<tool id="eal_table_template" name="Make templates for data tables" version="0.1.1+galaxy0" profile="22.05">
    <description>attributes and categorical variables 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 
         '$__tool_directory__/eal_table_templates.R'
         '$table'
    
    ]]></command>
    <inputs>
         <param name="inputdata" type="data_collection"  collection_type="list"  label="Upload all data files wich are data table" help= "Input a data collection."/>
    </inputs>
    <outputs>
       <collection name="templates" type="list" label="Data table templates">
             <discover_datasets pattern="(?P&lt;designation&gt;.+\.txt)" format="txt"/>
       </collection>
    </outputs>
    <tests>
        <test>
           <param name="inputdata">
              <collection type="list">
                 <element name="datafile_1.tsv" value="datafile_1.tsv" />
              </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 data table used to build EML metadata. It produces the following eal files: 

- attibutes_my_datatable.txt (describe the attributes of your data table)
- catvars_mydatatable.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 data table 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 data table (one or more). To do so, you can select the **Upload file** tool, select the *Collection* tab, upload all your data table file, 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>
</tool>