Mercurial > repos > ecology > xarray_mapplot

annotate xarray_mapplot.xml @ 2:adc0367f7cb1 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
author ecology
date Sun, 31 Jul 2022 21:17:52 +0000
parents 65621a6c85e9
children
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65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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1 <tool id="xarray_mapplot" name="NetCDF xarray map plotting" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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2 <description>Visualize netCDF variables on a geographical map</description>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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3 <macros>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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4 <import>macros.xml</import>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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5 <import>macros_mapplot.xml</import>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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6 </macros>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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7 <expand macro="edam_ontology"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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8 <requirements>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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9 <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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10 <requirement type="package" version="3">python</requirement>
2
adc0367f7cb1 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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11 <requirement type="package" version="1.6.0">netcdf4</requirement>
adc0367f7cb1 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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12 <requirement type="package" version="0.20.3">cartopy</requirement>
adc0367f7cb1 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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13 <requirement type="package" version="3.5.2">matplotlib</requirement>
adc0367f7cb1 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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14 <requirement type="package" version="1.4">cmcrameri</requirement>
adc0367f7cb1 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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15 <requirement type="package" version="2022.7.0">dask</requirement>
1
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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16 </requirements>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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17 <command detect_errors="exit_code"><![CDATA[
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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18 mkdir output_dir &&
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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19 mkdir -p `pwd`/mlp_tmpdir &&
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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20 MPLCONFIGDIR=`pwd`/mlp_tmpdir &&
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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21 echo "Galaxy xarray version @TOOL_VERSION@" > $version &&
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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22 python '$__tool_directory__/xarray_mapplot.py' '$input' '$var'
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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23 --config '$map_customization' --proj '$map_projection'
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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24 #if $shift
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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25 --shift
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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26 #end if
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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27 --output plot.png
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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28 --verbose &&
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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29 mv *.png output_dir
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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30 ]]></command>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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31 <expand macro="config_map"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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32 <inputs>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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33 <param type="data" name="input" label="Input netcdf file" format="netcdf"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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34 <param type="data" label="Tabular of variables" name="var_tab" format="tabular" help="Select the tabular file which summarize the available variables and dimensions."/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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35 <param name="var" type="select" label="Choose the variable to plot">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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36 <options from_dataset="var_tab">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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37 <column name="name" index="0"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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38 <column name="value" index="0"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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39 </options>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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40 </param>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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41 <param name="lat_dim" type="select" label="Name of latitude coordinate" >
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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42 <options from_dataset="var_tab">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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43 <column name="value" index="0"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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44 </options>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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45 </param>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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46 <param name="lon_dim" type="select" label="Name of longitude coordinate" >
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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47 <options from_dataset="var_tab">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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48 <column name="value" index="0"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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49 </options>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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50 </param>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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51 <conditional name="condi_datetime">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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52 <param name="datetime" type="select" label="Datetime selection" help="Use this option when your dataset contains multiple times/dates">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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53 <option value="no">No</option>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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54 <option value="yes">Yes</option>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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55 </param>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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56 <when value="no"></when>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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57 <when value="yes">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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58 <param type="data" label="Tabular of time values" name="time_tab" format="tabular" help="File containing time values."/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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59 <param name="time_values" type="select" multiple="true" label="Choose the times to plot">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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60 <options from_dataset="time_tab">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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61 <column name="name" index="1"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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62 <column name="value" index="0"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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63 </options>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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64 </param>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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65 </when>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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66 </conditional>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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67 <param name="xlim" type="text" optional="true" label="longitudes values 'lonW,lonE' for limited geographical area (optional and only available with some projections)" />
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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68 <param name="ylim" type="text" value="" optional="true" label="latitudes values 'latS,latN' for limited geographical area (optional and only available with some projections)" />
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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69 <param name="shift" type="select" display="radio" label="Shift longitudes [0,360] --> [-180,180]">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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70 <option value="" selected="true">No</option>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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71 <option value="Yes">Yes</option>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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72 </param>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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73 <param name="range" type="text" optional="true" label="Range of values for plotting e.g. minimum value and maximum value (minval,maxval) (optional)" />
