<tool id="view_chip" name="ChipView" version="1.0.0">
  <description>looking into the chip</description>
  <command interpreter="python">Raw_data.py $input $output $numerical_column_PM  $numerical_column_x $numerical_column_y $title</command>
 <inputs>
    <param format="tabular" name="input" type="data" label="Source file (*.pair file)"/>
    <param name="numerical_column_PM" type="data_column" data_ref="input" numerical="False" value="c10" label="Numerical column for PM" />
    <param name="numerical_column_x" type="data_column" data_ref="input" numerical="False" value="c6" label="Numerical column for x axis" />
    <param name="numerical_column_y" type="data_column" data_ref="input" numerical="False" value="c7" label="Numerical column for y axis" />
  	<param name="title" type="text" size="30" value="Image" label="Plot title"/>
  </inputs>
  <outputs>
     <data format="pdf" name="output" />
  </outputs>
	<help> 
.. class:: infomark

**What it does**

This tool creates the image of the array to make sure that no artifacts are present on the surface.

PLEASE, for more detailed information refer to the CARPET user Manual:
click to download_ it.

.. _download: /static/example_file/CARPET_userManual.zip

-----

.. class:: warningmark

This tool requires at least three numerical column **"X position"**, **"Y position"** (the position coordinates on the chip of each probe) and **"PM value"** (the raw signal of each probe). 

-----

**Example**

- On **Get Data** section it is possible to upload your files clicking on **"Upload File from your computer"**.
  
  Click here_ to download a pair_file example.

.. _here: /static/example_file/Pair_file.txt.zip	

- Input dataset pair_file from NimbleGen contained all these informations (eleven columns: c1, c2, c3, c4, c5... c11)::

   c1              c2                  c3      c4                  c5          c6    c7   c8             c9        c10      c11
   IMAGE_ID        GENE_EXPR_OPTION    SEQ_ID  PROBE_ID            POSITION    X     Y    MATCH_INDEX    SEQ_URL   PM       MM
   1251702_635     FORWARD             CHR19   CHR1900P000011001   11001       565   381  64160375       ____      5459.89  0.00
   1251702_635     FORWARD             CHR19   CHR1900P000011050   11050       610   656  64160376       ____      865.75   0.00


- Chose column **c10** for "PM value", **c6** for "X position" and **c7** for "Y position". 


   
.. image:: static/images/CARPET/chip.jpg

	</help>
</tool>

