--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/normalizeMedianNegCntrl.xml	Wed Jun 01 03:52:52 2016 -0400
@@ -0,0 +1,135 @@
+<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>