diff calculateZPrimeFactor.xml @ 5:d7efb5d5352a draft default tip

Uploaded
author jason-ellul
date Wed, 01 Jun 2016 02:40:16 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/calculateZPrimeFactor.xml	Wed Jun 01 02:40:16 2016 -0400
@@ -0,0 +1,91 @@
+<tool id="calculateZPrimeFactor" name="Calculate Z Prime Factor" version="1.0.0">
+  
+  <command interpreter="perl">
+  	calculateZPrimeFactor.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="calc_z_prime.tabular"/> 
+  </test>
+  </tests>
+
+  	
+  <help> 
+
+.. class:: infomark
+
+**What it does**
+
+This program takes a linear plate table and a plate config file and then calculates the Z Prime Factors for your data.
+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	mock
	B02	negcontr	mock
	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	mock
	O02	poscontr	ASCIZ
	P02	negcontr	NT2
	A23	negcontr	mock
	B23	negcontr	mock
	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	mock
	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::
+
+	plate	control.duo	z.prime.factor
+	Table_1	mock/ASCIZ	-64.34
+	Table_2	mock/ASCIZ	-Inf
+	Table_1	mock/PARP	-10.78
+	Table_2	mock/PARP	-0.67
+	Table_1	NT2/ASCIZ	-55.97
+	Table_2	NT2/ASCIZ	-9.38
+	Table_1	NT2/PARP	-16.79
+	Table_2	NT2/PARP	-0.32
+
+  </help>  
+  
+</tool>