Mercurial > repos > climate > mean_per_zone

annotate mean-per-zone.xml @ 1:4bb2f6091660 draft default tip

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planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit a5d176b7d0dc81bae07569d396edced43cfa2702
author climate
date Mon, 24 Jun 2019 02:41:30 -0400
parents 4f14b5b97262
children
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4bb2f6091660 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit a5d176b7d0dc81bae07569d396edced43cfa2702
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1 <tool id="mean_per_zone" name="zonal statistics" version="0.2.0">
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2 <description>over each area</description>
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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="0.13.1">rasterstats</requirement>
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6 <requirement type="package" version="0.4.1">geopandas</requirement>
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7 <requirement type="package" version="0.11.3">xarray</requirement>
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8 <requirement type="package" version="1.5.1.2">netcdf4</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 python3 '$__tool_directory__/zonal_statistics.py'
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12 '$ifilename'
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13 '$shapefile.extra_files_path'
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14 '$variable'
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15 '$ofilename'
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16 --stat '$stat_type'
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17 #if str($title).strip() != ''
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18 --title '$title'
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19 #end if
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20 ]]></command>
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21 <inputs>
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22 <param name="ifilename" type="data" format="netcdf,h5" label="input with geographical coordinates (netCDF format)"/>
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23 <param name="shapefile" type="data" format="shp" label="shapefile (shp) with polygons for which statistics will be computed"/>
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24 <!--param name="name" type="text" value="" label="Shapefile name" /-->
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25 <param name="variable" type="text" value="TS" label="variable name as given in the netCDF file" />
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26 <param name="title" type="text" value="" label="Title of the generated plot" />
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27 <param name="stat_type" type="select">
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28 <option value="min">minimum</option>
4bb2f6091660 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit a5d176b7d0dc81bae07569d396edced43cfa2702
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29 <option value="max">maximum</option>
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30 <option value="mean" selected="true">mean</option>
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31 <option value="count">count</option>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data name="ofilename" format="png"></data>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.180.nc" />
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40 <param name="variable" value="TS" />
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41 <param name="title" value="Mean Surface Temperature per country" />
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42 <param name="shapefile" value="TM_WORLD_BORDERS_SIMPL-0.3.html" ftype="shp" >
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43 <composite_data value="TM_WORLD_BORDERS_SIMPL-0.3/TM_WORLD_BORDERS_SIMPL-0.3.shp"/>
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44 <composite_data value="TM_WORLD_BORDERS_SIMPL-0.3/TM_WORLD_BORDERS_SIMPL-0.3.shx"/>
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45 <composite_data value="TM_WORLD_BORDERS_SIMPL-0.3/TM_WORLD_BORDERS_SIMPL-0.3.dbf"/>
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46 <composite_data value="TM_WORLD_BORDERS_SIMPL-0.3/TM_WORLD_BORDERS_SIMPL-0.3.prj"/>
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47 </param>
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48 <!--param name="name" value="TM_WORLD_BORDERS_SIMPL-0.3" /-->
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49 <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12.180.png" compare="sim_size" delta="1500"/>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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53
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54 **Plot statistics**
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55 ================================================
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56
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57 This tool wraps the functionality of ``zonal-statistics.py``.
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58
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59
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60 .. class:: infomark
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61
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62 The wrapper aims at providing a utility to extract information
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63 from geospatial raster data based on vector geometries (shapefile).
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64 The raster input file must be in netCDF format with geographical coordinates
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65 (latitudes, longitudes) with the same coordinate reference system as the
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66 shapefile.
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67
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68 **What it does**
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69 ----------------
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70
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71 This tools creates a png image showing statistic over areas as defined in the
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72 vector file.
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74 **Usage**
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76 ::
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78 usage: zonal-statistics.py [-h] [-v] [-t] raster vector variable output
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81 Positional arguments:
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82 ~~~~~~~~~~~~~~~~~~~~~
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83
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84 - **raster**: input raster filename with geographical coordinates (netCDF format)
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85 - **vector**: input shapefile filename with polygons
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86 - **variable**: variable used from raster file to compute statistics
4f14b5b97262 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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87 - **output**: output filename for png file containing the resulting plot.
4f14b5b97262 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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88
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89 Optional arguments:
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90 ~~~~~~~~~~~~~~~~~~~~~
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91
4f14b5b97262 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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92 -h, --help show this help message and exit
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93 -v, --verbose switch on verbose mode
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94 -t, --type statistic type [min, max, mean, count]
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95
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96 It uses ``rasterstats`` python package to compute zonal statistics.
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97 More information about ``rasterstats`` can be found at https://pythonhosted.org/rasterstats
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98
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99 ]]></help>
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100 <citations>
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101 </citations>
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102 </tool>