Mercurial > repos > climate > psy_maps

annotate 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
parents
children 706666d912d5
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0
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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1 <tool id="psy_maps" name="map plot" version="1.2.0">
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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2 <description>gridded (lat/lon) netCDF data</description>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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3 <requirements>
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4 <requirement type="package" version="3">python</requirement>
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5 <requirement type="package" version="1.2.0">psy-maps</requirement>
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6 <requirement type="package" version="1.2.0">psy-reg</requirement>
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7 <requirement type="package" version="1.2.2">psyplot-gui</requirement>
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8 <requirement type="package" version="1.4.1">netcdf4</requirement>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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11 python3 '$__tool_directory__/psymap_simple.py'
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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12 '$ifilename' '$variable'
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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13 --proj '$adv.projection'
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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14 --cmap '$adv.colormap'
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15 --output image.png
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16 ]]></command>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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17 <inputs>
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18 <param name="ifilename" type="data" format="netcdf" label="input with geographical coordinates (netCDF format)"></param>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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19 <param name="variable" type="text" value="TS" label="variable name as given in the netCDF file" />
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20 <section name="adv" title="Advanced Options" expanded="false">
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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21 <param name="projection" type="select">
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22 <option value="" selected="true">PlateCarree</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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23 <option value="robin">Robinson</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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24 <option value="moll">Mollweide</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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25 <option value="geo">Geostationary</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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26 <option value="northpole">NorthPolarStereo</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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27 <option value="southpole">SouthPolarStereo</option>
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28 <option value="ortho">Orthographic</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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29 <option value="stereo">Stereographic</option>
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30 <option value="near">NearsidePerspective</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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31 </param>
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32 <param name="colormap" type="select">
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33 <option value="Accent">Accent</option>
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34 <option value="Blues">Blues</option>
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35 <option value="BrBG">BrBG</option>
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36 <option value="BuGn">BuGn</option>
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37 <option value="BuPu">BuPu</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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38 <option value="CMRmap">CMRmap</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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39 <option value="Dark2">Dark2</option>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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40 <option value="GnBu">GnBu</option>
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41 <option value="Greens">Greens</option>
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42 <option value="Greys">Greys</option>
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43 <option value="OrRd">OrRd</option>
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44 <option value="Oranges">Oranges</option>
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45 <option value="PRGn">PRGn</option>
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46 <option value="Paired">Paired</option>
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47 <option value="Pastel1">Pastel1</option>
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48 <option value="Pastel2">Pastel2</option>
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49 <option value="PiYG">PiYG</option>
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50 <option value="PuBu">PuBu</option>
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51 <option value="PuBuGn">PuBuGn</option>
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52 <option value="PuOr">PuOr</option>
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53 <option value="PuRd">PuRd</option>
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54 <option value="Purples">Purples</option>
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55 <option value="RdBu">RdBu</option>
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56 <option value="RdGy">RdGy</option>
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57 <option value="RdPu">RdPu</option>
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58 <option value="RdYlBu">RdYlBu</option>
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59 <option value="RdYlGn">RdYlGn</option>
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60 <option value="Reds">Reds</option>
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61 <option value="Set1">Set1</option>
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62 <option value="Set2">Set2</option>
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63 <option value="Set3">Set3</option>
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64 <option value="Spectral">Spectral</option>
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65 <option value="Wistia">Wistia</option>
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66 <option value="YlGn">YlGn</option>
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67 <option value="YlGnBu">YlGnBu</option>
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68 <option value="YlOrBr">YlOrBr</option>
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69 <option value="YlOrRd">YlOrRd</option>
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70 <option value="afmhot">afmhot</option>
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71 <option value="autumn">autumn</option>
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72 <option value="binary">binary</option>
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73 <option value="bone">bone</option>
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74 <option value="brg">brg</option>
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75 <option value="bwr">bwr</option>
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76 <option value="cool">cool</option>
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77 <option value="coolwarm">coolwarm</option>
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78 <option value="copper">copper</option>
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79 <option value="cubehelix">cubehelix</option>
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80 <option value="flag">flag</option>
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81 <option value="gist_earth">gist_earth</option>
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82 <option value="gist_gray">gist_gray</option>
