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comparison xarray_mapplot.xml @ 1:dc05bf0af58f draft

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"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
author ecology
date Thu, 20 Jan 2022 17:09:04 +0000
parents d7479b6dfbe8
children 506b6d6880ff
comparison
equal deleted inserted replaced
0:d7479b6dfbe8 1:dc05bf0af58f
1 <tool id="xarray_mapplot" name="NetCDF xarray map plotting" profile="20.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="xarray_mapplot" name="NetCDF xarray map plotting" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Visualize netCDF variables on a geographical map</description> 2 <description>Visualize netCDF variables on a geographical map</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <import>macros_mapplot.xml</import>
5 </macros> 6 </macros>
6 <expand macro="edam_ontology"/> 7 <expand macro="edam_ontology"/>
7 <requirements> 8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
8 <requirement type="package" version="3">python</requirement> 10 <requirement type="package" version="3">python</requirement>
9 <requirement type="package" version="1.5.6">netcdf4</requirement> 11 <requirement type="package" version="1.5.6">netcdf4</requirement>
10 <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
11 <requirement type="package" version="0.19.0">cartopy</requirement> 12 <requirement type="package" version="0.19.0">cartopy</requirement>
12 <requirement type="package" version="3.4.2">matplotlib</requirement> 13 <requirement type="package" version="3.4.2">matplotlib</requirement>
13 <requirement type="package" version="1.2">cmcrameri</requirement> 14 <requirement type="package" version="1.2">cmcrameri</requirement>
15 <requirement type="package" version="2021.12.0">dask</requirement>
14 </requirements> 16 </requirements>
15 <command detect_errors="exit_code"><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
16 mkdir output_dir && 18 mkdir output_dir &&
17 mkdir -p `pwd`/mlp_tmpdir && 19 mkdir -p `pwd`/mlp_tmpdir &&
18 MPLCONFIGDIR=`pwd`/mlp_tmpdir && 20 MPLCONFIGDIR=`pwd`/mlp_tmpdir &&
19 echo "Galaxy xarray version @TOOL_VERSION@" > $version && 21 echo "Galaxy xarray version @TOOL_VERSION@" > $version &&
20 python '$__tool_directory__/xarray_mapplot.py' '$input' '$var' 22 python '$__tool_directory__/xarray_mapplot.py' '$input' '$var'
21 #if $condi_datetime.datetime=="yes" 23 --config '$map_customization' --proj '$map_projection'
22 --time="$condi_datetime.time_values"
23 #end if
24 --latitude='$lat_dim'
25 --longitude='$lon_dim'
26 #if $colorbar_label
27 --label='$colorbar_label'
28 #end if
29 #if $title
30 --title=$title
31 #end if
32 #if $cmap
33 --cmap='$cmap'
34 #end if
35 #if $proj
36 --proj='$proj'
37 #end if
38 #if $land
39 --land='$land'
40 #end if
41 #if $ocean
42 --ocean='$ocean'
43 #end if
44 #if $coastline
45 --coastline='$coastline'
46 #end if
47 #if $borders
48 --borders='$borders'
49 #end if
50 #if $threshold
51 --threshold='$threshold'
52 #end if
53 #if $range
54 --range='$range'
55 #end if
56 #if $xlim
57 --xlim='$xlim'
58 #end if
59 #if $ylim
60 --ylim='$ylim'
61 #end if
62 #if $shift 24 #if $shift
63 --shift 25 --shift
64 #end if 26 #end if
65 --output plot.png 27 --output plot.png
66 --verbose && 28 --verbose &&
67 mv *.png output_dir 29 mv *.png output_dir
68 ]]></command> 30 ]]></command>
31 <expand macro="config_map"/>
69 <inputs> 32 <inputs>
70 <param type="data" name="input" label="Input netcdf file" format="netcdf"/> 33 <param type="data" name="input" label="Input netcdf file" format="netcdf"/>
71 <param type="data" label="Tabular of variables" name="var_tab" format="tabular" help="Select the tabular file which summarize the available variables and dimensions."/> 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."/>
72 <param name="var" type="select" label="Choose the variable to plot"> 35 <param name="var" type="select" label="Choose the variable to plot">
73 <options from_dataset="var_tab"> 36 <options from_dataset="var_tab">
101 </param> 64 </param>
102 </when> 65 </when>
103 </conditional> 66 </conditional>
