view eco_map.xml @ 1:b38b954b92b9 draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 459ba1277acd7d8d4a02f90dbd7ff444bf8eac92

<tool id="ecoregion_eco_map" name="EcoMap" version="0.1.0+galaxy0" profile="22.05">
    <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>
</tool>