Mercurial > repos > climate > psy_maps

annotate psy-maps.xml @ 2:e6d1e9d6b399 draft

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planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
author climate
date Thu, 26 Sep 2024 10:32:08 +0000
parents 706666d912d5
children 988212a7466a
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e6d1e9d6b399 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
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1 <tool id="psy_maps" name="map plot" version="1.3.0" profile="23.0">
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2 <description>gridded (lat/lon) netCDF data</description>
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3 <edam_topics>
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4 <edam_topic>topic_3855</edam_topic>
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5 <edam_topic>topic_3318</edam_topic>
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6 </edam_topics>
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7 <edam_operations>
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8 <edam_operation>operation_0573</edam_operation>
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9 </edam_operations>
0
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10 <requirements>
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11 <requirement type="package" version="3">python</requirement>
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12 <requirement type="package" version="1.4.3">psyplot</requirement>
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13 <requirement type="package" version="1.4.2">psy-maps</requirement>
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14 <requirement type="package" version="1.4.0">psy-reg</requirement>
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15 <requirement type="package" version="1.6.5">netcdf4</requirement>
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16 </requirements>
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17 <command detect_errors="exit_code"><![CDATA[
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18 python3 '$__tool_directory__/psymap_simple.py'
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19 '$ifilename' '$variable'
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20 --logscale '$adv.logscale'
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21 --proj '$adv.projection'
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22 --cmap '$adv.colormap'
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23 --output image.png
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24 #if str($adv.multiple_plot.selector) == 'yes'
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25 --time '$adv.multiple_plot.time'
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26 --format '$adv.multiple_plot.format'
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27 --ncol '$adv.multiple_plot.ncol'
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28 --nrow '$adv.multiple_plot.nrow'
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29 #end if
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30 #if str($adv.multiple_plot.title).strip()
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31 --title '$adv.multiple_plot.title'
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32 #end if
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33 ]]></command>
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34 <inputs>
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35 <param name="ifilename" type="data" format="netcdf" label="input with geographical coordinates (netCDF format)"></param>
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36 <param name="variable" type="text" value="TS" label="variable name as given in the netCDF file" />
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37 <section name="adv" title="Advanced Options" expanded="false">
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38 <conditional name="multiple_plot">
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39 <param name="selector" type="select" label="multiple times">
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40 <option value="yes">yes</option>
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41 <option value="no" selected="true">no</option>
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42 </param>
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43 <when value="yes">
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44 <param name="time" type="text" value="0" label="comma separated list of indexes for fields to plot" />
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45 <param name="format" type="text" value="%Y-%m-%d %H:%M:%S" label="date and time format" />
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46 <param name="ncol" type="integer" value="1" min="1" max="4" label="number of columns for subplot grid" />
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47 <param name="nrow" type="integer" value="1" min="1" max="20" label="number of rows for subplot grid" />
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48 <param name="title" type="text" value="" label="subplot title (repeated on each subplot)" />
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49 </when>
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50 <when value="no">
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51 <param name="title" type="text" value="" label="plot title" />
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52 </when>
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53 </conditional>
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54 <param name="logscale" type="select" label="log scale the data">
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55 <option value="yes">yes</option>
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56 <option value="no" selected="true">no</option>
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57 </param>
0
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58 <param name="projection" type="select">
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59 <option value="" selected="true">PlateCarree</option>
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60 <option value="robin">Robinson</option>
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61 <option value="moll">Mollweide</option>
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62 <option value="geo">Geostationary</option>
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63 <option value="northpole">NorthPolarStereo</option>
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64 <option value="southpole">SouthPolarStereo</option>
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65 <option value="ortho">Orthographic</option>
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66 <option value="stereo">Stereographic</option>
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67 <option value="near">NearsidePerspective</option>
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68 </param>
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69 <param name="colormap" type="select">
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70 <option value="Accent">Accent</option>
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71 <option value="Blues">Blues</option>
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72 <option value="BrBG">BrBG</option>
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73 <option value="BuGn">BuGn</option>
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74 <option value="BuPu">BuPu</option>
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75 <option value="CMRmap">CMRmap</option>