104 <param name="xlim" type="text" optional="true" label="longitudes values 'lonW,lonE' for limited geographical area (optional and only available with some projections)" /> 67 <param name="xlim" type="text" optional="true" label="longitudes values 'lonW,lonE' for limited geographical area (optional and only available with some projections)" />
105 <param name="ylim" type="text" value="" optional="true" label="latitudes values 'latS,latN' for limited geographical area (optional and only available with some projections)" /> 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)" />
106 <param name="shift" type="select" optional="true" display="radio" label="Shift longitudes [0,360] --> [-180,180]"> 69 <param name="shift" type="select" display="radio" label="Shift longitudes [0,360] --> [-180,180]">
107 <option value="" selected="true">No</option> 70 <option value="" selected="true">No</option>
108 <option value="Yes">Yes</option> 71 <option value="Yes">Yes</option>
109 </param> 72 </param>
110 <param name="range" type="text" optional="true" label="Range of values for plotting e.g. minimum value abd maximum value (minval,maxval) (optional)" /> 73 <param name="range" type="text" optional="true" label="Range of values for plotting e.g. minimum value and maximum value (minval,maxval) (optional)" />
111 <param name="threshold" type="float" optional="true" label="Do not plot values below this threshold (optional)" /> 74 <param name="threshold" type="float" optional="true" label="Do not plot values below this threshold (optional)" />
112 <expand macro="customize_appearance_plots" /> 75 <expand macro="customize_appearance_plots" />
113 <param name="proj" type="text" optional="true" label='Specify the projection (proj4) on which we draw e.g. {"proj":"PlateCarree"} with double quote (optional)'> 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)'>
114 <sanitizer> 77 <sanitizer>
115 <valid initial="string.ascii_letters,string.digits,string.punctuation,string.whitespace"> 78 <valid initial="string.ascii_letters,string.digits,string.punctuation,string.whitespace">
170 <element name="plot_time0" ftype="png" file="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time0.png"/> 133 <element name="plot_time0" ftype="png" file="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time0.png"/>
171 <element name="plot_time1" ftype="png" file="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time1.png"/> 134 <element name="plot_time1" ftype="png" file="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time1.png"/>
172 </output_collection> 135 </output_collection>
173 <output name="version" ftype="tabular" file="version.tabular"/> 136 <output name="version" ftype="tabular" file="version.tabular"/>
174 </test> 137 </test>
138 <test>
139 <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
140 <param name="var" value="chl"/>
141 <param name="var_tab" value="var_tab_dataset-ibi"/>
142 <param name="lat_dim" value="latitude"/>
143 <param name="lon_dim" value="longitude"/>
144 <conditional name="condi_datetime">
145 <param name="datetime" value="yes"/>
146 <param name="time_tab" value="time.tabular"/>
147 <param name="time_values" value="0"/>
148 </conditional>
149 <param name="cmap" value="vik_r"/>
150 <param name="proj" value='{"proj":"EquidistantConic", "central_longitude": 20.0, "central_latitude": 70.0 }'/>
151 <param name="land" value="0.1"/>
152 <param name="ocean" value="0.1"/>
153 <param name="coastline" value="0.2"/>
154 <param name="borders" value="0.5"/>
155 <param name="title" value="Xarray map test"/>
156 <param name="colorbar_label" value="My personal label (X)" />
157 <output_collection name="output_dir" type="list" count="1">
158 <element name="plot_time0" ftype="png" file="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time0_title.png"/>
159 </output_collection>
160 <output name="version" ftype="tabular" file="version.tabular"/>
161 </test>
175 </tests> 162 </tests>
176 <help><![CDATA[ 163 <help><![CDATA[
177 **What it does** 164 **What it does**
178 165
179 This tool plots a variable on a geographical map. It must be a 2D variable (latitude, longitude) and eventually with 166 This tool plots a variable on a geographical map. It must be a 2D variable (latitude, longitude) and eventually with