<tool id="Get_Datasets" name="Query GEO Database" version="20181028">
    <description> Query Gene Expression Omnibus (GEO) Database using accession code. </description>    
    <requirements>
        <requirement type="package" version="3.4.1_0">r-base</requirement>
        <requirement type="package" version="1.1_4">r-batch</requirement>
        <requirement type="package" version="2.42.0">bioconductor-geoquery</requirement>
    </requirements>
    <command>
        <![CDATA[
        Rscript '$__tool_directory__/GetDatasets.R' GeoCode $GeoCode
            ]]>
    </command> 
    <inputs>
	<param name="GeoCode" size="40" type="text" value="GSE50628" label="GEO accession" help="Gene Expression Omnibus (GEO) accession code">
      <sanitizer>
        <valid initial="string.printable,string.digits">
        </valid>
      </sanitizer>
    </param>
    </inputs>
    <outputs>
    <data format="microarray" type="microarray" name="Geo Raw">
      <discover_datasets pattern="(?P&lt;name&gt;.*)" ext="microarray" format="microarray" type="microarray" visible="true" assign_primary_output="true" directory="CEL" />
    </data>
    </outputs>
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
    <help>
		
.. class:: infomark

**Authors**  Bensellak Taoufik bensellak.taoufik@gmail.com, El Messaoudi Idrissi Mohcine mohcine.elmessaoudi@gmail.com , Ahmed Moussa ahmed.moussa2@gmail.com . 

---------------------------------------------------

==================================================================
Query Gene Expression Omnibus (GEO) Database.
==================================================================

-----------
Description
-----------

This tool is used for querying Gene Expression Omnibus Database.

**GEO accession**

GEO Accession code 

-----------------
Workflow position
-----------------

**Upstream tools**

+------------------------+------------------+--------+-----------+
| Name                   | output file      |format  | parameter |
+========================+==================+========+===========+
| NA                     |  NA              | NA     | NA	 |			
+------------------------+------------------+--------+-----------+


**Downstream tools**

+-----------------------------------------------+------------------------------------------------+------------+
| Name                                          | Output file                                    | Format     |
+===============================================+================================================+============+
| Create Desig                                  | DataSet.Design.tsv,DataSet.Informations.RData  | tsv,RData  |
+-----------------------------------------------+------------------------------------------------+------------+

-----------
Input files
-----------

+---------------------------+------------+
| Parameter : num + label   |   Format   |
+===========================+============+
| GEO accession             |   String   |
+---------------------------+------------+

------------
Output files
------------

**Set of raw samples**

------------------------------
General schema of the workflow
------------------------------

.. image:: ./workflow.jpg 
          :height: 800 
          :width: 700

   </help>
</tool>