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83 <option value="gist_heat">gist_heat</option>
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84 <option value="gist_ncar">gist_ncar</option>
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85 <option value="gist_rainbow">gist_rainbow</option>
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86 <option value="gist_stern">gist_stern</option>
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87 <option value="gist_yarg">gist_yarg</option>
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88 <option value="gnuplot">gnuplot</option>
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89 <option value="gnuplot2">gnuplot2</option>
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90 <option value="gray">gray</option>
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91 <option value="hot">hot</option>
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92 <option value="hsv">hsv</option>
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93 <option value="jet" selected="true">jet</option>
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94 <option value="nipy_spectral">nipy_spectral</option>
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95 <option value="ocean">ocean</option>
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96 <option value="pink">pink</option>
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97 <option value="prism">prism</option>
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98 <option value="rainbow">rainbow</option>
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99 <option value="seismic">seismic</option>
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100 <option value="spring">spring</option>
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101 <option value="summer">summer</option>
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102 <option value="tab10">tab10</option>
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103 <option value="tab20">tab20</option>
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104 <option value="tab20b">tab20b</option>
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105 <option value="tab20c">tab20c</option>
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106 <option value="terrain">terrain</option>
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107 <option value="winter">winter</option>
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108 </param>
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109 </section>
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110 </inputs>
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111 <outputs>
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112 <data name="ofilename" format="png" from_work_dir="image.png"/>
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113 </outputs>
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114 <tests>
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115 <test>
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116 <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" />
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117 <param name="variable" value="TS" />
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118 <param name="adv.projection" value="" />
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119 <param name="adv.colormap" value="jet" />
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120 <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12.png" compare="sim_size" delta="500"/>
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121 </test>
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122 <test>
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123 <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" />
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124 <param name="variable" value="TS" />
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125 <param name="adv.projection" value="ortho" />
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126 <param name="adv.colormap" value="jet" />
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127 <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12.png" compare="sim_size" delta="500"/>
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128 </test>
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129 </tests>
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130 <help><![CDATA[
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131
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132 **Visualization on a map with psyplot**
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133 =========================================
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134
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135 This tool wraps the functionality of ``psyplot.plot.mapplot``.
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136
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137
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138 .. class:: infomark
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139
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140 The wrappers aims at providing the same functionality as ``psyplot.plot.mapplot`` but it has some limitations.
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141 The input file must be in netCDF format and must contain 2D arrays with geographical coordinatates
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142 (latitudes, longitudes) given in degrees.
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143 TODO: Fill in help.
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144
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145 **What it does**
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146 ----------------
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147
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148 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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149 netCDF file (input file). By default, the projection is ``PlateCarree`` and colormap is ``jet``. These settings can be changed in *Advanced settings*.
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150
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151
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152 **Usage**
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153
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154 ::
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155
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156 usage: psymap_simple.py [-h] [--proj PROJ] [--cmap CMAP] [--output OUTPUT] [-v] input varname
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157
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158
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159 Positional arguments:
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160 ~~~~~~~~~~~~~~~~~~~~~
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161
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162 - **input**: input filename with geographical coordinates (netCDF format)
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163 - **varname**: Specify which variable to plot (case sensitive)
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164
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165 Optional arguments:
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166 ~~~~~~~~~~~~~~~~~~~~~
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167
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168 -h, --help show this help message and exit
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169 --proj PROJ Specify the projection on which we draw
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170 --cmap CMAP Specify which colormap to use for plotting
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171 --output OUTPUT output filename to store resulting image (png format)
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172 -v, --verbose switch on verbose mode
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173
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174 It uses psy-maps, a python package to generate plots. More information about
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175 psyplot and psy-maps can be found at https://psyplot.readthedocs.io/projects/psy-maps/en/latest/
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176
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177 ]]></help>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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178 <citations>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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179 </citations>
db8d76da4174 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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180 </tool>