annotate geo_cov_template.xml @ 4:d53b708cb348 draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb

<tool id="geo_cov_template" name="Make geographic coverage template" version="0.1.0+galaxy0" profile="22.05">
    <description>for EML metadata creation</description>
     <requirements>
        <requirement type="package" version="4.3.1">r-base</requirement>
        <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    
    mkdir data_files && 
    ln -s '$inputdata' 'data_files/${inputdata.element_identifier}' &&
    #set $table = $inputdata.element_identifier
    
        Rscript 
         '$__tool_directory__/geo_cov_temp.R'
         '$inputdata'
         '$table'
         '$lat_col' 
         '$long_col' 
         '$site_col' 
         '$empty'
         
    ]]></command>
    <inputs>
         <param name="inputdata" type="data" format="tabular" label="Upload table containing geographic coordinates" />
         <param name="lat_col" type="data_column"  label="What column of your table contains latitude coordinates in decimal degrees?" data_ref="inputdata" use_header_names="true"/>
         <param name="long_col" type="data_column"  label="What column of your table contains longitude coordinates in decimal degrees ?" data_ref="inputdata" use_header_names="true"/>
         <param name="site_col" type="data_column"  label="What column of your table contains site names ?" data_ref="inputdata" use_header_names="true"/>
         <param name="empty" type="boolean"  label="Write an empty template file ?" />
    </inputs>
    <outputs>
         <data name="output" from_work_dir="geographic_coverage.txt" format="txt" label="geographic_coverage.txt"/>
    </outputs>
    <tests>
        <test>
            <param name="inputdata" value="test_geocov.tsv"/>
            <param name="lat_col" value="2"/>
            <param name="long_col" value="3"/>
            <param name="site_col" value="1"/>
            <param name="empty" value="false"/>
            <output name="output" value="geographic_coverage.txt"/>
        </test>
    </tests>
    <help><![CDATA[
    
**What it does?**
--------------------

This tool produce template for EML metadata. It produce template for geographic coverage. 
After that, these files can be edited to add information about your data and then be used in the make eml tool to produce EML metadata.

**How to use it?**
--------------------
To use this tool, you need to upload a table containing geographic coordinates (the decimal separator must be ".", example below), then select wich column of your table contains latitude, longitude and site names. You can also decide to make an empty geografical coverage templates.


**Example of geographic table :** 
-----------------------------------------

+------+------+----------------------+
| long | lat  |         site         | 
+------+------+----------------------+
|139.22|-65.57|     name of site 1   |
+------+------+----------------------+
|139.22|-65.57|     name of site 2   |
+------+------+----------------------+
| ...  | ...  |          ...         |
+------+------+----------------------+
 ]]></help>
    <citations>
       <citation type="bibtex">@Manual{,
       title = {EMLassemblyline: A tool kit for building EML metadata workflows},
       author = {Colin Smith},
       year = {2022},
       note = {https://github.com/EDIorg/EMLassemblyline,
       https://ediorg.github.io/EMLassemblyline/},
       }</citation>
    </citations>
</tool>