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76 <option value="Dark2">Dark2</option>
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77 <option value="GnBu">GnBu</option>
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78 <option value="Greens">Greens</option>
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79 <option value="Greys">Greys</option>
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80 <option value="OrRd">OrRd</option>
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81 <option value="Oranges">Oranges</option>
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82 <option value="PRGn">PRGn</option>
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83 <option value="Paired">Paired</option>
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84 <option value="Pastel1">Pastel1</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
85 <option value="Pastel2">Pastel2</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
86 <option value="PiYG">PiYG</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
87 <option value="PuBu">PuBu</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
88 <option value="PuBuGn">PuBuGn</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
89 <option value="PuOr">PuOr</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
90 <option value="PuRd">PuRd</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
91 <option value="Purples">Purples</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
92 <option value="RdBu">RdBu</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
93 <option value="RdGy">RdGy</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
94 <option value="RdPu">RdPu</option>
1
706666d912d5 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
climate
parents: 0
diff changeset
95 <option value="RdBu_r">RdBu_r</option>
706666d912d5 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
climate
parents: 0
diff changeset
96 <option value="RdGy_r">RdGy_r</option>
706666d912d5 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
climate
parents: 0
diff changeset
97 <option value="RdPu_r">RdPu_r</option>
0
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
98 <option value="RdYlBu">RdYlBu</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
99 <option value="RdYlGn">RdYlGn</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
100 <option value="Reds">Reds</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
101 <option value="Set1">Set1</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
102 <option value="Set2">Set2</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
103 <option value="Set3">Set3</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
104 <option value="Spectral">Spectral</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
105 <option value="Wistia">Wistia</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
106 <option value="YlGn">YlGn</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
107 <option value="YlGnBu">YlGnBu</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
108 <option value="YlOrBr">YlOrBr</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
109 <option value="YlOrRd">YlOrRd</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
110 <option value="afmhot">afmhot</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
111 <option value="autumn">autumn</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
112 <option value="binary">binary</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
113 <option value="bone">bone</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
114 <option value="brg">brg</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
115 <option value="bwr">bwr</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
116 <option value="cool">cool</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
117 <option value="coolwarm">coolwarm</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
118 <option value="copper">copper</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
119 <option value="cubehelix">cubehelix</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
120 <option value="flag">flag</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
121 <option value="gist_earth">gist_earth</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
122 <option value="gist_gray">gist_gray</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
123 <option value="gist_heat">gist_heat</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
124 <option value="gist_ncar">gist_ncar</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
125 <option value="gist_rainbow">gist_rainbow</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
126 <option value="gist_stern">gist_stern</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
127 <option value="gist_yarg">gist_yarg</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
128 <option value="gnuplot">gnuplot</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
129 <option value="gnuplot2">gnuplot2</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
130 <option value="gray">gray</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
131 <option value="hot">hot</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
132 <option value="hsv">hsv</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
133 <option value="jet" selected="true">jet</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
134 <option value="nipy_spectral">nipy_spectral</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
135 <option value="ocean">ocean</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
136 <option value="pink">pink</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
137 <option value="prism">prism</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
138 <option value="rainbow">rainbow</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
139 <option value="seismic">seismic</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
140 <option value="spring">spring</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
141 <option value="summer">summer</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
142 <option value="tab10">tab10</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
143 <option value="tab20">tab20</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
144 <option value="tab20b">tab20b</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
145 <option value="tab20c">tab20c</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
146 <option value="terrain">terrain</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
147 <option value="winter">winter</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
148 </param>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
149 </section>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
150 </inputs>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
151 <outputs>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
152 <data name="ofilename" format="png" from_work_dir="image.png"/>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
153 </outputs>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
154 <tests>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
155 <test>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
156 <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" />
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
157 <param name="variable" value="TS" />
1
706666d912d5 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
climate
parents: 0
diff changeset
158 <param name="projection" value="" />
706666d912d5 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
climate
parents: 0
diff changeset
159 <param name="colormap" value="jet" />
0
