Mercurial > repos > ecology > srs_global_indices

annotate biodiv_indices_global.xml @ 0:8963cac500ac draft default tip

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planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
author ecology
date Mon, 09 Jan 2023 13:53:55 +0000
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8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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1 <tool id="srs_global_indices" name="Compute biodiversity indices" version="@VERSION@" profile = "20.01">
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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2 <description>from remote sensing data</description>
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3 <macros>
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4 <import>macro.xml</import>
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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5 </macros>
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6 <requirements>
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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7 <requirement type="package" version="4.2.2">r-base</requirement>
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8 <requirement type="package" version="3.5_21">r-raster</requirement>
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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9 <requirement type="package" version="1.5_32">r-rgdal</requirement>
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10 <requirement type="package" version="1.5_1">r-sp</requirement>
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11 <requirement type="package" version="0.3.1">r-rasterdiv</requirement>
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12 <requirement type="package" version="3.4.0">r-ggplot2</requirement>
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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13 <!--requirement type="package" version="1.5_21">r-terra</requirement-->
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14 </requirements>
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15 <command detect_errors="exit_code"><![CDATA[
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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16 #import re
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17 #if $method.type == 'envi_bil':
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18 #set input_raster = $method.input_raster
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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19 #set input_raster_identifier = re.sub('[^\s\w\-]', '_', str($input_raster.element_identifier))
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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20 #set input_header = $method.input_header
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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21 #set input_header_identifier = re.sub('[^\s\w\-]+[^.hdr]', '_', str($input_header.element_identifier))
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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22 cp '${input_raster}' '${input_raster_identifier}' &&
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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23 cp '${input_header}' '${input_header_identifier}' &&
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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24 #end if
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25 Rscript
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26 '$__tool_directory__/biodiv_indices_global.r'
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27 #if $method.type == 'envi_bil':
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28 '$input_raster_identifier'
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29 '$input_header_identifier'
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30 ''
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31 #else:
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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32 ''
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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33 ''
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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34 '$method.input'
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35 #end if
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36 '$alpha'
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37 '$__tool_directory__/functions.r'
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38 '$output_indices'
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39 '$plots_png'
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40 ]]>
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41 </command>
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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42 <inputs>
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43 <conditional name="method">
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44 <param name="type" type="select" label="In which format are your data ?">
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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45 <option value="zipper">The data you are using are in a zip folder Reflectance</option>
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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46 <option value="envi_bil">Your already have the files in ENVI BIL format</option>
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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47 </param>
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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48 <when value="zipper">
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49 <param name="input" type="data" format="zip" multiple="true" label="Input data"/>
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50 </when>
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51 <when value="envi_bil">
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52 <param name="input_raster" type="data" format="bil" label="Input raster" help="It can be the raw data in bil or the PCA raster layer in bil"/>
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53 <param name="input_header" type="data" format="hdr" label="Input header"/>
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54 </when>
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55 </conditional>
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56 <param name="alpha" type="text" label="Write a number of the value of alpha you want to calculate Renyi, Prao and Hill indicators (between 0 and 5)"/>
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57 </inputs>
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58 <outputs>
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59 <data name="output_indices" from_work_dir="BiodivIndex.tabular" format="tabular" label="Biodiversity indices tabular">
8963cac500ac planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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60 </data>
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61 <collection type="list" name="plots_png" label="Biodiversity indices plots">
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62 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
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63 </collection>
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="type" value="envi_bil"/>
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68 <param name="input_raster" value="S2A_Subset"/>
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69 <param name="input_header" value="S2A_Subset.hdr"/>
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70 <param name="alpha" value="1"/>
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71 <output name="output_indices">
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72 <assert_contents>
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73 <has_n_lines n="2501"/>
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74 </assert_contents>
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75 </output>
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76 <output_collection name="plots_png" type="list" count="7"/>
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77 </test>
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78 </tests>
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79 <help><![CDATA[
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80 =========================================================================
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81 Computes global biodiversity indices from satellite remote sensing data
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82 =========================================================================
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83
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84
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85 **What it does**
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86
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87 This tool aims to provide functions to apply Information Theory based diversity indexes on RasterLayer such as Shannon's entropy or Cumulative Residual Entropy (CRE).
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88
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89
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90 **Input description**
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91
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92 It expects an image file as input, with a specific data format. ENVI HDR image with BIL interleave required.
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93 The image is an ENVI raster including :
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94
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95 - A binary file (which has no extension here).
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96
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97 - A header file (with .hdr extension).
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98
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99 The header file is a text file including all necessary metadata which can be read with a text editor. It includes image dimensions, projection, and the name and central wavelength for each spectral band.
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100
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101 In order to get such input we advise to use the tool preprocessing sentinel 2 data. If you did so you can directly enter the "Reflectance" output from this tool and thus select the otpion "The data you are using are in a zip folder Reflectance".
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102
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103 ⚠️ If you do not use this Reflectance folder make sure that your data are respectively in bil and hdr format in the datatypes.
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104
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105 - A number for the alpha indice which used to calculate the following indicators : Renyi, Hill and Prao.
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106
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107 +--------------+----------+---------------+
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108 | BIL | ENVI HDR | Number alpha |
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109 +==============+==========+===============+
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110 | raster stack | Metadata | 1 |
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111 +--------------+----------+---------------+
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112 | ... | ... | ... |
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113 +--------------+----------+---------------+
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114
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115 **Output**
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116
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117 - One tabular with 9 columns longitude, latitude columns and one for each indices.
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118
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119 - Seven png graph one for each indices.
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120
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121 ]]> </help>
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122 <expand macro="SRS_rasterdivref"/>
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123 </tool>