<tool id="raster_template" name="Make templates for raster files" version="0.1.1+galaxy0" profile="22.05">
    <description>attributes for EML metadata creation</description>
    <requirements>
        <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    
    #set $table = ""
    mkdir data_files && 
    #for $indata in $inputdata
        ln -s '$indata' 'data_files/${indata.element_identifier}';
        #set $table += $indata.element_identifier + " ";
    #end for
    
    Rscript 
         '$__tool_directory__/raster_templates.R'
         '$table'
    
    ]]></command>
    <inputs>
         <param name="inputdata" type="data_collection"  collection_type="list"  label="Upload all data files wich are raster files" help= "Input a data collection."/>
    </inputs>
    <outputs>
       <collection name="templates" type="list" label="Raster data templates">
             <discover_datasets pattern="(?P&lt;designation&gt;.+\.txt)" format="txt"/>
       </collection>
    </outputs>
    <tests>
        <test>
           <param name="inputdata">
              <collection type="list">
                 <element name="Present_Surface_pH.tif" value="Present_Surface_pH.tif"/>
              </collection>
           </param>
           <output_collection name='templates' type = "list" count="2"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does?**
--------------------
This tool is used to produce EAL templates for raster data used to build EML metadata. It produces the following eal files: 

- attibutes_my_raster.txt (describe the attributes of your data table)
- catvars_my_raster.txt (only if there are one or more catégorical variable in your data table)
- custom_units.txt (made to describe custom units if there are any)

After that, these files can be edited to add information about your raster 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 select, in your history a data collection with your raster data (one or more).To do so, you can select the **Upload file** tool, select the *Collection* tab, upload all your templates, click on the *Start* button to integrate the files to Galaxy and then click on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates.
You also can upload your files to Galaxy, select them in the history by clicking the *Select items* button, click on the newly appeared box on the right and select *Build dataset list*.
    ]]></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>