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
160 <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12.png" compare="sim_size" delta="500"/>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
161 </test>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
162 <test>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
163 <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" />
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
164 <param name="variable" value="TS" />
1
706666d912d5 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
climate
parents: 0
diff changeset
165 <param name="projection" value="ortho" />
706666d912d5 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
climate
parents: 0
diff changeset
166 <param name="colormap" value="RdBu_r" />
706666d912d5 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
climate
parents: 0
diff changeset
167 <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12_ortho.png" compare="sim_size" delta="500"/>
0
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
climate
parents:
diff changeset
168 </test>
2
e6d1e9d6b399 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
climate
parents: 1
diff changeset
169 <test>
e6d1e9d6b399 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
climate
parents: 1
diff changeset
170 <param name="ifilename" value="ESACCI-OC-L3S-CHLOR_A-20220601-RESIZED-fv6.0.nc" />
e6d1e9d6b399 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
climate
parents: 1
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171 <param name="variable" value="chlor_a" />
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172 <param name="projection" value="" />
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173 <param name="colormap" value="jet" />
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174 <param name="logscale" value="yes" />
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175 <output name="ofilename" ftype="png" file="ESACCI-OC-L3S-CHLOR_A-20220601-RESIZED-fv6.0.png" compare="sim_size" delta="1500"/>
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176 </test>
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177 </tests>
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178 <help><![CDATA[
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179
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180 **Visualization on a map with psyplot**
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181 =========================================
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182
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183 This tool wraps the functionality of ``psyplot.plot.mapplot``.
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184
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185
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186 .. class:: infomark
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187
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188 The wrappers aims at providing the same functionality as ``psyplot.plot.mapplot`` but it has some limitations.
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189 The input file must be in netCDF format and must contain 2D arrays with geographical coordinatates
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190 (latitudes, longitudes) given in degrees.
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191 The code may fail when the data is significantly different from what has been tested.
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192
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193 **What it does**
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194 ----------------
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195
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196 This tools creates an image (png format) corresponding to the visualization on a geographical map of a variable extracted from a
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197 netCDF file (input file).
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198 By default, the projection is ``PlateCarree`` and colormap is ``jet``.
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199 These settings can be changed in *Advanced settings* alongside an option to log scale the plot.
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200
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201
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202 **Usage**
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203
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204 ::
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205
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206 usage: psymap_simple.py [-h] [--proj PROJ] [--cmap CMAP] [--output OUTPUT] [--time TIME]
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207 [--format FORMAT] [--title TITLE] [--ncol NCOL] [--nrow NROW] [-l] [-v] input varname
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208
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209
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210 Positional arguments:
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211 ~~~~~~~~~~~~~~~~~~~~~
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212
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213 - **input**: input filename with geographical coordinates (netCDF format)
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214 - **varname**: specify which variable to plot (case sensitive)
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215
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216 Optional arguments:
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217 ~~~~~~~~~~~~~~~~~~~~~
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218
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219 -h, --help show this help message and exit
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220 -l, --logscale log scale the data
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221 --proj PROJ specify the projection on which we draw
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222 --cmap CMAP specify which colormap to use for plotting
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223 --output OUTPUT output filename to store resulting image (png format)
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224 -v, --verbose switch on verbose mode
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225 --time TIME list of times to plot for multiple plots
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226 --format FORMAT format for date/time (default is Month d, yyyy)
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227 --title TITLE plot title
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228 --ncol NCOL number of columns for multiple plots
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229 --nrow NROW number of rows for multiple plots
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230
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231 It uses psy-maps, a python package to generate plots. More information about
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232 psyplot and psy-maps can be found at https://psyplot.readthedocs.io/projects/psy-maps/en/latest/
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233
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234 ]]></help>
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235 <citations>
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236 <citation type="doi">10.21105/joss.00363</citation>
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237 </citations>
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238 </tool>