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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74 <param name="threshold" type="float" optional="true" label="Do not plot values below this threshold (optional)" />
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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75 <expand macro="customize_appearance_plots" />
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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76 <param name="proj" type="text" optional="true" label='Specify the projection (proj4) on which we draw e.g. {"proj":"PlateCarree"} with double quote (optional)'>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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77 <sanitizer>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
78 <valid initial="string.ascii_letters,string.digits,string.punctuation,string.whitespace">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
79 <add value="{" />
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
80 <add value="}" />
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
81 </valid>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
82 </sanitizer>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
83 </param>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
84
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
85 </inputs>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
86 <outputs>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
87 <data name="version" format="tabular" label="Tool version"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
88 <collection type="list" name="output_dir" label="Map plots">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
89 <discover_datasets pattern="__name_and_ext__" directory="output_dir"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
90 </collection>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
91 </outputs>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
92 <tests>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
93 <test>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
94 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
95 <param name="var" value="nh4"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
96 <param name="var_tab" value="var_tab_dataset-ibi"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
97 <param name="lat_dim" value="latitude"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
98 <param name="lon_dim" value="longitude"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
99 <conditional name="condi_datetime">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
100 <param name="datetime" value="yes"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
101 <param name="time_tab" value="time.tabular"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
102 <param name="time_values" value="50"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
103 </conditional>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
104 <param name="cmap" value="cm.devon_r"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
105 <param name="proj" value='{"proj":"PlateCarree"}'/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
106 <param name="land" value="0.1"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
107 <param name="ocean" value="0.1"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
108 <param name="coastline" value="0.2"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
109 <param name="borders" value="0.5"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
110 <output_collection name="output_dir" type="list" count="1">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
111 <element name="plot_time50" ftype='png' file="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time50.png"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
112 </output_collection>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
113 <output name="version" ftype='tabular' file="version.tabular"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
114 </test>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
115 <test>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
116 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
117 <param name="var" value="chl"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
118 <param name="var_tab" value="var_tab_dataset-ibi"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
119 <param name="lat_dim" value="latitude"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
120 <param name="lon_dim" value="longitude"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
121 <conditional name="condi_datetime">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
122 <param name="datetime" value="yes"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
123 <param name="time_tab" value="time.tabular"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
124 <param name="time_values" value="0,1"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
125 </conditional>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
126 <param name="cmap" value="Greens"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
127 <param name="proj" value='{"proj":"PlateCarree"}'/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
128 <param name="land" value="0.1"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
129 <param name="ocean" value="0.1"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
130 <param name="coastline" value="0.2"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
131 <param name="borders" value="0.5"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
132 <output_collection name="output_dir" type="list" count="2">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
133 <element name="plot_time0" ftype="png" file="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time0.png"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
134 <element name="plot_time1" ftype="png" file="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time1.png"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
135 </output_collection>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
136 <output name="version" ftype="tabular" file="version.tabular"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
137 </test>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
138 <test>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
139 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
140 <param name="var" value="chl"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
141 <param name="var_tab" value="var_tab_dataset-ibi"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
142 <param name="lat_dim" value="latitude"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
143 <param name="lon_dim" value="longitude"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
144 <conditional name="condi_datetime">
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
145 <param name="datetime" value="yes"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
146 <param name="time_tab" value="time.tabular"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
147 <param name="time_values" value="0"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
148 </conditional>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
149 <param name="cmap" value="vik_r"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
150 <param name="proj" value='{"proj":"EquidistantConic", "central_longitude": 20.0, "central_latitude": 70.0 }'/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
151 <param name="land" value="0.1"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
152 <param name="ocean" value="0.1"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
153 <param name="coastline" value="0.2"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
154 <param name="borders" value="0.5"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
155 <param name="title" value="Xarray map test"/>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
156 <param name="colorbar_label" value="My personal label (X)" />
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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157 <output_collection name="output_dir" type="list" count="1">
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158 <element name="plot_time0" ftype="png" file="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time0_title.png"/>
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159 </output_collection>
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160 <output name="version" ftype="tabular" file="version.tabular"/>
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161 </test>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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162 </tests>
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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163 <help><![CDATA[
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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164 **What it does**
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165
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166 This tool plots a variable on a geographical map. It must be a 2D variable (latitude, longitude) and eventually with
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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167 and additional time dimension (specific time to plot should then be selected).
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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168
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169 The appearance of plots can be customized with options as well at the projection.
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170 The projection needs to be given as a PROJ dictionary such as:
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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171 - {"proj":"EquidistantConic", "central_longitude": 20.0, "central_latitude": 70.0 }
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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172 - {"proj":"AlbersEqualArea", "central_longitude": 20.0, "central_latitude": 70.0 }
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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173 - {"proj":"EuroPP"}
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174
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175 The output is a collection of plots (png format); one per selected times.
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176
65621a6c85e9 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
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177 -------------------------------------------------
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178
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179 The xarray select tool can be used after the xarray Info and xarray coord.
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180 ]]></help>
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181 <expand macro="citations"/>
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182 </tool>