:706666d912d5 draft

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"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
author climate
date Sat, 05 Oct 2019 17:11:18 -0400
parents db8d76da4174
children e6d1e9d6b399
comparison
equal deleted inserted replaced
0:db8d76da4174 1:706666d912d5
1 <tool id="psy_maps" name="map plot" version="1.2.0"> 1 <tool id="psy_maps" name="map plot" version="1.2.1">
2 <description>gridded (lat/lon) netCDF data</description> 2 <description>gridded (lat/lon) netCDF data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3">python</requirement> 4 <requirement type="package" version="3">python</requirement>
5 <requirement type="package" version="1.2.1">psyplot</requirement>
5 <requirement type="package" version="1.2.0">psy-maps</requirement> 6 <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="1.2.0">psy-reg</requirement>
7 <requirement type="package" version="1.2.2">psyplot-gui</requirement> 8 <requirement type="package" version="1.4.2">netcdf4</requirement>
8 <requirement type="package" version="1.4.1">netcdf4</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 HOME=`pwd` &&
11 python3 '$__tool_directory__/psymap_simple.py' 12 python3 '$__tool_directory__/psymap_simple.py'
12 '$ifilename' '$variable' 13 '$ifilename' '$variable'
13 --proj '$adv.projection' 14 --proj '$adv.projection'
14 --cmap '$adv.colormap' 15 --cmap '$adv.colormap'
15 --output image.png 16 --output image.png
17 #if str($adv.multiple_plot.selector) == 'yes'
18 --time '$adv.multiple_plot.time'
19 --format '$adv.multiple_plot.format'
20 --ncol '$adv.multiple_plot.ncol'
21 --nrow '$adv.multiple_plot.nrow'
22 #end if
23 #if str($adv.multiple_plot.title).strip()
24 --title '$adv.multiple_plot.title'
25 #end if
16 ]]></command> 26 ]]></command>
17 <inputs> 27 <inputs>
18 <param name="ifilename" type="data" format="netcdf" label="input with geographical coordinates (netCDF format)"></param> 28 <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" /> 29 <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"> 30 <section name="adv" title="Advanced Options" expanded="false">
31 <conditional name="multiple_plot">
32 <param name="selector" type="select" label="multiple times">
33 <option value="yes">yes</option>
34 <option value="no" selected="true">no</option>
35 </param>
36 <when value="yes">
37 <param name="time" type="text" value="0" label="comma separated list of indexes for fields to plot" />
38 <param name="format" type="text" value="%Y-%m-%d %H:%M:%S" label="date and time format" />
39 <param name="ncol" type="integer" value="1" min="1" max="4" label="number of columns for subplot grid" />
40 <param name="nrow" type="integer" value="1" min="1" max="20" label="number of rows for subplot grid" />
41 <param name="title" type="text" value="" label="subplot title (repeated on each subplot)" />
42 </when>
43 <when value="no">
44 <param name="title" type="text" value="" label="plot title" />
45 </when>
46 </conditional>
21 <param name="projection" type="select"> 47 <param name="projection" type="select">
22 <option value="" selected="true">PlateCarree</option> 48 <option value="" selected="true">PlateCarree</option>
23 <option value="robin">Robinson</option> 49 <option value="robin">Robinson</option>
24 <option value="moll">Mollweide</option> 50 <option value="moll">Mollweide</option>
25 <option value="geo">Geostationary</option> 51 <option value="geo">Geostationary</option>
53 <option value="PuRd">PuRd</option> 79 <option value="PuRd">PuRd</option>
54 <option value="Purples">Purples</option> 80 <option value="Purples">Purples</option>
55 <option value="RdBu">RdBu</option> 81 <option value="RdBu">RdBu</option>
56 <option value="RdGy">RdGy</option> 82 <option value="RdGy">RdGy</option>
57 <option value="RdPu">RdPu</option> 83 <option value="RdPu">RdPu</option>
84 <option value="RdBu_r">RdBu_r</option>
85 <option value="RdGy_r">RdGy_r</option>
86 <option value="RdPu_r">RdPu_r</option>
58 <option value="RdYlBu">RdYlBu</option> 87 <option value="RdYlBu">RdYlBu</option>
59 <option value="RdYlGn">RdYlGn</option> 88 <option value="RdYlGn">RdYlGn</option>
60 <option value="Reds">Reds</option> 89 <option value="Reds">Reds</option>
61 <option value="Set1">Set1</option> 90 <option value="Set1">Set1</option>
62 <option value="Set2">Set2</option> 91 <option value="Set2">Set2</option>
113 </outputs> 142 </outputs>
114 <tests> 143 <tests>
115 <test> 144 <test>
116 <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" /> 145 <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" />
117 <param name="variable" value="TS" /> 146 <param name="variable" value="TS" />
118 <param name="adv.projection" value="" /> 147 <param name="projection" value="" />
119 <param name="adv.colormap" value="jet" /> 148 <param name="colormap" value="jet" />
120 <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12.png" compare="sim_size" delta="500"/> 149 <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12.png" compare="sim_size" delta="500"/>
121 </test> 150 </test>
122 <test> 151 <test>
123 <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" /> 152 <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" />
124 <param name="variable" value="TS" /> 153 <param name="variable" value="TS" />
125 <param name="adv.projection" value="ortho" /> 154 <param name="projection" value="ortho" />
126 <param name="adv.colormap" value="jet" /> 155 <param name="colormap" value="RdBu_r" />
127 <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12.png" compare="sim_size" delta="500"/> 156 <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12_ortho.png" compare="sim_size" delta="500"/>
128 </test> 157 </test>
129 </tests> 158 </tests>
130 <help><![CDATA[ 159 <help><![CDATA[
131 160
132 **Visualization on a map with psyplot** 161 **Visualization on a map with psyplot**
151 180
152 **Usage** 181 **Usage**
153 182
154 :: 183 ::
155 184
156 usage: psymap_simple.py [-h] [--proj PROJ] [--cmap CMAP] [--output OUTPUT] [-v] input varname 185 usage: psymap_simple.py [-h] [--proj PROJ] [--cmap CMAP] [--output OUTPUT] [--time TIME]
186 [--format FORMAT] [--title TITLE] [--ncol NCOL] [--nrow NROW] [-v] input varname
157 187
158 188
159 Positional arguments: 189 Positional arguments:
160 ~~~~~~~~~~~~~~~~~~~~~ 190 ~~~~~~~~~~~~~~~~~~~~~
161 191
168 -h, --help show this help message and exit 198 -h, --help show this help message and exit
169 --proj PROJ Specify the projection on which we draw 199 --proj PROJ Specify the projection on which we draw
170 --cmap CMAP Specify which colormap to use for plotting 200 --cmap CMAP Specify which colormap to use for plotting
171 --output OUTPUT output filename to store resulting image (png format) 201 --output OUTPUT output filename to store resulting image (png format)
172 -v, --verbose switch on verbose mode 202 -v, --verbose switch on verbose mode
203 --time TIME list of times to plot for multiple plots
204 --format FORMAT format for date/time (default is Month d, yyyy)
205 --title TITLE plot title
206 --ncol NCOL number of columns for multiple plots
207 --nrow NROW number of rows for multiple plots
173 208
174 It uses psy-maps, a python package to generate plots. More information about 209 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/ 210 psyplot and psy-maps can be found at https://psyplot.readthedocs.io/projects/psy-maps/en/latest/
176 211
177 ]]></help> 212 ]]></help>