--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/eal_table_template.xml	Tue Sep 10 12:48:04 2024 +0000
@@ -0,0 +1,64 @@
+<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>
+    <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>