comparison Format_Dream.xml @ 0:4eb60f0a4fdb draft

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0:4eb60f0a4fdb

<tool id="Format_Dream" name="Dream Tabular" version="20181019" hidden="false">
    <description> Read DataSet into Rdata Binary for the Preprocessing Step. </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="1.11.4" owner="defaults">r-data.table</requirement>
    </requirements> 
    <command>
    <![CDATA[
       Rscript '$__tool_directory__/FormatDream.R'
        datasetsource $inputdata  
            ]]>
        
    </command> 
    <inputs>
    <param name="inputdata" type="data"  format="tabular"  label="Select  File."/>
    
    </inputs>
    <outputs>
        <data name="Format_Dream.tsv" format="tabular" from_work_dir="Format_Dream.tsv" label="Format_Dream.tsv">        
	</data>
    </outputs>
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
    <help>
		
.. class:: infomark

**Authors**  Bensellak Taoufik [e-mail], El Messaoudi Idrissi Mohcine [e-mail], Ahmed Moussa [e-mail] . 

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

==================================
Read Microarray DataSet
==================================

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

This tool is used for reading  choosen dataset in order to process, dataset could be imported or selected from available datasets.

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

**Upstream tools**

+------------------------+--------------------------------------------------+--------+
| Name                   | output file                                      |format  |
+========================+==================================================+========+
| Get List Datasets      |  Projects.Informations.on.technology.RData       | Rdata  |			
+------------------------+--------------------------------------------------+--------+
| Get List Datasets      |  Get.List.DataSets.Microarrays.on.technology.tsv | Tabular|			
+------------------------+--------------------------------------------------+--------+
| Make Design            |  Imported.Project.Informations.RData             | Rdata  |			
+------------------------+--------------------------------------------------+--------+


**Downstream tools**

+-------------------------------------------+----------------------------------+----------+
| Name                                      | Output file                      | Format   |
+===========================================+==================================+==========+
|Preprocess.DataSet.Microarray              | Preprocess.Project.Data.RData    | RData    |
+-------------------------------------------+----------------------------------+----------+
|Matrix.Data                                | Matrix.Data.tsv                  | Tabular  |
+-------------------------------------------+----------------------------------+----------+

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

+---------------------------------+------------+
| Parameter : num + label         |   Format   |
+=================================+============+
| image (both intern and exterm ) |   Rdata    |
+---------------------------------+------------+
| datasetsnames (only intern)     |   Tabular  |
+---------------------------------+------------+

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

**MicroArrayObject.RData** Both for intern and extern datasets

**design.tsv** Only for extern datasets

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

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

   </help>
</tool>