<tool id="normalizeMedianNegCntrl" name="Normalize Using Median Negative Controls" version="1.0.0">
  
  <command interpreter="perl">
  	normalizeMedianNegCntrl.pl $inputFile1 $inputFile2 $outputFile1
  </command>

  <inputs>
  	<param format="tabular" name="inputFile1" type="data" label="Select the linear plates file"/>
  	<param format="tabular" name="inputFile2" type="data" label="Select the plate configuration file"/>
  </inputs>
  
  <outputs>
    <data format="tabular" name="outputFile1"/>
  </outputs>

  <tests>
    <test>
      <param name="inputFile1" value="150615-HR-12015-01A.linear"/>
      <param name="inputFile2" value="plate_config.txt"/>
      <output name="outputFile1" file="normalized_using_median.tabular"/> 
    </test>
  </tests>
  	
  <help> 

.. class:: infomark

**What it does**

This program takes a linear plate table and a plate config file as input and then normalizes each plate in the table to the negative controls in the config.
The plate config file **must** contain the columns Well, Type and Name in that order. Further the data in column Type must be **exclude**, **negcontr** or **poscontr**.

**Example**

If the plates table consisted of::

	#Well	Table_1	Table_2
	A01	1654	6
	A02	1719	8
	A03	1624	19
	A04	1518	6
	A05	1587	12
	A06	1517	8
	A07	1638	9
	A08	1733	7
	A09	1617	6
	A10	1722	8
	...
	P14	1630	6
	P15	1576	6
	P16	1740	7
	P17	1578	6
	P18	1544	6
	P19	1692	6
	P20	1560	6
	P21	1552	6
	P22	1790	7
	P23	1537	6
	P24	NA	NA
	
and the plates config was::
	
	#Well	Type	Name
	A02	negcontr	NT2
	B02	negcontr	NT2
	C02	poscontr	ASCIZ
	D02	poscontr	PARP
	E02	negcontr	NT2
	F02	poscontr	ASCIZ
	G02	poscontr	PARP
	H02	negcontr	NT2
	I02	poscontr	ASCIZ
	J02	poscontr	PARP
	K02	negcontr	NT2
	L02	poscontr	ASCIZ
	M02	poscontr	PARP
	N02	negcontr	NT2
	O02	poscontr	ASCIZ
	P02	negcontr	NT2
	A23	negcontr	NT2
	B23	negcontr	NT2
	C23	poscontr	ASCIZ
	D23	poscontr	PARP
	E23	negcontr	NT2
	F23	poscontr	ASCIZ
	G23	poscontr	PARP
	H23	negcontr	NT2
	I23	poscontr	ASCIZ
	J23	poscontr	PARP
	K23	negcontr	NT2
	L23	poscontr	ASCIZ
	M23	poscontr	PARP
	N23	negcontr	NT2
	O23	poscontr	ASCIZ
	P23	negcontr	NT2
	A01	exclude	exclude
	A24	exclude	exclude
	B01	exclude	exclude
	B24	exclude	exclude
	C01	exclude	exclude
	C24	exclude	exclude
	D01	exclude	exclude
	D24	exclude	exclude
	E01	exclude	exclude
	E24	exclude	exclude
	F01	exclude	exclude
	F24	exclude	exclude
	G01	exclude	exclude
	G24	exclude	exclude
	H01	exclude	exclude
	H24	exclude	exclude
	I01	exclude	exclude
	I24	exclude	exclude
	J01	exclude	exclude
	J24	exclude	exclude
	K01	exclude	exclude
	K24	exclude	exclude
	L01	exclude	exclude
	L24	exclude	exclude
	M01	exclude	exclude
	M24	exclude	exclude
	N01	exclude	exclude
	N24	exclude	exclude
	O01	exclude	exclude
	O24	exclude	exclude
	P01	exclude	exclude
	P24	exclude	exclude
	
Running the program will give the following output::

	#Well	Table_1	Table_2
	A01	1.03	0.75
	A02	1.07	1
	A03	1.02	2.38
	A04	0.95	0.75
	A05	0.99	1.5
	A06	0.95	1
	A07	1.02	1.12
	A08	1.08	0.88
	A09	1.01	0.75
	A10	1.08	1
	...
	P14	1.02	0.75
	P15	0.99	0.75
	P16	1.09	0.88
	P17	0.99	0.75
	P18	0.97	0.75
	P19	1.06	0.75
	P20	0.98	0.75
	P21	0.97	0.75
	P22	1.12	0.88
	P23	0.96	0.75
	P24	NA	NA

  </help>  
  
</tool>