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1 <tool id="srs_preprocess_s2" name="Preprocess sentinel 2 data" version="@VERSION@" profile="20.01">
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2 <description>read, crop, resample and write it as a raster stack</description>
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3 <macros>
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4 <import>macro.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="4.2.2">r-base</requirement>
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8 <requirement type="package" version="1.0_7">r-sf</requirement>
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9 <requirement type="package" version="0.6_1">r-rgeos</requirement>
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10 <requirement type="package" version="0.5_5">r-stars</requirement>
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11 <requirement type="package" version="1.5.0">r-stringr</requirement>
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12 <requirement type="package" version="1.2.3">r-jqr</requirement>
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13 <requirement type="package" version="2.1.3">r-protolite</requirement>
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14 <requirement type="package" version="1.5.3">r-sen2r</requirement>
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15 <requirement type="package" version="1.2.2">r-progress</requirement>
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16 <requirement type="package" version="2.0.3">r-gdalutils</requirement>
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17 <requirement type="package" version="1.0.4">r-fasterize</requirement>
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18 <requirement type="package" version="3.99_0.13">r-xml</requirement>
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19 <requirement type="package" version="1.3.3">r-xml2</requirement>
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20 <requirement type="package" version="2.2.2">r-zip</requirement>
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21 </requirements>
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22 <command detect_errors="exit_code"><![CDATA[
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23 Rscript
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24 '$__tool_directory__/preprocess_S2.r'
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25 '$input'
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26 '$__tool_directory__/Lib_preprocess_S2.r'
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27 '$source_s2'
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28 '$type_s2'
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29 '$output'
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30 '$output_refl'
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31 '$output_cloud'
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32 ]]>
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33 </command>
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34 <inputs>
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35 <param name="input" type="data" format="zip" multiple="true" label="Input data"/>
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36 <param name="source_s2" type="select" label="Where does your data come from ?">
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37 <option value="SAFE">From Scihub or Peps</option>
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38 <option value="THEIA">From Theia</option>
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39 </param>
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40 <param name="type_s2" type="select" label="From which satellite are the data ?">
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41 <option value="2A">Sentinel 2A</option>
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42 <option value="2B">Sentinel 2B</option>
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43 </param>
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44 </inputs>
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45 <outputs>
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46 <data name="output" from_work_dir="Mission.csv" format="csv" label="Mission source"/>
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47 <data name="output_refl" from_work_dir="Refl.zip" format="zip" label="Reflectance"/>
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48 <data name="output_cloud" from_work_dir="Cloud.zip" format="zip" label="Cloud Mask"/>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="input" value="S2A_MSIL2A_20200306T015621_N0214_R117_T51JXN_20200306T034744.zip"/>
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53 <param name="source_s2" value="SAFE"/>
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54 <param name="type_s2" value="2A"/>
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55 <output name="output" value="Mission.csv"/>
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56 <output name="output_refl">
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57 <assert_contents>
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58 <has_size value="12923807" delta="100"/>
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59 </assert_contents>
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60 </output>
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61 <output name="output_cloud">
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62 <assert_contents>
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63 <has_size value="235912" delta="100"/>
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64 </assert_contents>
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65 </output>
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66 </test>
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67 </tests>
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68 <help><![CDATA[
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69 ==========================
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70 Preprocess Sentinel 2 data
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71 ==========================
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72
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73
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74 **What it does**
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75
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76 The goal of this tool (using the package preprocS2) is to provide a common framework for the preprocessing of Level-2A Sentinel-2 images (does not work yet for Level 1C).
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77 Sentinel-2 L2A images can be produced or obtained from various data hubs or atmospheric correction methods. PreprocS2 provides a unique function to read, crop, resample the original image directory, and write it as a raster stack.
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78
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79 **Input description**
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80
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81 A zip folder with Sentinel 2 data.
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82 These data can be dowloaded on 3 different platforms:
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83
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84 - Copernicus Open Access Hub, Scihub, which provides complete, free and open access to Sentinel-2 data : https://scihub.copernicus.eu/dhus/#/home
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85
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86 - PEPS, la 'Plateforme d'Exploitation de Produits Sentinel' : https://peps.cnes.fr/rocket/#/search
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87
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88 - Theia : https://theia.cnes.fr/atdistrib/rocket/#/search
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89
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90 For each of those 3 platforms you will need to create an account.
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91
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92 You need to select from where you dowloaded your data in order for the tool to know the format of the folder once it unzips it.
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93
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94 +----------+----------+
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95 | ZIP | Source |
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96 +==========+==========+
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97 |folder.zip|Character |
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98 +----------+----------+
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99 | ... | ... |
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100 +----------+----------+
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101
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102 **Output**
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103
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104 A zip folder containing the refelctance data with a raster stack pile in BIL format (no extension), a header with the metadata (.hdr extension) and 2 other files in .xml.
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105
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106 A zip folder containing the cloud mask with the 2 files for the raw data (.RAW) and 2 files containing the metadata (.hdr).
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107 ]]> </help>
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108 <expand macro="SRS_S2ref"/>
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109 </tool>
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