<tool id="Map_shp" name="Make a map with a shapefile" version="0.1.0+galaxy0">
    <requirements>
       <requirement type="package" version="4.3.2">r-base</requirement>
       <requirement type="package" version="3.4.4">r-ggplot2</requirement>
       <requirement type="package" version="1.0_14">r-sf</requirement>
       <requirement type="package" version="1.1.9">r-ggspatial</requirement>
       <requirement type="package" version="1.1.3">r-dplyr</requirement>
       <requirement type="package" version="1.1_3">r-rcolorbrewer</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript
         "$__tool_directory__/Map_shp.R"
          #if $input1.is_of_type("shp") 
             ${os.path.join( $input1.extra_files_path, "shapefile.shp" )} 
          #else
            "$input1" 
          #end if
         "$input2"
         "$input3"
         "$input4"
         "$input5"
         "$output"
          
    ]]></command>
    <inputs>
       <param name="input1" type="data" format="shp" label="Shapefile"/>
       <param name="input2" type="data" format="tabular" label="Data to represent"/>
       <param name="input3" type="text" label="What is the title of your map ?">
          <sanitizer invalid_char="">
              <valid initial="string.printable">
                  <add value="é"/>
                  <add value="è"/>
              </valid>
          </sanitizer>
       </param>
       <param name="input4" type="text" label="What is the legend of your map ?">
          <sanitizer invalid_char="">
              <valid initial="string.printable">
                  <add value="é"/>
                  <add value="è"/>
              </valid>
         </sanitizer>
        </param>
       <param name="input5" type="boolean" label="Display the geographical coordinates ?"/>
    </inputs>
    <outputs>
       <data name="output" from_work_dir="map.pdf" format="pdf" label="map.pdf"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="GRECO/GRECO_l93.html" ftype="shp">
                 <composite_data value="GRECO/GRECO_l93.shp"/>
                 <composite_data value="GRECO/GRECO_l93.shx"/>
                 <composite_data value="GRECO/GRECO_l93.dbf"/>
                 <composite_data value="GRECO/GRECO_l93.prj"/>
            </param>
            <param name='input2' value="evolution_rate.tsv"/>
            <param name='input3' value="Taux d'évolution du volume des bois favorables à la biodiversité par GRECO"/>
            <param name='input4' value="Taux d'évolution (%) \nentre les périodes \n2008-2012 et 2013-2017"/>
            <param name='input5' value="true"/>
            <output name='output' value="map.pdf"/>
        </test>
    </tests>
    <help><![CDATA[
==================    
**What it does ?**
==================

This tool allows to build a map from a shapefile and color the areas according to a percentage (case study dead wood evolution rate).

    ]]></help>
</tool>