Mercurial > repos > taoufik > dream_challenge

changeset 0:4eb60f0a4fdb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author taoufik
date Sat, 26 Jan 2019 19:01:54 -0500
parents
children 7c746038ed87
files Format_Dream.xml
diffstat 1 files changed, 100 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Format_Dream.xml	Sat Jan 26 19:01:54 2019 -0500
@@ -0,0 +1,100 @@
+<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 bensellak@ensat.ac.ma, El Messaoudi Idrissi Mohcine mohcine.elmessaoudi@gmail.com, Ahmed Moussa ahmed.moussa2@gmail.com . 
+
+---------------------------------------------------
+
+==================================
+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>