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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
author ecology
date Wed, 23 Jul 2025 14:36:18 +0000
parents c2856067ee72
children
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<tool id="ecoregion_eco_map" name="EcoMap" version="0.1.2+galaxy0" profile="23.2">
    <description>Create map from cluster to visualize ecoregions</description>
    <requirements>
       <requirement type="package" version="4.2.3">r-base</requirement>
       <requirement type="package" version="3.3">r-tmap</requirement>
       <requirement type="package" version="1.0_12">r-sf</requirement>
       <requirement type="package" version="1.1.1">r-dplyr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript
        '$__tool_directory__/crea_carte_G.R'
        '$cluster'
        '$output'
    ]]>
    </command>
    <inputs>
      <param name="cluster" type="data" format="tabular" label="Source file (File 'cluster points' from previous step)" help="See example below"/>
    </inputs>
    <outputs>
      <data name="output" from_work_dir="ecoregions.png" format="png" label="Map"/>
    </outputs>
    <tests>
        <test>
            <param name='cluster' value="points_clus.tsv"/>
            <output name='output' value="ecoregions.png"/>
        </test>
    </tests>
    <help><![CDATA[
==================    
**What it does ?**
==================

The clusters obtained in the previous step are projected on a map to obtain the spatial distribution of each ecoregion.

===================         
**How to use it ?**
===================

This script takes as input a file containing for each environmental pixel its associated cluster. See example below. The output of this script is a map representing ecoregions.

+--------+--------+---------+
|  lat   | long   | cluster |
+--------+--------+---------+
| -65.57 | 139.22 |    1    |
+--------+--------+---------+
| -65.57 | 139.22 |    1    |
+--------+--------+---------+
|   ...  |  ...   |   ...   |
+--------+--------+---------+

    ]]></help>
    <citations>
       <citation type="doi">10.32614/CRAN.package.dplyr</citation>
       <citation type="doi">10.32614/CRAN.package.sf</citation>
       <citation type="doi">10.32614/CRAN.package.tmap</citation>
    </citations>
</tool>