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planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7

<tool id="srs_preprocess_s2" name="Preprocess sentinel 2 data" version="@VERSION@" profile="20.01">
    <description>read, crop, resample and write it as a raster stack</description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="4.2.2">r-base</requirement>
        <requirement type="package" version="1.0_7">r-sf</requirement>
        <requirement type="package" version="0.6_1">r-rgeos</requirement>
        <requirement type="package" version="0.5_5">r-stars</requirement>
        <requirement type="package" version="1.5.0">r-stringr</requirement>
        <requirement type="package" version="1.2.3">r-jqr</requirement>
        <requirement type="package" version="2.1.3">r-protolite</requirement>
        <requirement type="package" version="1.5.3">r-sen2r</requirement>
        <requirement type="package" version="1.2.2">r-progress</requirement>
        <requirement type="package" version="2.0.3">r-gdalutils</requirement>
        <requirement type="package" version="1.0.4">r-fasterize</requirement> 
        <requirement type="package" version="3.99_0.13">r-xml</requirement> 
        <requirement type="package" version="1.3.3">r-xml2</requirement>
        <requirement type="package" version="2.2.2">r-zip</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript
            '$__tool_directory__/preprocess_S2.r'
            '$input'
            '$__tool_directory__/Lib_preprocess_S2.r'
            '$source_s2'
            '$type_s2'
            '$output'
            '$output_refl'
            '$output_cloud'
        ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="zip" multiple="true" label="Input data"/>
        <param name="source_s2" type="select" label="Where does your data come from ?">
            <option value="SAFE">From Scihub or Peps</option>
            <option value="THEIA">From Theia</option>
        </param>     
        <param name="type_s2" type="select" label="From which satellite are the data ?">
            <option value="2A">Sentinel 2A</option>
            <option value="2B">Sentinel 2B</option>
        </param> 
    </inputs>
    <outputs>
        <data name="output" from_work_dir="Mission.csv" format="csv" label="Mission source"/>
        <data name="output_refl" from_work_dir="Refl.zip" format="zip" label="Reflectance"/>
        <data name="output_cloud" from_work_dir="Cloud.zip" format="zip" label="Cloud Mask"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="S2A_MSIL2A_20200306T015621_N0214_R117_T51JXN_20200306T034744.zip"/>
            <param name="source_s2" value="SAFE"/>
            <param name="type_s2" value="2A"/>
            <output name="output" value="Mission.csv"/>
            <output name="output_refl">
                <assert_contents>
                    <has_size value="12923807" delta="100"/>
                </assert_contents>
            </output>
            <output name="output_cloud">
                <assert_contents>
                    <has_size value="235912" delta="100"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
==========================
Preprocess Sentinel 2 data
==========================


**What it does**

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).
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.

**Input description**

A zip folder with Sentinel 2 data. 
These data can be dowloaded on 3 different platforms: 

- Copernicus Open Access Hub, Scihub, which provides complete, free and open access to Sentinel-2 data : https://scihub.copernicus.eu/dhus/#/home

- PEPS, la 'Plateforme d'Exploitation de Produits Sentinel' : https://peps.cnes.fr/rocket/#/search

- Theia : https://theia.cnes.fr/atdistrib/rocket/#/search

For each of those 3 platforms you will need to create an account.

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.

+----------+----------+
|   ZIP    |  Source  |
+==========+==========+
|folder.zip|Character |
+----------+----------+
|   ...    |    ...   |
+----------+----------+

**Output**

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.

A zip folder containing the cloud mask with the 2 files for the raw data (.RAW) and 2 files containing the metadata (.hdr).
    ]]>    </help>
        <expand macro="SRS_S2ref"/>
</tool>